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Bio 181

By mrunquis Jan 29, 2013 19910 Words
Bio
8.23.10
Chapter 1 Intro: The study of Life
Properties of Life
1. Precise organization (Order)
2. Ability to take in energy and use it. (Energy utilization) 3. Ability to respond to stimuli ( Response to the environment) 4. Capacity for growth and development
5. Ability to reproduce
6. Ability to regulate internal environment (Homeostasis) 7. Ability to evolve ( Evolutionary adaptation)
8. Living organisms are cell based, made of one or more cells 9. Life is DNA based
Gray Areas….lots of gray areas in biology
For example virus are not cell based although some do have DNA wrapped in protein coat and other viruses have double stranded RNA.
Prion is mad cow disease and it is only a rod of protein

Themes of Biology
1. Emergent Properties- life is very complex, as complexity gets bigger more emerge3nt properties reveal. Life itself is an emergent properties. If things are not put together in the right way, the emergent properties will not emerge. a. Molecules

i. In your body we have glucose and water
ii. Every molecule has properties, depending on the atom and how the atoms are arranged

b. Organelle
iii. A nucleus is an organelle, and a chloroplast is also an organelle iv. Organelles are made up of many molecules
c. Cells
d. Tissue
e. Organ
f. Community
2. Cell is the simplest unit of life
g. The cell is the lowest level of structure that is capable of performing all the activities of life v. Unicellular- made of one cell
vi. Multi cellular- many cells
h. The first cells were observed and named by Robert Hooke in 1665 from a slice of cork.. made from the bark of a cork oak tree. vii. He named them cells because they reminded him about jail cells i. Anton van Leeuwenhoek was the first person to see single-celled organisms in pond water and observe cells in blood and sperm. j. The cell theory: first proposed in 1839. (Schwann)

viii. A theory is an explination that is put together from lots and lots expieriments. Based on data collected, not a best guess or a best belief ix. The theory stated that all living things consist of cells k. In 1855, the cell theory was extended ( Theorys are and can be modified )—All cells come from other cells, new cells are produced by the division of existing cells. l. Cells reproduce, grow, and repair…….

3. Life is based on heritable information in the form of DNA – Life is DNA based m. Biological instructions for life are encoded in DNA (deoxyribonucleic acid) n. DNA is the ‘substance’ of genes

o. DNA double helix
p. Single strand of DNA (Nucleotide) **Fig 1.10
x. G
xi. T
xii. A
xiii. C
q. Genomes (Human and Others)
xiv. The entire library of genetic instructions that an organism inherits is called its genome. 1. The Human genome is 3 billion chemical letters long (3 billion letters of the nucleotides (4 letters)) 2. The rough draft of the sequence of nucleotides in the human genome was published in 2001 3. Biologists are learning the functions of thousands of genes and how their activities are coordinat3ed in the development of an organism. a. Our closest relative shares 98% of the same sequence it is a chimpanzee that lives in Africa 4. Structure/Function

r. Form fits structure, so the shape of something fits is function xv. For example a hammer is structured very well to pound in hammers s. Understanding the structure gives clues about function xvi. For example a bird, the bones in the bird are honeycombed inside, which makes them strong yet lightweight xvii. Example 2 nerve cells or neurons the hair like extensions make it very efficient xviii. Mitochondria is an organelle inside the cell, and its structure is very well suited for its function, the membrane is folded up, which allows for a huge surface area in a little area. Along the folds are molecules. 5. Open Systems ** Fig 1.5

t. This means energy enters and leaves—it is not recycled xix. For humans we eat the energy and it leaves us by heat 6. Regulation
u. One level of regulation are the chemical reactions in your body, they are all tightly regulated v. When fire burns if burns unorganized
xx. Wood is made up dead plant cells, the outside of the cell is made of cellulose which is made of glucose xxi. When wood burns, Glucose reacts with oxygen and it produces Carbon Dioxide (colorless ordorless gas) and water ……..energy is released when the reaction occurs, this same reaction occurs in your body every day, we get glucose by eating, oxygen by breathing, we release energy as heat and the rest of the energy is used by work or movement of muscles, and also breathe out the carbon dioxide and water by sweating and peeing, but in humans this same reaction is VERY TIGHTLY regulated. When you are active this reaction happens much faster than when you are not active. w. An organism regulates the chemical reactions within its cells xxii. Like ph value in blood, how much sodium and potassium in cells x. Regulat3 the inte3rnal environment even when external environment changes (Homeostasis). xxiii. For example Oryx maintains body temp and lood concentration in the very hot and dry naim desert 7. Unity and Diversity

y. All the species on earth are very diverse but also very unified z. Diversity:
xxiv. There are about 1.5 or 1.8 million species described 4. About a third of a million are plant species
5. 50,000 vertebrates ( mammals and reptiles birds fish and anphibians) 6. Almost 1 million insects most of which are beetles xxv. Estimates 5-30 million species that are undescribed most of which are believed to be microscopic xxvi. Diversity decreasing as species go extinct. (bees are endangered, much of the food we eat depends on the pollination from the bees, pollution and pestacides are some of the reason they are going extinct, because these pollutions and pesticides weaken the bees immune system, the pollination that the bees do is called an ecosystem services) xxvii. Plants are one living organism, bacteria animal protists fungi, nautalist shell crustation xxviii. A part of biology is Taxonomy: classifying and organizing forms of life Based on shared characteristics KPCOFGS (king phil came over for good spaghetti) 7. Kingdom: Animalia- based on a wolf

i. Multi-cellular
ii. Heterotrophic, which means that we eat or consume other organisms iii. NO cell wall around cells
8. Phylum: Chordata
b. All have a backbone
9. Class: Mammalia
c. Hair
d. 3 inner ear bones
e. Suckle young ( feed young with a boob)
10. Order: Carnivora
11. Family: Carideae
12. Genus: Canis
13. Species: lupus
f. The scientific name comes from the genus and the species, must be underlined and Genus must be capitalized and the species does not need to be capitalized, both are in latin xxix. Examples from the Fungal Kingdom

xxx. Ophiognomonia crypticica Wilson & Barr
14. This is a fungus that Professor Wilson found up in globe {. 5 Kingdoms
xxxi. Monera= Bacteria (Prokaryotes
xxxii. Plante= Plants
xxxiii. Animalia=Animals
xxxiv. Fungi= Fungi
xxxv. Protista= Protists ( single celled)
BUT
|. Domains
xxxvi. Bacteria- Have Prokaryotic cell type
xxxvii. Archea – also has prokaryotic cell type( ancient bacteria, like the first cells on earth, find them in deep ocean, or high temps, or high pressures) xxxviii. Eukarya- each have Eukaryotic Cell Type (cells have nucleus) 15. Plante

16. Animalia
17. Fungi
18. Protista
}. Unity within diversity
xxxix. DNA as the common information molecule
xl. Eukaryotes all share common cellular architecture 8. Evolution
~. Mechanism which explains both diversity and unity.
xli. Evolution is a scientific theory:
19. Species change over time
20. The mechanisms of change
Graphic of the ape to man
Does not say that the human species came from apes, but that both humans and apes evolved from a common ancestor
Homo SapienP.p. (sci Ape)

4.5 mill yago
Australopithicus africanus (1st known)
12 million years ago
9. Scientific Method
Def. “Science is a process of inquiry that includes repeatable observations and testable hypotheses” . Discovery Science and Induction
xlii. Making observations
xliii. Collecting data
21. EXAMPLES
g. “Egg eater” frog
h. Red eyed Costa Rican tree frog
i. Eyelash pit viper (3 morphs)
j. Coconut crab ( called coconut crab because it climbs up coconut trees.) They are called a hermit crab but when they are adult, they are too big for a shell, and no longer have shells k. Howler monkey (the worlds 2nd loudest animal) l. Leaf cutter ants

m. Leapord
n. Cheetah
. Hypothetico-Deductive Science
xliv. Scientific method
22. Observation
23. Ask Questions
o. The questions must be specific and precise p. Ask how or why questions
q. Generate Hypotheses
iv. Plausible, testable, possible or potential answers to our question v. When you propose a hypotheses you must make more than one, come up with as many possible answers as we can. vi. List as H1, H2, H3…etc and write them down r. Make predictions

vii. Every hypothesis must have a prediction P1, P2, P3 viii. Use If ….And….Then statement
1. Example IF there are more nutrients in the mound of soil(hypothesis) AND I measure nutrients in mound and non mound soil (possible experiment) THEN I will find more nutrients in the mound soil. (Prediction) s. Experimentation

t. Get results from data collected
u. Conclusions
xlv. Formal process
xlvi. Experimentation
. Limitations of Scientific Method
xlvii. Remember
24. Science seeks natural causes for natural phenomena 25. The scope of science is limited to the study of structures and processes that we can observe and measure, either directly or indirectly 26. Verifiable observations and measurements are part of science 27. You must be able to test and retest by doing the same thing 28. Scientists publish their findings in journals, so other scientists can verify them)

Chapter 2
The Chemical Context of Life
The antibiotic chemical formula we looked at azithromyicin works by preventing protein synthesis by inactivating the bacterial 50s ribosomes, it doesn’t kill us because we have different ribosomes than the bacteria Another antibiotic ( Omnicef) interfears with the cell walls by removing some but not all B-lactamase enzymes, which make the cell wall, therefore the bacteria cannot make a cell wall, and our immune system can kill the bacteria easily Amoxicillin is structured very much like Omnicef and also works the same way The structure of molecules fit their function

1. Matter = chemical elements & compounds
a. Matter is defined as anything that has mass
b. An element is a substance that cannot be broken down into other substances by chemical reactions. i. Example : my diamond , made up of carbon atoms, and cannot be broken down into anything else ii. There are 92 naturally occurring elements

iii. Each element is named
1. Sodium( silver soft metal) + Chlorine (Poisonous gas) = sodium chloride (table salt) 2. Both sodium and chlorine are very rare to find in nature because they are highly reactive and make compounds instantly c. A compound is a substance consisting of 2 or more elements 2. Life requires about 25 chemical elements

d. 96% of living matter = 4 elements- C carbon, O oxygen, H hydrogen, N nitrogen iv. HONC C-4 bonds H- 1 bond O-2 bonds N-3 bonds
e. 4% of an organism’s mass = phosphorus P, sulfur S, calcium Ca and potassium K f. Trace elements present in minute amount less than .01% g. Refer to table 2.1 on pg 32
3. Atomic structure determines the behavior of an element h. An atom is the smallest unit of measure
i. Atoms are composed of even smaller parts, called subatomic particles v. Neutronsno charge1.009 Dalton
vi. Protons(+)1.007 Dalton
vii. Electrons(-)1/2000 Dalton* = unit to express mass (1.66 x 10-24g) Refer to figure 2.5 on pg 33 of the helium (He) atom
j. Nucleus contains protons and any neutrons if the atom has any k. Electron shell(s) electrons
viii. Can be called an electron cloud
ix. Electron energy levels:
3. 1st shell fills with 2 electrons
4. 2nd shell fills with 8 electrons
5. 3rd shell fills with 8 electrons
l. Atomic Number- Number of protons in an atom.
m. In a neutral atom, the number of protons = the number of electrons n. Mass number – the number of protons plus the number of neutrons x. The number of neutrons in an element can vary ISOTOPES o. Electrons are negatively (-) charged particles that orbit around the nucleus p. Electrons have orbitals

q. Each orbital is a certain distance from nucleus and can only contain certain # of electrons r. The chemical behavior of an atom is determined by its electron configuration s. Elements in the periodic table are grouped together based on their valence shell electrons xi. When their outer shell is full we call them inert or nonreactive 4. Isotopes

t. Elements occur as mixtures of isotopes.
eg. Carbon
98.9% have 6 neutrons 12C STABLE
1.11% have 7 neutrons 13C STABLE
.0000000001% have 8 neutrons 14C : RADIOACTIVE
xii. Every element atom has the same number of protons, but with different isotopes the number of neutrons can vary u. Different isotopes of the same element react in the same way v. Some isotopes are unstable and thus are radioactive xiii. Radioactive carbon gets less as time goes by

5. Chemical bonding to form molecules
w. Atoms form bonds by sharing or transferring of electrons x. Chemical bonds is how atoms are held together
y. Chemical bond types:
xiv. Covalent bonds= share bonds, strong bonds
6. C-H the – is a covalent bond
xv. Ionic bonds= transfer bonds, strong bonds but in water they have weak bonds xvi. Weak bonds – not formed by transferring or sharing z. A Covalent bond is the sharing of a pair of electrons by two atoms xvii. Rules about covalent bonds

7. Why do they share?
a. An atom likes to fill its outer electron shell, when an atom has a full outer electron shell it is relatively stable {. Every atom has a characteristic total numb3er of covalent bonds that it can form – an atom’s valence fl atomic number is 9 so it has 7 electrons in the outer shell therefore it can have 1 covalent bond before the last electron shell is full |. The attraction of an atom for the electrons of another atom is called electronegativity

Measure of the strength of the bond
Electronegativity scale (FYI)
F = 4.0
O = 3.5
N = 3.0
S AND C = 2.5
P AND H = 2.0
Li= 1.0
Number of protons and the size of the atom determine the electronegativity All atoms if they have the same number of electron shells have the same diameter more of an attraction means higher electronegativity

}. Nonpolar covale3nt bonds
xviii. The electrons are shared equally, electrons are shared by the same atoms or atoms that have similar electronegativities ~. Polar covalent bonds
xix. The unequal sharing of electrons between 2 atoms xx. Between atoms with different electronegativities H—:O:—H 8. Shared electrons are closer to the atom with the highest electronegativity xxi. This is why water has the many properties that it does 9. Good solvent, cohesive which means water molecules like to stick together, also very adhesive they like to stick to some other things not all things but some, etc xxii. With the polar charges remember that the positive end will attract the negative end and so on . Covalent bond summary:

xxiii. Atoms share electrons to fill valence shells xxiv. Nonpolar covalent bonds
10. Atoms have same or similoiar electronegativity xxv. Polar covalent bonds
11. Atoms have dissimilar electronegativity
12. Gives molecule unique properties
. Ionic Bonds- weak bonds when in water
xxvi. The complete transfer of one or more electrons from one atom to another xxvii. If unequal in their el3ectronegativity one aton strips an electron completely from the other xxviii. Charged atom is what we call an ion

xxix. So when Na gives up its one electron to Cl the Na now has a positive charge (ion) and the Cl takes on a negative charge ( ion) xxx. And the charges attract each other, and that’s what holds the atoms together, Ionic bonds are not represented with a – xxxi. Compounds formed by ionic bonds are called salts . Biologically important weak bonds

xxxii. 1. Hydrogen 2.Ionic (weak in water) 3. Van der Waals xxxiii. Hydrogen bonds
xxxiv. Van der Waals
xxxv. These are weak because it doesn’t take much energy to break them xxxvi. Because these bonds are transient and easily broken, they can be used for, 13. When you change the shape of the molecule, you change the function of the molecule 14. Cell Signaling

b. NERVE CELL realeases neurotransmitters, where weak bonds are impoertang, then they change shape, and then they effect the nerve impulse, and then they change shape and don’t effect the nerve impulse 15. Linking molecules together

c. In the structure of dna
16. 3 D Shape
d. Determined by weak bonds
xxxvii. Hydrogen bonds
17. Formed by a charge attraction between a hydrogen atom that is covalently bonded to an electronegative atom and another electronegative atom. 18. The charge attraction represented by dotted lines. xxxviii. Weak bond: about 5% of the strength of a covalent bond 19. Allows water to remain as a liquid over a wide range of temperatures e. Because it takes a lot of energy to break these hydrogen bonds f. One water molecule is capable of making 4 hydrogen bonds, 2 off each hydrogen and 2 off the oxygen ( to 2 other hydrogen bonds) g. Which is why a paperclip floats on water.

EXAM 1 HERE
6. Molecules function is related to shape
. Morphine is shaped much like an endorphin, which is why they act the same . Shape is a result of the atoms present and how they bond . The shape determines its function
7. Chemcical reactions
. Process of making and breaking chemical bonds
xxxix. The starting molecules=reactants and the end molecules are = products xl. Requires energy to break bonds
xli. Making new bonds releases energy
20. Example, methane (it burns) combine it with oxygen and it produces carbon dioxide and water, when it burns energy is released as heat and a little bit of light 21. Takes much less energy to break bonds, than it does to make the bonds xlii. In a chemical reaction, all of the atoms in the reactans must be accounted for in the products xliii. The reactions must be balanced (p42)

xliv. Matter is neither created nor destroyed
22. That means that the atoms that exist today, will exist forever.. and new atoms will not be created h. Tiny exception nuclear reactions
23. Photosynthesis is a chemical reaction
i. 6CO2 + 6H2O------------ C6H12O6 + 6O2
j. The opposite one is cellular respiration
k. Plants use energy from light to convert carbon dioxide and water into glucose (sugar) and oxygen Chapter 3
Water
1. Water & Hydrogen Bonding
a. Properties of water result from hydrogen bonding
i. Takes a lot of energy to raise the temp of water 1. Takes more energy to raise water 1 degree celcius than most other liquids, because of the hydrogen bonds figure 3.2 pg 47 2. Cohesion and Adhesion

b. Water molecules tend to stick together: cohesion
c. Water likes to stick to other things, Adhesion
ii. Which is why water can travel up the roots and trunk to the leaves of trees 2. A big tall oak tree can take 80 to 100 gallons of water a day iii. Also how bugs can walk on water

3. Water and ice: liquid and solid
d. Water is most dense at 4 degrees celcius
iv. Which is why ice floats
e. Least dense at 0 degrees celcius
4. Water is the solvent of life
f. All chemical reactions in your body occur in water
g. We refer to a water rich environment as aqueous
h. Solvent means dissolving agent (means things dissolve into) i. Oils and metals do not dilute in water
j. Solute: is the substance that dissolves into the solvent k. The sphere of water molecules around each dissolved ion is called a hydration shell
1. Ch 5
2. The structure and function of large biological molecules 3. Legos example
4. Macromolecules work the same way as legos
5. How the building blocks are put together and taken apart, their functions, and the combonations 6. Ever6y chemical reaction we discuss is mediated by enzymes (biological catalysts) 7. Enzymes them selves are proteins, make chemical reactions occur, and they are not used in the reaction which is why they are a catalysts, it just speeds up the reaction 8. 1.Polymer ( all polymers are macromolecules but not all macromolucles are polymers) A. Macro molecules are large organic molecules

B. Most macromolucles are polymers ( do you know any examples) i. EX carbohydrates, lipids, nucleaic acids, proteins 1. Of these lipids are not polymers, the other 3 are polymers C. Polymer: large molecules containing many repeating subunits covalently linked together D. Monomers: subunits (building blocks) of a polymer

2. Construction and deconstruction of Polymers
a. Construction (anabolic): anabolic is used for building up ii. Find our if these anabolic require energy or release energy?????????? b. Deconstruction (catabolic):

c. Condensation (dehydration) reaction
i. Chemically similar process of construction. 9. II. this is when we take 2 monomers and add them together to get a polymer and water is released ii. condensation reaction ( dehydrateion reaction: linking monomers together via covalent bonding 3. 1.One monomer provides a hydroxyl. Group and the other a hydrogen =??? 4. Requires energy and is aided by enzymes

iii. Hydrolysis reaction
5. 1.Breaking down polymers is chemically similar for all macromolecules 6. Hydrolysis: the reaction that splits monomers 7. In hydrolysis water is split, the hydrogen and hydroxyl groups are returned to the monomers 8. Hydrolysis reactions dominat3 the digestive process, driven by specific enzymes * Polymers (macromolecules)

* Carbohydrates
* Large organic molecules that are made up of sugars and their polymers * Used for fuel
* Used Carbon source
* Monomers : are simple sugars called monosaccharides or simple carbohydrates * Ex: Fructose, glucose
* Sugar polymers are joined together by condensation reactions. * Complex carbohydrates are the product. * Ex: starches, fibers, cellulose

* Monosaccharides: simple sugar
* C:H:O ratio is 1:2:1 CH2O
* Example : glucose is C6H12O6
* Usually end in –ose
* Simple sugars are the main nutrients for cells. * Glucose is the most common
* Store energy in chemical bonds
* Carbon hydrogen is the high energy bond which means lots of calories associated with it * Make new bonds release energy, break bonds require energy * Monosaccharides are also raw materials to synthesize monomers of amino acids and fatty acids etc. * Refer to fig 5.3 on pg 70

* Disaccharides
* Disaccharide: a double sugar consisting of 2 monosaccharides * Fig 5.5 pg 71
* Each carbon has a specific number pertaining based on where it is located in the molecule * So 2 glucose added together to form the disaccharide maltose has a alpha 1-4 glycosidic linkage * Polysaccharides

* Polysaccharides: polymers of monosaccharides. * Formed by dehydration reactions
* Huge molecules
* 2 very important biological functions:
* Energy storage (starch and glycogen)
* Structural support (cellose and chitin) pronounced kaitin * Plant cells lined with cellulose
* Starch
* Starch : a glucose polysaccharide in plants * 5.6 a pg 72
* Linear shaped molecule
* Monomers are joined by an Alpha 1-4 linkage between the glucose molecules. * The plant makes the starch because it doenst dissolve, which makes it easy to store, because if they would keep the glucose the glucose would dissolve . * Plants store starch within plastids, including chloroplasts. * Plants can store surplus glucose in stach and withdraw it when ne33ded for energy or carbon * Animals that feed on plants can also access this starch and break it down into glucose * And the glucose we use as energy * Glycogen: a glucose polysaccharide in animals * See 5.6 b on pg 72

* Very highly branched molecule
* Enzymes, which is what breaks up the bonds, can only break bonds on the terminal side of the molecule there for the complication within the branches allow for more enzymes to break down the glycogen much faster than starch * This can be illustrated by the fight or flight * Cellulose a glucose polysaccharide in plants * Very rigid and strong, used for structural support for cell walls * This has a beta 1-4 glycosidic linkage, because every other glucose monomer is flipped upside down, * Humans cannot break the beta 1-4 glycosidic linkage * Linear (unbranced)

* Cellulose is a major component of th3e tough cell walls in the plant * Cellulose is biologically inactive 5to humans we don’t have the enzymes to break it down (fiber) * Groups of polymers from strong strands, microfibrils, that are basic building materials for plants ( and humans) fig 5.8 pg 73 * Chitin

* Chitin: a structural polysaccharide used in the exoskeletons of anthropods (including incects, spiders, and crustaceans). * Like cellulose, chitin is a glucose polymer tht is linked by beta 1-4 bonds. * Chitin also forms the structural support * Summary

* Polymers and monomers
* Construction and deconstruction dehydration and hydrolysis * Carboyhdates
* Monosaccharides
* Disaccharides
* Polysaccharides
* Starch
* Glycogen
* Celluclose
* Chitin
* LIPIDS
* Lipids- macromolecules that are insoluble in water (hydrophobic). * They are hydrophobic because their structures are dominated by nonpolar covalent bonds * What type of solvents would dissolve lipids

* Alochol, acetone,n (non-polar)
* 3 important groups of lipids
* Fart and oils
* Phospholipids
* Steroids ( hormones)
* FAT
* Fat: a macromolecule composed of glycerol( an alcohol) linked to a fatty acid * Fig 5.11 a on pg 75
* Fatty acid: a carboxyl group attached to a long carbon skeleton, often 16-18 carbons long * Triaclyglycerol( which is a triglyceride)
* Triaglycerol:P a fat composed of 3 fatty acids linked to one glycerol molecule * Characteristics of fats
* Fats are water insoluable (why?)
* Fatty acids may svary in length ( number of carbons) and in the number and locations of double bonds * 2 main types of fats:
* Saturated ( all C bonds taken by H)
* Unsaturated ( jnot all C bonds taken by H) * Saturated fat
* No double bonds between carbons
* Butter fig 5.12 a
* Straight chains, so they can be packed tightly, and they don’t move past each other very well * Maximum (saturated) number of hydrogens
* Solid at room temp.
* Mostly found in animal fats ( lard, fat on bacon etc) * Unsaturated fat
* One or more double bonds between carbons, which causes it to kink or bend, which causes more space inbetween them, so they tend to be liquid at room temp * Ex veg oil, corn

* Mostly plant fats
* Tail kinked at double bond
* Fig 5.12 b pt 75
* More healthy for you, don’t clog arteries * Trans fats( very bad for you)
* These live in your blood for a very long time * In processed foods
* Chemically ( man made) we break the double bonds and add H * Such as margarine,peanut butter
* Build up and plaque our arteries
* Cis are the good ones
* Function of fats
* Long term fuel storage
* Hold much more than carbohydrates
* Stored in adipose (fat cells)
* Also fats act as a cushion for vital organs * Insulation against heat loss
* The blue whale has much blubber
* Lizards hold fat in their tail
* Phospholipids
* Phospholipids are made up of glycerol, 2 fatty acid chains ( one of these chains has a double bond) and a phosphate group on carbon number 3 * Hydrocarbon ( fatty acid) tails are hydrophobic * Phosphate group (head) is hydrophilic

* ( not quite liquid not quite solid)
* What happens when phospholipids are placed in water? * When phospolpds are added to water, they form a circle3 with the phosphate (hydrophilic) side out and the hydrophobic tails in the center of the circle this type of structure is called a micelle * Phospholipds are the major component of membranes. * They are arranged as a phospholipid bilayer (fig 5.14 pg 77) * Steroids

* Steroids are lipids with a carbon skeleton consisting of 4 fused carbon rings * Hundreds of different steroids
* Cholesterol is the precursor for all steroids synthesis fig 5.15 pg 77 * There is very little structural difference among steroids * Estregn and testorone look very much alike * Proteins

* Most complex molecules known to exist
* 100’s of 1000’s of different kinds
* Variety of proteins = variety of life on earth
* Polymers of amino acids ( 20 different kinds)
* Amino acids are the monomers of proteins
* Examples of roles of proteins
* Structural support ( keratin )
* Ex hair, skin, nails, hoofs on a horse, horn on a rhino, feathers on a bird, scales on a lizard * Storage of AA (albumin)
* Very hard to store protein
* Birds and reptiles store protein in eggs, the white of the egg is called albumin * Transport (hemoglobin)
* Hemoglobin is a protein with iron in it, it transports oxygen from lungs to the rest of the tissues, and picks up carbon dioxide and drops it off in our lungs so we can breathe it out * Carbon monoxide kills you because it bonds to the hemoglobin very storng, therefore the hemoglobin cannot carry oxygen or carbon dioxide * Signaling (insulin)

* Sends signals to remove glucose from blood
* Stimuli (receptors)
* A protein in the retina in your eye called rhodopsin and the stimuli that it receives is light * Look at the sun, and when you look away you can still see the sun, and it takes awhile to convert the rhodopsin back to rhodopsin * Movement (myosin)

* Muscles are made of the protein called myosin, which enables movement, the myosin acutally gets shorter, which causes contraction * Immune (antibody)
* Enzymes (catalyst)
* Speed up the rate of reactions
* Polypeptide chains: polymers of amino acids (monomers) arranged in a linear sequence and joined by peptide bonds * Proteins are combined of one or more polypeptide chains, the chains are folded into a very specific 3 dimetial shape * Take a closer look at amino acids they have a center carbon which has a H attached and a carboxyl group and also an amino group…(EVERY AMINO ACID HAS THIS) plus (this is what varies) the R group…he will show us what the r group can be later * The bond that hold the N to the C after dehydtration is called the peptide bond * Learn how to draw this

* Carbon Hydrogen bonds are non polar, which is why they don’t mix well with water * Amino acids are joined by covalent bonds: peptide bond formed by condensation reactions. * The backbone of the peptide bonds is the sthe amino group and carboxyl group * The Side Chain is the R group(variable group)

* Protein conformation: 3 D Structure (shape) of a protein * 3 dimensial shape… very complicated, we must break it down * Determined by the sequence of amino acids
* Dertermines protein function
* Formed by folding and coiling of the polypeptide chain ( results from the different pro;perties of amino acids) * Ribbon diagram (fig 5.19 a pg 81)
* The backbone is the same in every amino acid
* A proteins specific conformation determines its function. * In almost every case, the function depends on its ability to recognize and bind to some other molecule * In the same way that a key fits a lock, proteins function only if they can recognize and bind. * Enzymes recognize and bind to specific substrates, facilitating a chemical reaction * The sequence of our genes determines amino acid sequence * 4 differnet levels of organization

* Primary aka 1o
* Linear sequence of amino acids:
* Determined by genes ( DNA sequence)
* Can be sequenced to determine the order of amino acids * (hemoglobin mutation) sickle cell anemia * If you have sickle cell anemia you cannot get maleria * Secondary aka 2o

* Resuts from hydrogen bonding between amino acids along the backbone * This secondary structure forms the coils called * Formed by regular intervals of hydrogen bonds along the backbone * Alpha Helix Beta pleated sheets

* The structural proper4ties of silk are due to betaq sheets * The presence of so many hydrogen bonds make each silk fiber stronger than steel * Tertiary aka 3o

* gives us the 3D shape of the protein
* formed by interactions between the R groups only * di sulfide group
* hydrogen bonds
* very hydrophobic nonpolar covalent bonds, are forced away from the center because these are in aqueous solutions * van der waALS INTERACTIONS _ very weak forces of attraction * stabilize the final protein structure

* Quaternary 4o
* Structures formed when two or more polypeptide subunits * Examples
* Collagen
* Hemoglobin
* Nucleic acids
* Polymers of nucleotids
* Nucleotides are made up of nucleotides (monomers are nucleotides ) and they are polymers * Nucleotides are themselves made from subunits * Nitrogen base

* Sugar
* Phosphate group
* Examples
* DNA
* RNA
* ATP
* Chapter 6 a tour of the cell
* Amazing facts about cells
* How many cells in :
* A new born baby?
* Adult?
* Retina? 125 million
* The smallest cell is 0.2 Mm and it is a bacteria cell * The gram stain we did in lab each bacteria is 2Mm * The biggest cell is an ostrage cell—shell is very thick * The white part of an egg is called albumin

* How we study cells
* Light microscope
* First cells “discovered” Robert Hooke in 1665 using a compound * Important concepts in microscopy
* Magnification ratio of objects image to real size * Resolution : minimum distance between 2 points that can still be distinguished as 2 separate points * The limit of resolution of a light microscope is 0.2 micrometers ( UM:P one millionth of a meter’ 10-6 * This makes 1000x the maximum magnification possible. * Can see objects down to bacteria and some organelles of the cell * Electron microscope:

* Introduced in 1950
* Uses beams of electrons .. not light
* Electron beams have shorter wavelenths and therefore better resolution * The resoluti9on of an electron microscope is 0.2 nano meters (nM: one billionth of a meter: 10-9) 1000x better than a light microscope * This magnification can resolve viruses proteins and evens some small molecules * Study and know fig 6.2 pg 95

* Transmission electron microscopy (TEM)
* TEM aims a beam at a thin cross-section (sliced) of a specimen ( stained with metal particles) * The image is then focused onto a viewing thin film * 2 d image

* Common stain used OsO4 osmium tetroxide
* If electrons pass easily it will look much different * Scanning electron microscopy (SEM)
* Sem aims a beam at the surface of a specimen (stained with metal particles (gold)) * Used to study the surface of a specimen
* Provides a 3D image
* Cell fractionation
* Cello fractionation separate major or\ganelles to study the function of each * Disrupt cells, then centerfiuge to seperat3e cellular componets * Seperates based on difference size or density or shape * Study this more from lab

* 2 basic cell types
* Prokaryote literally means before nucleus
* Pro- before and karyon = nucleus
* Have no membrane bound organelles
* Bacteria and monera are the only ones to have this cell type * Eukaryote:
* Eu=true and karyon= nucleus
* Do have nucleus
* And have membrane bound organelles
* Prokaryotic Cells
* Refer to fig 6.6 pg 98
* There is organization but everything is floating in jelly like cytoplasm * Eukaryotic cell
* More membrous compartments and they tend to be bigger * Limits to cell size(why are cells so small)
* Fig 6.8 pg 79
* Must understand proportional and ratios
* Cells must have a certain surface area to volume ratio to function correctly * Surface to volume (s:v) ratio limits cell size * Eukaryotic cells have 1000x the volume of prokaryotic cells, but only 100x the surface area( compensate w/ organelles) * Cells can only be so big or so small

* Can only be so small because they need to fit everything in * Focus on the eukaryotic cell
* Internal Membranes
* Partition the cell into compartments
* Provide necessary localized environments
* Sequester reactions, stop interference
* Eukaryotic cell is like a kitchen, have a fridge, and an oven, and a microwave, and we have compartments for sugar, and baking soda, and cereal so everything is separated * Nucleus

* Contains most genes
* About 5 micrometers in diameter
* Nuclear envelope is a double membrane
* Nuclear membrane is studded with pores-protein complex * DNA as chromatin
* Chromatin: DNA and proteins (histones) which make up chromosomes * Dna is wrapped around histone
* Nucleolus: area of the nucleus where riibosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm * So ribosomes are made in nucleus
* Ribosomes: organelles/molecules (RNA + Protein) that are sites for protein synthesis * Assembly station for protein synthesis
* Ribosomes are made up of 2 parts, a large subunit and a small subunit * 2 types 1. Free 2. Bound
* Endomembrane system
* Many membranes of the eukaryotic cell are part of an endomembrane system * These membranes are either directly linked (physically attached) or indirectly linked (via transport vesicles) * Vesicle: a small membrane bound sacs that are the delivery system of the cell (UPS of the cell) * From the movie he showed the vesicle was the thing being drug by that motor molecule * Membranes are constantly changing in thickness, composition, and behavior * In response to their environment.

* Endomembrane system includes:
* Nuclear envelope
* Endoplasmic reticulum
* Golgi apparatus
* These three nuclear envelope, endoplasmic reticulum and the golgi apparatus are all connected togethe3r * Lysosomes
* Very specific vesicles
* Vacuoles
* Huge vesicle in cell, a bit more permanent * Not all cells have these
* Endolplasmic reticulum: membranous network of tubules and sacs ( cisternae) that separate its internal lumen (cisternal space) from the cytosol * Continuous with the outer membrane of the nuclear envelope * 2 regions:

* ROUGH
* SMOOTH
* SMOOTH endoplasmic reticulum (ER)
* Why is it called smooth?
* No ribosomes
* Wide varity of functions:
* Synthesis of lipids, phospholipids, and steroids * Carbohydrate metabolism
* In liver cells, catalyzes a key step in the mobilization of glucose from stored glycogen in the liver * Detoxification of drugs, and poisons * In liver cells, the ER gets bigger in response to alcohol etc, thus increasing tolerance * Stores calcium ions used for muscle contraction * Showed a pic of a liver, and the gall bladder, liver is very vascular * ROUGH endoplasmic reticulum ER

* Why is it called rough?
* Ribosomes
* Functions:
* Manufactures secretory proteins: * Secretory proteins are proteins that are produced in the cell and then exported out of the cell 1) Ribosomes synthesize proteins

2) Protein folds into its correct structure 3) Proteins are often modified with carbohydrates to form glycoproteins (glyco=sugar) 4) Packaged in vesicles (boxed up) for transport to other parts of the cell 5) Vesicles fuse to membrane to release its d. Makes membranes for use in other organelles iii. By expanding its own membrane)

iv. Golgi Apparatus
9. Golgi apparatus: Made of stacked, flatten sacs (cisternae) that manufactures, store, sort, and ship and modify products from the rough ER. e. Cis face is the receiving side of the golgi apparatus and trans face is the shipping side of the golgi apparatus f. Has kind of a one way traffic

10. Vesicles transport proteins between the golgi and the other cell structures: 11. Has polarity ( receiving side: shipping side) g. Products (proteins are modified in stages as they pass through the Cis to the Trans Face v. Lysosomes

12. Lysosome: Membrane enclosed bag of hydrolytic enzymes that digest maqcromolecules ( acidic pH=5) 13. Four types of enzymes:
h. Carbohydrases, Proteases, Lipases, and Nucleases 14. Enzymes and lysomal membranes are made in the R-ER and processed in the Golgi 15. The ph of 5 makes the enzymes inactive by breaking some of the bonds which makes it able to store the enzymes. 16. White blood cells lysosomkes, ‘eat the bacteria” which requlates ph, and then activate the enzymes 17. Lysosome function

i. Digest external organic matter via phagocytosis j. White blood cells digest bacteria
k. Autophagy: Breaks down damaged organelles and recycling l. Apoptosis- where a cell completely destroys itself, (embryotic cells skin between fingers) they commit suicide using lysosomes iv. Tadpole….reabsorbs tail to make legs vi. Endomemebranes

18. Chemical instructions leave nucleus and go go rough er where the ribosomes tell it to make proteins, go therou vesicles to gthe golgi and sometimes get modified or stored there or go to the trans side of the golgi and goes to a vacuole, or maybe a lysosme that was made, where will then hang out and do their job fig 6.16 pg 109 19. Glycoproteins is what makes mouth all slimy, in saliva.we make about 2 pints each day, most of saliva is water and there are some glycoproteins vii. Mitochondria

20. Mitochonddria: sites of cellular respiration (o2 requiring process that uses energy from organic molecules to generate ATP) 21. CELLULAR RESPIRATION -----REMEMBER THIS
m. Oxygen + glucose -------carbon dioxide and water n. O2+
22. Only found in Eukaryotes (lots per cell)
o. How many is a lot
v. A heart muscle cell might have 500
vi. Sperm cell only has 1 mitochondria
6) To lighten the load
vii. A skin cell and bone cells, have low mitochondria numbers 23. Have their own dna
24. Have 2 membranes
p. Inner
q. Outer
viii. Function of these are for separation ix. Inbetween them is the intermembrane space viii. Chloroplasts
25. Found in plants and some protists (alge)
26. Chloroplast: Chlorophyll containing sits of photosynthesis (CO2 requiring process that stores energy in organic molecules) 27. Takes energy from sun, converts it to energy plants can use 28. Only found in plants and certain (protest) alge have lots per cell 29. Also have own dna

30. Stroma-contain dna, ribosomes and enzymes
r. Endosymbiosis
31. Thylakoids flattend sacks staced into grana that are critical for converting light into ix. Cytoskeleton
32. Component of every other cell
33. The cytoskeleton is a network of fibers extending throughout the cytoplasm 34. The cytoskeleton organizes structures and
s. The 3 parts of the cytoskeleton is flagellum, cilia, and intermediate filaments t. Microtubules
x. Straight hollow polymer fibers made of tubulin 7) Functions
a. Support
b. Tracks for organelles
c. Separation of chromosomes during cell division d. Cilia movement
i. Cilia are used for movement or to dra2 fluid across stationary cells (ex: windpipe sponge ii. Occur in large number (thousands) iii. Shorter in length than flagellum iv. Works like an oar, alternating power with a recovery stroke (back stroke) v. 9 x 2 arrangement

e. Flagellum movement
vi. Flagella are used for movement vii. Occur in small numbers (usually one or two per cell) viii. Longer in length than cilia ix. Undulating motion that creates force in the same direction as the axis of the flagellum (like a tiny motor) f. Intermediate filaments

x. Constructed from keratin molecules (more permanent than the other two cytoskeletal components)fig 6.26 pg 117 xi. Functions: bearing tension(cytoskeletal frame) and reinforce cell shape (nerve axons) and fix organelle positions (nucleus) xii. Pg 113 table 6.1

u. Microfilaments (actin)
xi. Solid rods made from actin (protieins) linked into chains, 2 actin chains are wound into a helix xii. Functions
8) Support
9) Muscle contraction
10) Localized contraction
g. Pinching of cells in two during division xiii. LIKE A RUBBERBAND AROUND A CELL h. Ameobid movement
xiv. White blood cells
i. Cytoplasmic streaming
xv. Chloroplasts around the cell wall x. Cell wall
35. Plants, bacteria, fungi, some protists,
36. Most plants produce a coat external to the plasma membrane 37. Constructed of cellulose fibers embedded in a matrix of polysaccharides and proteins 38. Functions 1) protection (fungi and bacteria really important) 2) rigidity 3) prevents excess H2O uptake 39. What other organisms have a cell wwall?

xi. Extracellular matrix (animal cells, ECM)
40. The ECM is a meshwork of macromolecules outside of cells(fills spaces between cells) 41. Constructed mainly of glycoproteins
42. Functions
v. Support
w. Cushioning
x. Communication
y. Fig 6.30 pg 120
z. Cell to cell attachment
TEST 2HERE
Chapter 7 Membrane Structure and Function
1. Membrane Structure
a. What is the distance between the living and nonliving? b. But how far are they separated?
i. Nonliving is separated by only a cell wall which is 8-9 nm c. The plasma membrane is the structure that separates the living cell from its non-living surroundings d. Phospholipid bilayer that is only 8 nm thick (10,000 x thinner than paper) e. Controls the traffic in and out of the cell

f. It is selectively permeable (some objects cross while others cannot) g. It has a unique structure which determines its function 2. Fluid Mosaic Model (1972)
h. Proteins are embedded in the membrane
i. Hydrophillic regions are exposed
j. Hydrophobic regions are inside
k. A mosaic of proteins that float around
3. Membrane structure (fluidity)
l. Lipids can move around freely or “flip” direction (rarely) m. Hybridized cells show homogeneous mixing of membrane proteins within 1 hour n. This fluidity is temp dependent
o. Membranes rich unsaturated fatty acids are more fluid p. Cholesterol is wedged between pphospholipds
ii. at high temp reduces fluidity
iii. at cool temps prevents freezing of membranes
q. to work properly membranes must remain fluid (~liquid = vegetable oil or warm butter r. cells alter lipid composition of membranes to cope with changes in fluidity to temp flux s. winter increawes percentages of unsat phospholipids just before winter

t. The membrane proteins are spatially arranged as: integral or peripheral u. Integral: transmembrane proteins with hydrophobic and hydrophobic regions span membrane v. Peripheral: proteins attached to the membrane surface w. The membrane is asymmetric (what does this mean)

iv. Not symmetrical
x. Integral membrane proteins
v. Integral membrane proteins (IMPs) have a variety of functions fig 7.9 pg 129 1. Transport
2. Enzymatic activity
3. Signal transduction
4. Intercellular joining
5. Cell-cell recognition
6. Attachment to the cytoskeleton and extracellular matrix (ECM) vi. Cell to cell recognition:
7. We looked at round worm or nema toad worm
8. Citrus trees much on tree roots
9. Rings trap nema toad
10. Lethal lollipops
vii. Transport
11. Lets set the stage
a. We3 understand membrane structure rememb3er structure often determines function b. Now lets exqamine how the membrane regulates the movement of substances into and out of the cell 12. Movement across the membrane: transport

c. Selectively permeable:
i. Pass through phospholipid
1. Small uncharged molecules pass easily 2. Carbon dioxide can pass easily
3. Oxygen can pass eisly
4. Large non polar molecules can pass easily (lipids) a. Sex hormones, steroids
ii. Things that cannot pass through the phospholipid, Use integral proteins 13. Transport proteins
d. Hydrophilic channel running through them
e. Sometimes the protein with physically move the thing moving through it, like a revolving door f. The proteins are specific for the substance that it moves, very specific. Each one is unique 14. Diffusion:

g. Diffusion is the movement of molecules from an area of high concentration to another area of lower concentration, diffusion really is the tendency of molecules to spread out evenly in space, typically move from an area of high concentration to low concentration,, passive process, which requires no energy, it just happens, and the diffusion of one substanve doesn’t impact the diffusion of another substance iii. Ex: molecules are in constant random motion, think about air particles, moving around randomly, even going in one direction, they still move …..SMOKING 5. We call that concentration graion, so substances diffuse down their concentration gradions iv. Another example, green and red balls in classroom v. The spreading will continue until its evenly distributed 15. Osmosis: special case of diffusion for water h. Diffusion of water molecules across a semi permeable membrane from a solution of low solute concentration to a solution of higher solute concentration i. Seems to be opposite, but really is not

j. Hypotonic: solution of lower solute concentration k. Hypertonic: solution of higher solute concentration l. Isotonic: the solutions have the same solute concentration m. Passive process

16. Osmosis
n. Selectively permeable memebrane
o. Water moves from hypotonic to hypertonic solution untl they are isotonic. p. It takes energy to maintain the higher water level in the u tube, although diffusion and osmosis do not require energ6y q. Osmotic Concentration: the concentration of all solutes combined vi. Ex, U tube, with selectively permeable membrane with 3 M nacl and .5 M glucose, has osmotic concentration of 3.5.. just the total of all solutes

r. Osmotic Pressure
vii. Osmosis can produce a pressure, which is what makes the water levels stay uneven.. s. Reverse osmosis: cleaning water, keeps solutes and lets pure water out t. The greater the concentration of solute, the greater osmotic pressure u. Animal cell- what would happen if we dunk the animal cell into a hypotonic solution , since it is hypertonic inside the cell the water would move into the cell, and it would burst (lyse) v. If we put it in isotonic solution, nothing would change. w. Shrink (shrivel) if we put it in hypertonic x. Plant cells are different though, they wont burst, because they can only take up water until they fit the cell wall y. Turgid (swollen; normal)

z. In isotonic solution the same amount of water will go in as goes out, and the cell will not push tight against cell wall, at this point plantws will wilt al little bit, and they become flaccid (soft : weak ) plants wilt {. Become plasmolysed (plasma lyses) plants may die |. The transfer of water happens quickly

17. Transport across cell membrane
}. Passive transport
viii. Diffusion
ix. Facilitated diffusion
6. Is where we have diffusion of substances in and out of the cell with the aid of membrane proteins 7. Transport protein with the open core, where molecules just pass through the open channel( these holes are called aquaporins) 8. Membrane proteins remember are very specific to what they allow though 9. Lots of these aquaporins

x. Facilitated diffusion (gated)
10. Doesn’t require energy
11. But its not an open channel it’s a gate, therefore the protein must change shape b. Usually transport amino acids (large molecules ) c. One gene makes one protein, if that gene is defective, the protein that it makes, may be defective. (sickle cell) d. Some inherited diseases result is defective transport proteins eg cystinuria i. Effects us in the kidney, where a lot of transports occur, the kidney removes everything that dissolves inblood, and then your body reabsorbs what we want. When that protein doesn’t work the cysteine builds up in our kidneys and will crystalize, and therefore will develop a certain kind of kidney stone e. Passive transport is diffusion and facilliated diffusion 18. Active Transport

~. Does require energy
. Transfers substances against where they naturally want to diffuse.. xi. A hole in the boat, water is going to naturally come in, you must put in energy to get rid of it, with a pail. . Fig 7.`6 pg 136

. Sodium potassium pump
xii. Once the protein flls with Na s the atp dropps offna phosphate group and turns into adp, which gives the protein energy to change shape and drop off the na, then k binds to the proteins, and as soon as the k binds, the phosphate is released, and then the shape of the protein bounces back, and then the k are dropped off inside the cell. viii. Transport summary review

19. Fig 7.17 pg 136
y. Voltage across membranes
ix. Used in body with nerve impulses, pump in lots of + ions and pump out lots of – ions x. Pumps often generate a voltage across a cell membrane 20. Sodium potassium pump:

21. Hydrogen pumps alsol called?: proton pump
22. Voltage can be used to do work
z. Exocytosis: Cell moves large amounts of a substance from the inside of the cell and releases it to the outside. xi. A good example is our saliva in our salivary glands 23. These cells are lined along a branch

{. Endocytosis: Cell brings in large volumes from the outside to the inside of the cell. xii. Pinocytosis- molecules like proteins ( liquids) cellular drinking xiii. Phagocytosis- particles like bacteria cellular eating 24. This reaches out and starts to form a vesicle, this “arm” is called pseudopodium, then it will completely engulf it, and pull it into the cell.

xiv. Paraguen falcon, fastest air creature, 200 mph dives cheeta is the fastest land xv. Biomimicry, nose of paragon with the cone, in the jet motor 25. Also Velcro
26. Using plants animals, microroganisms, structure to invent things

Metabolism (energy)
Life is organized into metabolic pathways
Metabolism-
Metabnolic pathway:
A B C D E etc
We can brerak down metabolism into metabolic pathway
The first 2 steps in the catabolic pathway that breaks down glucose, (very complex)
Cellular respipation take glucose combine it with oxygen, get carbon dioxide and water
2 main categories of metabolism
Catabolic- pathways where things get broken down requires energy
Anabolic – pathways were things get built up
Spontaneous Chemical Reactions -Proceed by themselves without the net input of energy
Does not mean instantaneous, sometimes may take a long time
EX a hot object always cools down
Gases always expand to fill avail space
Objects always roll down hill
When dennis bungee jumped there was potential energy when he was on the top of the bridge, then went to kinetic energy,
Free energy and metabolism (pg 147 fig 8.6
Exergonic: Output of energy
Good example is cellular respiration, the C6H12O6+O2---CO2 + H20
The glucose and oxygen has lots of energ6y, the co2 and water have less, the difference is the energy outpujt, that energy output is used to produce atp and the rest is lost as heat
Products always have less energy that the reactants
Reaction runs energetically downhill
Spontaneous reaction
G stands for Gibb Free Energy
And Delta G is negative
For the overall reaction of cellular respiration
C6H12O6+6O26CO2+ 6H2O
∆G=-686 kcal/mol
Where does energy go, atp and heat
Non spontaneous reactions- chemical reactions that will not proceed without a net input of energy
Examples, you don’t fall up
Cold coffee doesn’t get warm
Gasses don’t compress by themselves
Endergonic: the products have more energy that the reactants.
Reaction requires the net input of energy
∆G is positive
Photosynthesis is the reverse of cellular respiration
6CO2+6H2O- C6H12O6 + 6O2
+686 kcal
ATP
ATP adenosine triphosphate
Nucleotide:
Immediate source for energy that drives most cellular work including:
Transport protein pumps require atp energy
Contracting muscles Mechanical
Chemical the synthesis of proteins
ATP is the universal source of energy inside cell
Hydrolysis of ATP
ATPADP+P
This reaction releases 7.3 kcal of energy pr mole of ATP under standard conditions (room temp / Pressure)
In the cell it releases around 13 kcal/mol ( difference because of change in pressure and room temp)

Regeneration ATP
ATP is renewable
In a muscle cell, how many molecules of ADP get regenerat3d every second… LOOK UP
Regeneration is endergonic
And its use is exergonic
Where does energy come from to regenerate atp, glucose
Enzymes
Facilitate every chemical reaction in our body
Biological catalysts that accelerate a reaction
They just make it proceed faster then they all ready would have happened
Speed up exogonic reactions
They are proteins
Structure yields their function
Catalyst:
Accelerates reaction
Not consumed by reaction
Would enzymes speed the rate of an exergonic or endergonic reaction
Speed up exergonic reactions
They speed up reaction rat3es by lowering activation energy of the reaction
Every exergonic reaction requires Activation energy is the small imput of activation energy ( the spark that gets the reaction going)
Amount of activation energy, varies, enzymes lower the amount of activation energy needed to get the reaction going.
Before a reaction can occur it must have a certain amount of activation energy to start the reaction
Acitivation energy: amount of free energy that reactant molecules must gain to start a reaction
Enzymes work by lowering activation energy
Do enzymes change ∆G? NO
Enzymes are specifc for a particular substrate
Specifically depends on what? Shape of the enzyme
Sucrase
Sucrose + H2O ----------Glucose + fructose
Substrate is Sucrose
Enzymes are proteins (fig 8.16 pg 153)
Active site: region on the enzyme that binds to a substrate ( little pocket, groove, or fold) only a few amino acids at the active site, Induced fit….. as soon as the substrate fits in the enzyme, it changed shape slightly so the substrate fits perfectly , becaus3 of the induced fit change in shape, when it does fit perfect, that’s when the active site starts to tweek the substrate, stressing them, as a result it lowers the activation energy, once it changes it slightly it no longer fits perfect, therefore the enzyme opens, and allows for another substrate to enter the active site for another transformation Rate of enzymatic reactions

Temperature, Ph balance and Concentration of enzyme (refer to lab)
Temperature : is how much heat energy something has, But each enzyme has a temp optium, that means at temp at which they work at their fastest rate. So all enzymes have a temp optium, most of ours have an optium temp at 37 degrees celcius, the enzyme changes shape at high temps therefore may not work as well.

At about 60 degrees celcius, an enzyme shape changes, and it becomes denatured, and unrepairable. , explain why the graphs with optium temp are not symmetrical (pg 155 fig 8.18)

PH- each enzyme has its own optimal pH , our graph is much more symmetrical here 0|-----Xstomache acid 2----------------------------------|7-----amalayse works at 7.8----------digestive 9------------|14 Acid Base or alkaline Metabolism is regjulated because we regulate the concentration, ph, but we have a hard time using temp, 37.?O C Your tummy is acidic because that low pH in your stomach to kill parasites

When your sick and have a fever, you feel bad because your enzymes stop working as well because they have changed shape Why?(anything that effects shape or structure of enzyme can change the rate) Substrate randomly finds the active site, they don’t look for each other. Things that effect enzyme activity

Co factors – small inorganic non protein molecules (enzyme helpers)
Eg zinc, copper, magnesium and iron
Many enzymes in immune system do not work properly unless zinc is avail
Co enzymes – organic molecues eg vitamins ( help enzyme work properly)
Enzyme inhibitors ( substances that inhibits (prevents) the correct functions)- any molecule that inhibits or prevents the enzyme from working
COMPETITIVE it binds to the enzyme active site (competes with the substrate for the active site) AND NON COMPTEITIVE any molecule which binds to the enzyme away from the active site.. but causes the active site to change shape.

Can be used to regulate the production of things. By your body releasing natural inhibitors
Sometimes they bond with covalent bonds, this is an irreversible inhibitor, so that’s permanent.
Reversible if attached by weak bonds
(pH has influence on these weak bonds)
Some enzyme inhibitors are DDT (builds up in food chain) (insecticide)(irreversible enzyme inhibitior) and other poisons (parathion)(enzyme inhibitor (incecticide) antibiotics (betalactamase) prevents bacteria from building cell wall DDTs blocked the enzymes that help make the shell on the egg, therefore that’s why the birds that have become very rare.

Learning module, no more than 2 pages on chapter 8, must be hand drawn graphs..chapter summary. Include text and graphs and diagrams, and label and annotate, turn in within the first 2 minutes of exam,

Cellular respiration chapter 9
C6H12O6 + 6O2--- 6H20 + 6CO2
ADP to ATP
+
Phosphate
See glossary for definition
Cellular respiration-catabolic pathways of aerobic and anaerobic which breAk down organic molecules for the production of atp 3 major parts to cellular respiration
3. Glycolysis
4. Aerobic Respiration
A. Krebs (Citric Acid) cycle
B. Electron transport chain (ETC)
l. Glycolysis
v. Occurs in cytoplasm
vi. Requires no oxygen
vii. Occurs in all organisms
5. Prokaroyotes are the only organisms that DEPEND solely on this, they don’t have mitochondria 6. Eukaroyotes all do this, but this is only their first step viii. Glucose-- 2 molecules of Pyruvic Acid (Pyruvate) ( and each molecule has 3 carbons each ( THIS GIVES US ATP) 2 OF THEM AFTER WE Put in 2 ADP and 2P 7. The Pyruvic acid then enters the mitochondria m. (in mitochondria)

ix. 2 molecules of Pyruvate enter the mitochondria and then at this point we need to add O2 ( which has been dropped off to red blood cells) 8. Krebs Cycle (Citric Acid) Cycle

9. ETC
C. It essentially works like this, the pyruvate is very high energy, and the electrons in the glucose and pyruvate have a lot of energy as well, we harness the energy from them, we make the electrons jump from high levels to low levels, and the energy transferred are indirectly made into ATP, there are these little elctron carriers that take the energy and allow the ATP to absorb , and the oxygen that we breath in helps dispose of the excess C H and O … 10. Then the H2O and CO2 is released.

11. ADP and Phosphate groups are going to flood the the mitochondria by diffusion 12. And ATP leaves by diffusion
13. 36 total ATPs produced total for 1 molecule of glucose ( 2 from pyruvate) and 34 from Krebs Cycle and ETC x. Fungi do things slightly different, Fermentation 14. Where insufficient oxygen, the pyruvate cannot enter mitochondria, the pyruvate gets converted to, ethanol xi. In mammals

15. Where insufficient oxygen, pyruvate gets converted to lactic acid, and that lactic acid can build up in muscles…. Can give you a cramp.

Photosynthesis
Condensed version, where it occurs, and formula
Chapter 12 the cell cycle
1. Roles of cell cycle
a. Cell division functions in( 3 primary roles of Mitosis) i. Reproduction (reproduces its self as a result of Mitosis) 1. When an amoeba makes offspring by Mitosis.
2. Single celled organisms primarily reproduce by Mitosis ii. Growth and development
3. Multicellular grow and get bigger by Mitosis iii. Tissue repair and renewal
4. Smoke cigarettes, lousey diet,
b. Cell division
iv. (except)
v. First replicates DNA
5. Entire genome replicates itself
vi. DNA packatged into chromosomes, and then Seperates the chromolsome copies from one another vii. And then the cell divides into 2 identical daughter cells 6. Think of homologous chromosomes as a pair of shoes, they don’t have left or right, they have maternal and paternal chromosomes 7. Each chromosome is made up of 2 identical halfs they are called sister chromatids c. Genome – genetic instructions (all of DNA)

viii. Every cell has an identical copy of its genome 8. They way mitosis works, ensures that
9. Genomes can be small
a. Prokaroyotes have small, sometimes only 1 chromosome b. We have 23 pairs 46 total
10. Some genomes can be large
11. Large genomes are managed via organizational sub-units of DNA called chromosomes 12. We can only see chromosomes during cell division d. Eukaryotic chromosomes
ix. Made of chromatin
x. DNA has to be specially packated to fit the nucleus of each cell, xi. Our dna is 2 meters long, inside each cell nuclueus xii. Histone proteins
xiii. DNA + Histone proteins = chromatin ( histones are kinda like a bobbin and the dna is kinda like the thread around the bobbin) xiv. Chromatin makes up chromosomes
xv.
13. Find a diagram that shows the size of each.
2. Cell cycle overview
e. Interphase can be broken down into 3 sub categories: xvi. G1: 1st gap
xvii. S DNA synthesis
xviii. G2
f. Mitoic phase
xix. Refer to fig 12.5 the cell cycle pg 231
3. Cell division
g. S phase: genome is copied
4. Mitotic phase (M) can be broken down into 2 sub categories: h. Think of this as the chromosal separation
xx. Mitosis nuclear division
xxi. Cytokinesis: physically when the cell breaks into 2 i. Mitosis is a very reliable process with only one mistake per 100k divisions 5. Mitosiis is a continuous process that can be broken down into 5 stages j. Prophase- can see chromosomes

k. Prometaphase- nuclear envelope almost completely gone xxii. Centrioles move around to opposite sides of the cell l. Metaphase
xxiii. Metaphase all lined up
m. Anaphase
xxiv. Chromosomes split
xxv. The kinetochores (center of chromosome)
n. Telophase
6. The Cell Cycle
o. The cell cycle has 3 checkpoints to prevent uncontrolled cell growth xxvi. G1 checkpoint
xxvii. G2 checkpoint
xxviii. M checkpoint
p. VERY TIGHTYLY CONTROLLED
q. Molecular signals report:
xxix. Environment
xxx. Cell size
xxxi. DNA
r. At each checkpoint each cell gets these signals to tell the cell 7. G1 Checkpoint
s. G1 is important in mammalian cells
xxxii. G0 resting phase
xxxiii. Many cells at G0
xxxiv. They get called to wake up, for reasons when G1 are needed xxxv. Some cells can not
xxxvi. Some are never in G0
14. In a diagram itsa little extra side circle off of the G1 part of the circle 8. More cell cycle cues
t. Chemical : factors that can influence cell division xxxvii. Eg platelet derived growth factor (PDGF) arthrosclerosis (hardening of arteries ) and PDGF 15. (fig 12.8 pg 241)

16. LOOK UP AND READ ABOUT THEIR RELATIONSHIP
u. Physical : factors that can influence cell division xxxviii. Anchorage Dependence- to divide they must be attached to a substratum such as inside of a culture jar or the extracellular matrix of tissue xxxix. Density dependent inhibition- a phenomenon in which crowded cells stop dividing 17. Fig 12.19 pg 242

9. Cancer
v. What do you know about cancer?
xl. Uncontrolled grown of cells
w. US mortality 2006
xli. Heart disease 631,636 26% of all deaths
xlii. Cancer is next
10. Cancer cells
x. Form immortal cell lines
xliii. Normal cells, once they divide into 2 we no longer have the orig cell, we have 2 daughter cells, normal cells go through 30 maybe 40 rounds in the linage, then they die out, the cancer cells, have no limit….they just continually divide y. They keep dividing… there may be periods when they stop, but for the most part, they just keep dividing z. Products of normal cells, cant catch it, but you can catch viruses that can start the cancer {. They kill you by disrupting systems

|. 2 types
xliv. Benign:
xlv. Malignant:
18. Uncontrolled growth
19. Invasion- might start off as a small mass, but then they invade other tissues and organs 20. Metastasis- some cells break off from main tumor site, and then settle in another place and lodge themselves in and then start to divide c. Fig 12.20 pg 243

d. Once a cell turns cancerous, the checkpoints used to regulate the division stop working… and they continually divide e. The cancer can travel through blood vessels and lymph vessels and nodes 11. Cancer

}. What is it?
xlvi. Tumorgenesis- formation of a tumor
xlvii. Metastasis
xlviii. Angiogenesis- where stimulates and develops a blood supply to feed the tumor 21. Immortal
~. What causes cancer ?
xlix. Lots and lots of mutation
22. When the DNA gets damaged in some way
. What causes mutation?
l. Certain chemicals
23. Cig smoke
24. Charred meat
25. Chemicals inside house and industrial (gasoline) 26. Dioxin (agent orange) used in Vietnam war
f. Group of compounds
li. Radiation
27. Example x rays … and dental x rays
28. Sun (Ultra violet rays)
Natural decay of many radioactive isotopes Carbon 14
lii. Mutation of specific types of genes
29. Proto oncongenes
30. Tumor suppressing genes
g. It is possible to have inherited some of these mutated genes from your parents . Tumolr sujppressor genes tell them to stop dividing
liii. Eg p53 (guardian angel)
liv. Damanged DNA activates the guardian angel
31. Prevents the cell from dividing until repairs can be made (p21 gene) 32. Turns on repair genes
33. If damage is to great, suicide genes are activated 34. Has a role in the apoptosis (programed cell death) lv. Almost all cancers have a mutation in their p53 gene papillomavirus gene interferes with p53 genes protein and normal apoptosis . Mutation of a tumor stop suppressor gene

lvi. Stop dividing
lvii. Point mutation
lviii. Stop divding
lix. Means nothing, and keeps dividing
. Proto – oncongenes
lx. Proto means before, and they say continue dividing ( but a very quiet signal) lxi. When they get mutated, they begin to yell and amplified, and it tells DIVIDE DIVIDE DIVIDE DIVIDE DIVIDE lxii. Once it has been mutated it is called oncogene after is mutated 35. MYC

lxiii. Transcription factor responsible for turning on genes that prepare for cell division 36. A mutated cell, makes lots of transcription factors, a normal cell would not make so mjuch 37. 25% of mice

lxiv. Genes involved in various cancers
lxv. Tumor suppresors oncogenes
lxvi. -p53- myc
lxvii. -retinoblastoma RB- ras
. Cancer how is it treated
xlviii. Radiation
29. Don’t feel immediately.. fill later on, effects chromosomes. When a cell divides, the daughter cells are nonfunctioning 30. Problems with radiation
v. Kills cells indiscriminately (healthy or canceros) w. Risks causing mutation in healthy cells
xlix. Chemotherapy
31. Chemicals which prevent cells from dividing 32. Gives us wrong bases to make copies of dna or interfere with it during duplication 33. Example AGCTCTGA
34. TCIIIIIIIIICT
35. Interfears with necessary proteins for physical cell division 36. Eg microtubules ( spindle fibers)
Effects sperm cells, any cells with cilia
37. Problems with chemotherapy
38. Kills all cells that are dividing cancerous or not 39. Hair, skin blood
40. So how do we find out which of these u7nknown genes are involved in cancers 41. SEE LAB AND TEXT BOOK FOR MEIOSIS
Y THE EARLY 1930S SCIENTISTS HAD A GOOD IDEA THAT CHROMOSOMES DNA AND PROTEINS CONTAINED THE GENETIC MATERIAL, BUT THEY THOUGHT THAT PROTEINS (HISTONES) WERE RESPONSIBLE FOR INHERITANCE NOT DNA, BECAUSE PROTEINS WERE MORE COMPLICATED

IN 1926 FREDERICK GRIFFITH PERFORMD FOUR SETS OF EXPERIMENTS THAT HELPED SHOW THAT THE GENETIC MATERIAL WAS A SPECIFIC MOLECULE:
HE TOOK 2 DIFF STRAINS OF STEPTOCOCCUS PNEUMONIA (PNEUMON IA CAUSING BACTERIA)
ONE STRAIN (S) COULD (SMOOTH BOARDERS) FORMS CAPSULES BY-PASS THE IMMUNE SYSTEM AND CAUSE DISEASE. SICKNESS
THE OTHER STRAIN (R) (NO EXTRA CAPSLE AND LOOKED ROUGH) COULD NOT FORM CAPSLES AND WERE EASIL PHAGOCYTOSIED BY THE WHITE BLOOD CELLS -- MIGHT GET SICK BUT SHOULD SURVIVE gRIFFITH'S EXPERIMENT PG 306 FIG 16.2 (MICE)

WHATEVER CHEMICAL THAT TRANSFORMED THE R STRAIN TO THE S STRAIN MJUST BE THE GENETIC MATERIAL
GRIFFITHY CORRECTLY DEDUCTED THAT SOME MATEIAL FROM THYE DEAD S STRAIN WAS BEING TRANSFERRED TO THE R STRAIN TRANSFORMING

GENETIC MATERIAL REVEALED
IN 1953 ALFRED HERSHEY AND MARTHA CHASE SHOWED THAT DNA WAS THE GENETIC MATERIAL OF THE PHAGE (VIRUS) T2
FIG 16.3 PG 306
THE T2 PHAGE IS COMPOSED OF BOTH DNA AND PROTEINS. WHEN IT ATTACKS E. COLI IT INJECTS A MATERIAL. THIS QUICKLY TURNS THE BACTERIA INTO A T2-PRODUCING FACTORY THAT RELEASES PHAGES WHEN THE CELL RUPTURES (PAGE REFERS TO EATING, AND THIS IS A BACTERIA 'EATER" THEY DONT REALLY EAT THEM, WE KNOW THIS NOW, BUT BACK THEN THEY ONLY KNEW THAT THEY WERE MADE OF DNA AND PROTEIN, INFECT BACTERIA, KILL BACTERIA, THEN MAKES THE CELL PRODUCE MORE VIRUS PARTICLES... THATS ALL THEY KNEW BACK THEN.(VERY TINY PARTICLES)

HERSEY AND CHASE CONDUCTED EXPERIMENT FIG 16.4 PG 307

KNOW DETAILS OF BOTH OF THESE EXPERIMENTS
CHASE AND HERSHEY, CONCLUDED THAT DNA NOT PROTEIN FUNCTIONS AS THE GENETIC MATERIAL OF PHAGE T2

MORE EVIDENCE3 DNA WAS THE GENETIC MATERIAL
SUBSEQUENT EXPERIMENTS SHOWED THAT:
GAMETES ONLY HAD HALF THE AMOUNTO OF DNA S THE ORGANISM THAT PRODUCED THEM
THE AMOUNT OD DNA WAS DOUBLED IN CELLS PRIOR TO MITOSIS
SO THE NEXT STEP WAS TO FIGURE OUT HOW DNA WORKS

DNA THE MOLECULE OF LIFE
CELL THEN COMES CHROMOSOMES THEN COMES DNA THEN COMES GENE- LENGTH OR SECTION OF DNA THAT CODES FOR A PROTEIN TRILLIONS OF CELLS
EACH CELL
-46 HUMAN CHROMOSOMES
-2 METERS OF DNA
- 3 BILLIONS DNA SUBUNITS (BASES A,T,C,G)
-APPROXIMATLY 30,000 GENES CODE FOR PROTEINS TAT PERFORM MOST OF LIFE FUNCTIONS - ONLY ABOUT 3% (does vary a little bit) FORMS GENES, THE REST OF IT 97% (again varies a little) is non coding, which means it does not form genes ( JUNK DNA) DNA STRUCTURE

DNA REPLICATION
HOW PROTEINS ARE MADE FROM DNA

DNA STRUCTURE
IN 1953 CRICK AND WATSON CAME UP WITH THE STRUCTURE OF DNA
(PHOTO OF CRICK AND WATSON) (PHOTO OF THE MODEL)
THEN THERE WAS SCANDLE THAT THEY STOLE THE MODEL FROM ROSALIND FRANKLIN. A FRIEND OF THEM OR ONE OF CRICK AND WATSON CHECKED OUT HER RESULTS
DNA IS A POLYMER, MADE UP OF NUCLEOTIDES ( 4 DIFF TYPES OF NUCLEOTIDE) GENERICALLY A NUCLEOTIDE CONSISTS OF A NITROGEN BASE, A PHOSPHATE GROUP, AND A SUGAR. ( FIG 16.5 PG 308) IN THE CASE OF DNA THE SUGAR IS CALLED DEOXYRIBOSE SUGAR

AND THE NITROGEN BASES HAVE 4 TYPES : ADENINE, GUANINE, CYTOSINE, OR THYMINE
DNA STRUCTURE
DOUBLE HELIX , DOUBLE STRANDED, RULE A-T C-G
(DRAW A DOUBLE STRAND OF DNA HERE)
ALTERNATING PHOSPHATE SUGARS ARE THE BACKBONE
THE PHOSPAHTE SUGARS ARE BONDED BY COVALENT BONDS
THE NUCLEOTIDES ARE COMBIINED BY HYDDROGEN BONDS

CHARGAFFS RATIO
IRWIN CHARGAFF DNA OF ANY GIVIN SPECIES THE RATIOS BETWEEN A AND T AND G AND C REMAIN THE SAME, ONLY THE DIFF AMOUNTS OF COMBOS A-T AND G-C RATIOS CHAANGE
SO C-13% A-37%
G-13% T-37%
U TUBE VIDEOOF 5 YR OLD BRYCE SAYS DEOXYRIBONUCLEAIC ACID (DNA)

3' (PRIME) AND 5' PRIME ENDS
FIG 16.7 PART B
THESE RUN IN OPPOSITE DIRECTIONS THE 5' ENDS IN A PHOSPHATE GROUP AND THE 3' ENDS IN A SUGAR
THE POINTY PART OF THE SUGAR O POINTS TO THE PHOSPHAT3 GROUP (WHICH IS THE 5' END)
THESE STRANDS RUN ANIT PARALLEL
A-T HAVE 2 H BONDS ND G-C HAVE 3 H BONDS

THE NUMBERS REFER TO THE POSITION OF THE CARBON.

THIS CLASSIC DOUBLE HELIX DOESNT ALWAYS LOOK PERFECT, SOMETIMES CAN BE CURVED

DNA REPLICATION
1. HELIX UNZIPS
THIS BREAKS THE H BONDS BECAUSE OF HELICASE (ENZYME) THAT BREAKS THE H BONDS
2. USING THE 2 EXPOSED PARENT STRANDS AS TEMPLATES
THESE ARE CALLED PARENTAL STRANDS AND THEY ACT AS TEMPLATES
In nucleus cytoplasm, there are tons of extra nucleotides ( ready to assemble daughtr strands)
3. THEN DAUGHTER STRANDS ASSEMBLED A-T AND C-G
DNA Polymerase the enzyme that adds nucleotides
4. 2 IDENTICAL COPIES RESULT
Only 1%-5% of genome codes for proteins, about 25% is for genes, and the rest is unknown Video showing the replication origin, and replication bubbles. We start replication at many different origins .. and it happens very quickly Okazaki fragments – look up from movie

Keep this rule straight
DNA polymerase ONLY adds to the 3’ end
(the first one, that follows helicase, is called the leading strand. The strand that is copied “backwards” is called the lagging strand…
The lagging strand gets copied in segments, because polymerase has to jump up to follow helicase, these segments are called Okazaki fragments Key enzymes
Helicawse unzips dna heliz
Polymerase: joins nucleotides of the complimentary strand

How proteins are made from DNA ch17
Proteins are incredibly varied : 10-100 thousand different proteins We have about 30,000 genes
A gene is responsible for making proteins
Proteins are involved in every metabolic reaction
Metabolic reactions are what you tick and make you unique
In a nutshell
Here is how proteins are made from dna
The directions information is encoded in DNA: order of nucleotides in a gene
Genes vary in length
The sequence of the nucleotides is important
Genetic information is decoded: used to assemble amino acids in specific sequences to form a polypeptide gene, which will them form proteins
Each gene has a unique code, each gene will make a unique different polypeptide.
The sequence of nucleotides determine the amino acids
The protein will then perform i5ts function and have an effect on your phenotype
Huge chromosome ( tiny flies pull their head off, huge salavory glands)
Genes are lengths of DNA (we can map for genes)
The sequences of bases in dna encodes information
Dna remains in nucleus
Proteins are made in the cytoplasm
The information encoded in dna is transcribed into rna which them moves into cytoplasm
DNA stays in nucleus for lots of reasons
RNA STRUCTURE:
Phosphate – same as dna
Sugar- has ribose sugar not deoxyribose sugar
4 nitrogen bases – has cistine like dna, also guanine like dna and it has adenine like dna, has no thymine it has U uracil
RNA DIFFERS FROM DNA
RNA is single stranded
Has U not T

Similataries
Nucleac acids
Polymers of nucleotides
Both have phosphate, sugar, and 4 nitrogen bases
3 different kinds of RNA
38. mRNA structure
h. phosphate
i. sugar
j. 4 nitrogen bases
i. Differs to dna
A. Single stranded
B. Has U not T
k. Has 3’ and 5’ ends
lxviii. M Rna
l. Transcribed from dna in nucleus, leaves nucleus trhough nuclear pores, into cytoplasm then it goes to a ribosome and attaches, which is where proteins are made 39. tRNA

m. phosphate
n. sugar
o. 4 nitrogen bases
ii. Differs to dna
C. Single stranded
D. Has u not t
a. Made in nucleus, but spend virtually all their time in the cytoplasm, there job is to carry amino acids but the amino acid that they carry is specific to the anticodon sequence 40. rRNA

p. phosphate
q. sugar
r. 4 nitrogen bases
iii. Differs to dna
E. Single stranded
F. Has u not t
b. What ribosomes are made of
c. Produced in nucleolous by dna
d. Spend most of their time in cytoplasm, some on er. (rough er) e. Made separately but once the large subunit and the small subunit are joined together then they can make protein . Transcription DNA

lxix. Take a gene from dna and transcribe it into RNA mRNA lxx. DNA unzips at a specific gene ( the gene contains info to make proteins, therefore the gene is switched on, and transcribes) lxxi. An enzyme assembles a strand of Mrna ( USING THE DNA as a template) 41. Enzyme is called RNA polymerase

lxxii. A single gene is tanscribed into Mrna
42. The rule is A-U
43. C-G
lxxiii. HOW PROTEINS ARE MADE FROM DNA
44. rna polyermaise does both jobs of dna polermase and helicase 45. using the code in the dna as a template for rna, it unzips and reads, assembles the rna and then it zips it back up, when its done, it goes away, when the rna is complete it leaves nucleus to ribosome n 46. fig 17.7 and 17.8 pg 332 and 333

47. drew transcription of Mrna here
48. rna polymerase can only add to the 3’ end just like DNA POOLERMAISE . Translation
lxxiv. Literally turning the code of mrna and make it flesh and blood lxxv. translationL Mrna to proteions
49. information of rna is used…
50. to direct the sequence of amino acids
51. in a new polypeptide
52. take the sequence in the mrna and assemble it into the primary structure of the protein 53. we only have 4 nucleotides on mrna, so in groups of 3 code from amino acids ( pg 330 fig 17.5) 54. the amino acids are bonded by peptide bonds… 55. 3 bases form a codon on mRNA

56. tRNAs have anticodons that match mRNA codon 57. tRNAs carry amino acids specific to the anticodon 58. on ribosomes, amino acids are linked to form proteins 59. the sequence of amino acids is directed by the sequence of bases in mRNA and 5hus the sequences of bases in DNA lxxvi. How proteins are made from dna

60. He had a nice diagram ( maybe like 17.3 pg 337) 61. Some proteins are immediately functional, but others may need more modification from golgi, and pairing with another protein 62. USE 17.5 TABLE ON PG 330

s. Must have mrna in the correct 5’ to 3’ direction.. very important So far a gene is a sequence of dna, made into mrna, and trna Assists in making a protein so DNA goes to mRNA, which is transcription and

Exons – real coding part (exits)
Introns - non coding part
Only exons make it to rna, the introns are cut out during rna splicing

Showed the pics of the baby, testing for phenoalinine, (in diet soda) the gene that metabolizes this drug, sometimes, isn’t given the correct copy of the gene, and therefore the phenoalinine will build up in the body, and will cause mental retardation if you have the bad copy of the gene, you can moniter diet. ( aspartame, sweetner in diet soda, has high levels. (PHENALCOTURIA) 3000 human traits ( characteristics) determined by single genes

Cystic fibrosis
For every trait we have 2 genes
( inter protein that transports chloride) cystic fibrosis has a flawed gene that codes for this transport protein, therefore if you have 2 copies of this one single gene that are flawed then you have cystic fibrosis

Another thing from one gene, is polydactamy ( 6 fingers) baldness, clubbed fingers. Hemophilia ( blood wont clot) , color blindness hairy ears. Many of our traits (our height) are determined my multipal, genes, eye color is determined by a couple genes, The single gene determiniations are one or the other

Chapter 14
Mendelian genetics
Study of the inheritance of biologically expressed traits ( pic of white tiger and the black and orange tiger)
Tigers are rare now, but they used to be more common, populations in asia and india ( about 20 years ago) orange tigers were very common, india was divided into 2 provinces, Maharages were the ‘royalty’ they hunted tigers, form a big line, bang pots and pans, which would scare tigers, so they would run, the maharage seen a white tiger, and he thought it was marvelous, so he captured it, so he could breed it, he bread it with an orange tiger, to see if he could get more white tigers.

When he bread them, all the cubs were orange.
When one of the offspring mated with the white one, they got 4 white ones, and 4 orange ones.

How can we explain that and many other patterns of inheritance?

The first person to really study this is Gregor Mendel (a little more than 150 years ago, he was a monk) he was the first to investigate laws of inheritance In 1856 to 1863, published in 1865, he worked with garden peas, Pisum sativum ( scientific name for peas)

Key terms
Phenotype- any characteristic or trait that you might have
Ex; height, eye color, if your pee smells funny after eating asparagus) color of hair, skin, but it also applies to things you cant see, for example your blood type. Chemical, physical.
Your phenotype is determined by DNA ( genes) + environment.

Some phenotypes are determined 100% genetically
( cystic fibrosis, blood type, 5 or 6 fingers)
Some phenotypes are 100% determined by environmental
Ex( fetal alcohol syndrome, thalimide children, name of a drug that drs used to give mothers to rid morning sickness) Some phenotypes are determined by a combo of genes and environment IQ is 60% determined by genes and 40% environment

He showed us the pic of hydranges flower, the color of this flower is determined completely by environment, pH specifically, basic is blue, acidic is red.

There is a lot of debate about criminals, are they born bad or is it the environment, what we do know, is that it is caused by a combo of environment and genetic

With autism there is some genetic links to autism, but even if you have autistic genes, and do not have the environmental factors to activate the gene, you never get it

Mendels experiments
How can we figure out if genotype is environmental or genetic He decided to work with pea plants because
Plants with flowers are easy to cross (mate)
Used distinct characteristics
( he saw different colors of flowers, very distinct) ( like tall or dwarfs) unambiguous Controlled experiments – crossed plants by differing in only 1 trait at least at first. So he took pink flower plants with white flower plants, that’s the only difference. He was very quantatitative with his data, used large number of crosses, recorded data, and then used algerbraic methods to analaze.

Mendel’s observations, he called his plants true breeding lines. So he would ensure that the purple was all purple, no white in there past. Then he would take the true purple and the true white, and cross them

Used true breeding plants
Purple X White flowers =?????
He removed the stamens from the purple flower, and transfer the pollen from stamens of white flower to carpel of purple flowers, pollinated carpel matured into pod, planted seeds from pod, and examed offspring all purple flowers, so PxW F1 plants was 100% purple then he crossed F1plants with F1 plants so in the F2 he got purple and white flower plants, so the white color kinda reappeared , so he counted the number of each, and found that he got a 3:1 ratio ( 705 purple and 224 white plants) This made him curious, he wondered if he could repeat it, so when he looked back at his results, he determined that the white trait was masked by the purple flower, He came up with these terms, the masked factor is recessive and the expressed factor is dominant , when he repeated this he got the same ratio, when he followed these protocals exactly, Always saw a 3:1 ration in the F2 generation (when using CONSTANTs) Cystic fibrosis x cystic fibrosis=

F1xF1
Cystic fibrosis x normal =
F1 x F1
Back to mendel table 14.1 pg 265
We are looking at patterns of inheritance
We are trying to explain those patterns of inheritance
We discovered a consistant pattern for some phenotypes, for example cystic fibrosis, tounge rolling, flower color in pea plants, stem color in brassica plants (tangent)Asparagus, chemical pathway A -- B (which enzyme 1 changes) and then B C and enzyme 2 changes, and then CD , but some genes, don’t produce enzye 2, therefore it only goes from ab and b stinks True breeding parents, one with one of the phenotpyes the

So how do we explain this patern of inheritance?
So this is how we (and mendel ) explained it
Alternative forms of genes (DNA ) are responsible for variations in inherited characters called alleles These alleles occur at the same position (locus) on the chromosome fig 14.4 pg 265 Gene – flower color and the alleles –purple + white

Which ever is dominant we make (CAPITAL) and the recessive we make in (lower case) Purple – P and white is – p

For each character an organism inherits 2 alleles ( one from each parent’s chromosome) Called homologous chromosomes
The 2 alleles for each character segregate during gamete production ( meiosis ) this means half will get one allele and the the other half with get the other allele

If different alleles are present in the parent, then
There is a 50% chance that a gamete will receive the dominant allele
There is a 50% chance that the gamete will receive the recessive allele This is mendels first law, the law of segregation!!!!!!!!!!!!!!!!!!!!!! The law of segregation- the two alleles at a locus are separated during meiosis and only chance determines which will end in each gamete. Useful genetic terms

Homozygous: Having 2 identical alleles for a given trait.
Also known as true breeding ( for that trait)
Homozygous recessive ( both alleles are recessive) eg. Both alleles code for white flowers
Homozygous dominant ( both alleles are dominant) eg both alleles code for purple flowers Heterozygous: having 2 different alleles for a given trait
Eg one allele for white flowers and one for purple
Phenotype: traits that can be seen ( some things you cant see) eg. Purple flowers Genotype: an organisms genetic make up (eg. Alleles (PP))
So far
Predicting inheritance by using Punnett square fig 14.5 pg 266 A punnett square predicts the results of a genetic cross
Upper case letters= dominant allele ( P= dominant purple)
Lower case letters = recessive allele (p= recessive white)
PP= Homozygous dominant
Pp= Heterozygous
A pp= homozygous recessive
Phenotype and Genotype
Identical phenotype but different genotype fig 14.6 pg 267
Test cross: To determine unknown genotypes fig 14.7 pg 267
Mendelian Inheritance
Single gene with 2 alleles
Dominant and recessive alleles
BUT, not all traits are simple, Mendelian traits
Other mechanisms of inheritance that yield different patterns of inheritance. Other mechanisms of inheritance
Explain this result
Red true breeding parent crossed with white true breeding parent yields : 100%pink F1s fig 14.10 pg 272
Incomplete dominance :the dominant phenotype is not fully expressed in the heterozygote
Complete dominance:
Explain this
Heterozygous parents cross to yelid the flooling phenotypic ration: a phenotypic ratio of 2;1 yellow to brown
This concept is Lethality
Mice hair yellow or agouti (brown)
Yellow allele dominant over agouti allele
In 1904 Lucien Cenot found this
Found 2:1 ratio of yellow to agouti instead of expected 3:1
Test crosses revealed that all yellow mice are heterozygous, so they concluded that the homozygous yellow, is lethal, not compatable with life Hunntington’s disease also dominant lethal
Homozygotes never survive
Heterozygotes have disease does not manifest itself until later in life (30-60) Multiple alleles: it is possible to have more than 2 forms of an allele (blood type) fig 14.11 pg 273
Blood Group IA IB i
1 gene with 3 alleles (A,B, i)
Co dominance- 2 of the alleles are equal dominant. So if you have an A and a B ( and both are dominant) then you have AB blood The i allele is recessive

Genetic variation
* 2n where n= number of genes that a species or organism can have and 2 is the number of alleles * We have between 25,000 and 30,000
* So if we have 5 genes there are 32 different genotypes possible * 10 genes ( and that number is too simple) – 1048
* 30 000 genes = too big ( with 300 there are 2 x 1090)
* The chances of getting the same genes as somebody else.. is sooooooo small, in the human race there are sooo many different genotypes, that’s why you don’t look like anybody else

Chapter 20 Biotechnology
What is DNA technology?
Manipulation and exploration of DNA
Think of dna as software ( chemical) that tells body and cells what to do He was talking about craig ventor who was on the news, and he had invented synthetic cells. He took the basic cell of one bacteria, removed all of the genetic material, took material that he made himself, and put it in the cell, and got a functioning cell. (growing alge that use co2 to produce oil. ) Genetic engineering is where we take a gene from one organism from one species and place it into another species. Recombinant DNA – where we take dna of one species and mix it with another ( bacteria with human) DNA cloning – different than organism cloning, this is where we make copies of a fragment of DNA Gene therapy- ex if you have an individual with cystic fibrosis, inherited disease,what if some how we could shoot into their cells, a correctly functioning gene. Then we just fixed the disease The Human Genome project- a project that has now sequenced the entire human genome, all (just under) 3 billion. We don’t know what it does, but we know the sequence ( comparing DNA) Environmental Clean ups- think of the BP oil spill, so think about trains that go along train tracks, they drip oil, and they produce bacteria, that can eat the oil, put bacteria in the ground that may be able to produce natural fuels

GMO’s – genetically modified organism. ( some food companies put on food) Forensics – a unique dna sequence, for each individual

We use this a lot, and it is only going to get bigger, and its important that we know about them

What is biotechnology>
Genetically Manipulation of an organism or their components to make useful products Human insulin ( diabetic) they used to purify pig insulin, but now we pull out the gene to make insulin, we pop it into the bacteria, and then the bacteria make human insulin Same thing with human growth hormone.

Tissue plasminogen activator ( another substance that we can have bacteria make) Insecticidal plants – plants that produce their own insecticdes

Recombiant DNA technology
Recombinant DNA : recombining DNA from one (species) organism with another By placing the target gene into a host, the host can then make the protein\ express the desired characterisitic. How is this done? Plucking out the gene and putting it into another Most biotechnology work involves Bacteria, simple because bacteria are easy to grow and they only have 1 chromosome. So they only carry one allele, easy to reproduce Review bacteria; simple only have one circular chromosome

Often also have a plasmid= extra piece of circular DNA, smaller than the chromosome. Some have the plasmid… but some don’t, the plasmid does carry some extra genes, for example MRSA ( their resistant genes are carried on a plasmid)

Plasmids
Size varies, just a circle of dna that carries genes, genes vary Plasmids can jump from one cell into another = transformation Bacteria can replicate the plasmid, and then it will release the copy In the lab, we can add stretches of DNA such as a gene to a plasmid If a bacteria takes up that plasmid, we have successfully genetically engineered the bacteria Simply placing the dna from one species to another is genetic engineering, but once we put a plasmid into a bacteria, we can just have bacteria reproduce ( once every 20 min) So if the bacteria then divides and makes copies of the plasmid we have cloned the gene Gene cloning is where we make copies of genetically engineered DNa Terms thus far

Recombination
Recombinant DNA
Plasmid
Vector * anything with respect to DNA is whatever will carry the dna, so plasmids can be a vector, viruses can also be a carrier for our dna Gene cloning
Gel electrophoresis

Cotton, pictures of cotton, I bet everyone in the class has some sort of cotton on, cotton has the highest level of pesticides, because we don’t consume it as food, so it has a lot of chemicals appleied to it, there are a lot of insects pests, this one is a catapillar of a moth, and so the moth layes its 100 eggs, and then the catappillars mow down the cotton plant, the structure of the plant it eats, after a couple of month, we are gonna have thousands of them, theres a pic of the moth, so then our solution is spray spray spray, so we increase pesticsdes which are expensive, and we get a lot of run off, and lots of bugs killed So here is our solution there is a bacteria called bascillus thuringiensis Bt for short Looks like little rods, ( ibprophin tablets) very tiny, 2 or 3 microns if that Bt is very common but was first found in pine tree leaves (outside) what they noticed is that every now and again, some of these insects that feed on pine needles would increase, and then just go away, they didn’t know why, but when somebody looked the Bt was growing, and this Bt, produces this big structure inside it, and that big structure is an insecticide, and it is called a Bt toxin, and that toxin is a protein, this toxin kills the bugs that eat the leaves that they grow and live on. A natural but very potent, it is activated by alkaline pH of insect gut, inserts into gut cells membranes, and forms a big pore, so it makes holes in the guts, which just lets everything leak out, and the insect just dies. the gene encodes and makes the protein and the gene is located on a plasmid refer to fig 20.2 on pg 397 Showed us pic of round up ( chemical herbicide ( gets rid of weeds)) Can we make the cotton plants resistant to the round up ?

These cotton plants that can do this are cound round up ready. So now we have cotton plants that produce their own insecticide and are round up ready plants

In 1996 87% soy was round up ready
In 1998 RuR corn

Fig 20.2 again.
The vehicle used to insert the foreign DNA is called a vector Plasmids can be vectors as can viruses
Also you can put dna into a host, take tiny almost microscopic gold beads, then you use electricity and fire the beads into the cell. And hopefully it works, but you must do it a lot. Must have enough beads, dna and cells. Remember the t2 phage that’s how viruses work, they insert their dna into the organism There are some plasmids which bacteria have, where the plasmid infects the host Natures genetics engineers

Agrobacterium tumefaciens, also looks like rods
The bacteria has plasmids inside and what they do is infect rose, its on the stem and has Galls, what causes the calls is agrobacterium and all it takes is a little damage in the rose stem, if the bacteria gets in one of the wounds, the plasmid inserts itself into the plant genome, kinda like what a virus does, and any cells that are infected with that plasmid, periferate and grow and the bacteria lives inside that Gall and the plasmid have genes, that make the rose plant produce certain sugars, that the rose plant cannot use, but the bacteria can, so rose growers hate this, they have to clip it off and burn it. ( kinda like warts—viruses injected galls) Jumping genes: Transposons

(corn kernals, that have yellow and red pigments. Its not a bacterium or a virus but a transposons, which are short fragments of dna that plants and other organisims have, they are bizarrae, the fragments are able to replicate themselves, and then insert themselves into another part of the genome. )

So how do we do it?
How do we:
Find the target gene?
How did we find the gene in humans that code for insulin?
then once we find it how do we remove it?
How do we clone it?
How do we place it into a vector?
Insert it into a host genome???
In principal its quite straight forward, so lets look at some of the tools of biotechnology
The tools of biotechnology
Restriction enzymes- we have lots of different restriction enzymes, each one has a unique restriction site
Enzymes that cut DNA at specific sequences
Molecular sissors
One called E co (ecoli) R1 (restriction enzyme 1)
Eg EcoR1 cuts at GAATC
Sticky end fig 20.3 pg 398 Pay special attention to how it cuts ( between the G and AA)) Dennis drew this on the board ( must be important)
We find these in bacteria, our body doesn’t make these. Restriction site ( molecular biologists do it with their sticky ends!! )Where sequence of dna at which the restriction enzymes cut.
Site or sequence at which the restriction cuts eg. Eco R1 cuts at GAATTC
DNA Ligase – like molecular paste ( enzyme) joins DNA back together
Enzyme that rejoins DNA (Molecular paste)
Denaturation- simply means we separate the 2 strands of DNA
Southern Blot ( show us later what this is)
Probe
Restriction enzymes, DNA ligase, plasmids
Here dennis drew on the board the plasmid that was cut, and he showed us how the dna from the human cell would be inserted into the plasmid. Its very important that the restriction enzyme used to cut the human dna, is the same that we use to cut the plasmid, so the sticky ends are the same!!! That is very important because if the sticky ends are not the same the strands will not join, then in the test tube we will add the plasmids to bacteria, the bacteria will then suck up the plasmid, and then they will reproduce, wich will also reproduce the plasmids, and the gene we inserted ( in this case the the human insulin gene) again refer to fig 20.3 on pg 398 Here we talked about fig 20.2 on pg 397

Denaturation
Separate double stranded DNA into single stranded DNA
Eg with heat, also high salt and pH.
Probe
Short piece of single stranded DNA that is ‘hot” which means they are radioactively labeled)
Can bind to other single stranded DNA
Used to ‘tag’ target DNA sequences.
The ones we want to focus on is radioactive ( there are companies out there that will manufacture probes ( whatever kind you want) and send you millions and billions of them.
Usually use radioactive phosphorus
Constructing the probe
Lets say we want to find the gene that codes for insulin ( could be any protein) Fredrick sanger won 2 noble prizes in science. Dennis met him once, he got one by sequences proteins, (human insulin) and how to sequence DNA. 1918-2007 won 2 Nobel prizes in 1958 and 1980 ( sequenced dna and proteins) So we sequence the human insulin gene, we figure out the mRNA (using the codon for each amino acid table) sequence from the amino acid sequence.

Then we can figure out the dna sequence from the mrna sequence
Then construct the probe with a complimentary sequence and make radioactive.
Example Cys Cys Thr Ser ( amino acid sequence)
UGU UGU ACU UCU = mRNA
ACA ACA TGA AGA = DNA
TGT TGT ACT TCT = probe (radioactive)

Lo cating the Target Gene
Extract the DNA
( liver is a really good place to get DNA but we can do it from anything, cheek cells, if we have a chunk of tissue then we add liquid nitrogen, which will freeze them, then we grind it all up. )

Cut the DNA into small fragments ( with what) restriction enzymes.
Then lets run them on a gen to separate out the fragments
Southern Blotting
Fig 20.11 pg 407
Each of the tubes have dna, identical DNA, so maybe we took some liver tissue, ground it up, and extract DNA from tissue, put it in the tube, then we add restriction enzyme to tube 1, in tube 2 we add a different, and in tube 3 yet again, another restriction enzyme, which will cut the dna into fragments, lots of different fragments, then we run it on a gel, the differences in the gel patterns, are the different size pieces. So now we have the gel with the fragments, remember we are looking for a gene, if this is from a human, we know that one of the lanes will have the gene, then we use this lil concoction, looks more complicated than it is, get a tray, get a sponge, add a buffer solution with a pH of 9 or 10 ( very alkaline) high pH breaks h bonds and will denature the dna, then we put our gel ontop of the sponge, then we add nitrocellulose paper, and then the bio book, the alkaline will fuse to the gel, and then denature dna, we will still have the bands, but now the bands are single stranded. The nitrocellulose paper, feels like inkjet paper( very smooth paper) and what it does, its not sticky, but its sticky from a molecular paper, so big molecules stick to the paper. Some moves up through the gel and sticks to the paper, and its stuck there. We cant see the dna but if we could, the bands would be identical to whats on the gel. We peel the paper off the gel, and we have the paper with the dna stuck, next we put it in a plastic bag, and we add a solution that contains our probe. (remember we constructed the probe which is unique to the sequence that we are looking for. ) anytime the sequence is find, the probe is going to stick and remember the probe is radioactive. But then we lay the nitrocellulose paper to photographic film, ( and the radioactivitiy exposes the film) therefore anyplace that the probe bound to dna, that probe is going to stick there, and then it will expose the film, then we will have this dark bands which will then locate the fragments of dna that might have the dna sequence , then we take the scalpel and cut out that fragment out of the gel, and now we have what we were looking for. ( then we went back to fig 20.2 ) and applied that process. (forrest gump) cute Steps of southern blotting

DNA is denatured
Add the probe
ID ‘radioactive’ fragment
(its important that you remember where the fragment came from ( on the gel )so we know what size the fragment is and what enzyme we used.

Chapter 22
Decent with Modification A Darwinian View of Life
You have seen the huge diversity of species on earth
Graphics bacteria, protists, animilia fungi and plante, all similar how can we explain this diversity. DNA genetic material, all living orgainisms are cell based. But then we have massive diversity. How can we account for:

The species we have on earth
New species that arise (discovered, and evolution)
Similarities among closely related organisms
The closest relative to the human is a banobo chimpanzee share 98% similarity Evolution
Brainstorm everything that comes to mind when you hear evolution
Darwin, Genome, adaptations, environmental factors, god, dinosaurs, monkeys, Science is evidence based
Central (parts) tenents of evolution:
All living things are descended from common ancestors. So we have common ancestors we decedned from, and if you go back far enough you can trace first form of life, very ancient bacterial cells,
Groups of living things can change over time into species. They used to believe that species here on earth have always been here and will always be here, that has been proven false, human beings have not been on earth forever, and species change over time.

Misconceptions
The first misconception there is a believe that human beings evolved from monkeys, the evidence shows that humans and monkeys had a common ancestor and descended from a common ancestor, and that ancestor is not living today, it is extinct, showed graphic of evolution from ape to man, the ancestor of human beings was monkey or ape like, Dennis spent a lot of time in Africa, and south Africa is the beginning of himans, and one of the main discovery site, an awful lot of evidence was found there, the study of fossialized remains of homanids (Human ancestors) , is called paleoanthropology, Stirkfontaine is the place in Africa where the evidence was found, lets look at this picture he took from the museam, these sticks are like a timeline, goes from today, to 6 million years ago, dinosaurs went extinct 65 million years ago, the oldest rocks you can find at the grand canyon are 2 billion years old, the earth is 4.5 billion years old. When did all of north Americas wolly mammoth and sabertooths die out, 10000 years ago, they died, after ice age. So lets go back in time 7 to 8 million years ago, humans didn’t exist yet, nor did today apes and animans, but an ancestor from modern day apes and chimps and humans did survive then, a pic of a skull found 4.5 million years old, and the species Australopithecus africanus, she was affectionaly named mrs pess, this was our oldnest named ancestor out of the lineage of the apes. Up until about 20 years ago, only bone parts had been found, they did find a full skeleton about 20 years ago. The human species have been around on earth for 100,000 to 40,000 years. What defines a species, the ability to interbreed and produce fertal offspring, a donky and a horse can have a baby, called a mule, but the mule cannot make babies. A wolf and a dog, are similar enough to mate and have fertal offspring. The more finds you have the greater weight of the evidence Shwed pics of the caves and the itallians found them, when looking for limestone, not even 100 years ago. This used to be underwater, behind the gate is where they found the full skeleton. This is the skull of a juvenile ( a meter tall) stood upright, walked upright, but with its feet could still grasp branches, resembled humans and apes, lived in the planes of Africa. 4.5 million years ago. Then came “Rhodesian Man, so now this is the genus homo rhodesinsis, huge brow ridges, Australopithecus africanus artists picture looked very chimp/human like Darwin’s synthesis:

What Darwin put together from his overservations. He made observations, gathered samples, asked lots of questions 1. Show that closely related species evolve from and share a common ancestor 2. Propose a mechanism that would explain the process of evolution ( natural selection) He published all his info in a book the origin of species in 1842 Darwins observatons and deductions

1 Observatons : Populations have the potential to increase exponentially
Fairly obvious, not subject to doubt. Dennis drew a graph #’s|_(time) generations
Talked about fruit fly, start off with 2, make 30 eggs, they hatch feed, grow and turn into adults within 30 days, so in 30 days we have 30 fruit flies, after 60 days we have 450 (exponential growt) remember from math class starts rising slowly and then faster and faster.

2 Observations: Populations are fairly constant in size
Now they do fluctulate a lot, they might be in a growth and then may have a low period, but they fluctuate. Its impossible to grow indefinitely. 3 observations: 3 Natural resources are limited, only so much food, only so much space, only so much water, only so much shelter, Based on these 3 observations, Darwin made this deduction1 Only some organisms survive, there is a struggle for existence among individuals in a population.

So you can take bunny rabbits, worried about getting enough food and water and not getting eaten. Humans worried about food and water and disease.
4 observation: there is variation within a species, the phenotypes vary within species, and variation is inherited. Which led to the 2nd deduction
Deduction 2 individuals with favorable variations are more likely to survive and reproduce ( faster bunny more likely to survive) ( camelflauge ( color) ) and if they survive, they are more likely to reproduce, which their offspring will inherit. Fastest land animal in western hemisphere, it is the pronghorn antelope. Dennis was in the forrest wanting pics, and he gave up, they have very good eyesight, they cant jump. They can get up to somewhere between 40 and 60 mph but 40 is more accurate. Cheetas evolved in north America, and they died out. Antlers are shed each year, and horns are permanent, the pronghorn is in between has a permanent part but also has one that falls off. The most highly adapted are most likely to survive and have offspring. The less well adapted are most likely to be selected against. Die from disease, get eaten etc Deduction 3 Accumulation of favorable variations over many generations is evolution. And so when you look at species, they are well adapted for their environments, birds well adapted to fly, fish adapted to swim, and cheetas very well adapted to running.

Natural Selection
Differential survival based on characteristics that you possess The more favorable characterists for that environment, the more likely you are to survive, therefore the more likely you will produce What might be advantageous in one environment may not be advantageous in another, example being white in a polar environment vs a desert If your phenotypes are heritable, then you will pass on them advantageous characteristics, so we accumulate in further generations advantageous traits Natural selection causes eveloutionary change

Indirect eviden ec:
Animal and Plant breeding
Showed us the Auroch (extinct ancestor) (cow like)
Modern beef cow and Modern Dairy Cow ( these do not exist in nature, they exist by artificial breeding. Selective breeding, over generations What Darwin said is if over a couple hundred years or less, we can go from the auroch to the variety of cows we have now, natural selection will make much much much more changes over millions of years. Here we talked about 22.9 on pg 458 cauliflower, broccoli, brussel sprouts Also we talked about dogs, massive, to a beagle to a teacup poodle, artificial breeder, these don’t exist in nature. Also corn, is a grass, doesn’t exist in nature, there are some old relatives that exist in south America. Every agricultural animal and plant do not exist in nature. Indirect evidence #2

Fossil record. Evidence that firstly new species arise, and secondly species change over time, into other species. Showed graphic of bones, like a hand, then like a foot, then like a 3 fingered hoof, and then with shorter fingers, and then to a penis looking thing, and then then like a modern day hoof, speed was the main cause to change, with evolution the legs got faster Indirect evidence #3

Homologous structures
Structures that may apprear outwardly to be quite different, but they have the same basic underlying structure. Showed pic with center circle of common ancestors, which brances off to cat, human, dolphin, chicken, bats, horses, lizards

Lets compare the bat wing with the leg of a cat, or the fin on a dolphin,m or the leg of a human. Or a chicken wing, but when you look at the internal bone structure they all have the same structures, they all have a humerus, the only difference is the size, and dimensions, which are different in each. And that natural selection in different environments, selected for each structure. Dolphin swimming, bats flying, etc. (good evidence) Homologus structures are specif evidence for divergent evolution Divergent evolution- is evolution that says heres a common ancestor with certain proterties ( some shrew like organism) natural selection depends on the environment,

So divergent evolution is that bats and cats could diverge ( come out of, and become more different) from a common ancestor, Again no morphing, but slowly changing over time as a result of different environments. So they start off similar and change and become more different as time goes because the environment they adapt to is different This can only work on the variation that is there, cant invent new ones until they arise naturally. Indirect Evidence

Analogous structures outwardly appear very similar, like the fins on a dolphin and a shark, outwardly they seem very similar, but their underlying structures are very different, a dolphin has bones much like our hand, and the shark is just cartilage. So the ancestors of sharks were aquatic, but the ancestors of dolphins went to land and returned to the water, and because it was in the same environment as the shark, they are almost the same features Lets take not two different environments like air and ground, lets take the same environment (aquatic) So we might expect that organisms that had very different ancestors would change and adapt and get the same charactericts Analogous structures give specific evidence to convergent eveloution

Take 2 very different organisms, that have different ancestors, and converge to become similar because the environment they adapt to is the same, This is what we would predict by natural selection.

The Hawaiian islands are 6 million years ago.
The Hawaiian islands formed by volcanic eruptions
The big island is the youngest, there is another island being formed under the ocean water. Some islands are getting adding too, and others are not. When the first islands rose above the ocean water, there was no life, (maybe some marine life) Life arrived on the islands, from polianasians and north and south American, get carried on by wind, plant seeds or spores, birds, etc. Unique forms evolved by speciation

Forms of life that are no where else on earth, ONLY on the Hawaiian islands, this is because the environmental factors were much different then wehre the life originaly came from… which is why they are so much different.

Two models of allopatric speciation stippling indicates evolution of new species, the dumb bell model in which the ancestral species is divided into 2 roughly equal halves each of which forms a new species, the peripheral isolate model in which the new species fors from a population isolated at the edge of the ancestral species range Geographical barrier

A Ancesteral populationExample : The environment decides which charcteristics, say conditions are and chance play a part

Ancesteral Population

A disease came trough, we need to become resistant, doenst work like that, naturally we will just become resistant. Snails, no barrier, just one species, with variation, then a geographical barrier comes, a mountain range comes, now we have 2 populations of snails, that barrier prevents the snails from meeting up again, so each population reproduces with each other, and if the conditions are different on each side, and lets say when they got separated they were a little genetically different anyhow, and the sanils then will gradually change, the differences may be so great that after time that they are so different that they are different species. Butterflies in Europe Erebia epiphron, in the mountains, different colors designate different races or forms, note that teste races evolved in geographical isolation. All the same species, but have different colors, but they can still all interbreed with each other. Once they are left long enough, maybe they might change, once they can no longer interbreed with each other The kaibib squirrel is only found on the Kaibab plateau north of the grand canyon Colorado plateau is slowly moving up, the Colorado river was flowingtrough it, the rivers cause erosion, the elevation of the Colorado river is the same as it used to be, as the river dug down, the plateau moved up. As the river got wider and the canyon got deeper, there is a geographical barrier, and the squirrls became reproductive isolated;, now there is the kaibabeniss is only found on the Kaibab plateau north of the grand canyon And the scirus aberti si found on the south rim of the canyon, they are not 2 different species, they can still mate, but have supspecies names. And we will predict that eventually they will no longer be able to interbreed, and become different species. In south America on the amazon river, where the river is skinny they can mix, but on the main cannel of the amazon river, and it is massive, there is separation and now thy have started to diverge, because they do not interpreed. Speciation in progress

These four sub species of the deer mouse, the rockys mountains is the barrier,

Evolution in action, breeding tests with fruit flies. They breed very easily in cages, you can get 500 to 1000 in the cage, got 1/3 the flies and separated them, and put them in normal tem, elevated temp, and lower temp, left them for 20 years, but they could no longer interbreed. So we know species change over tiem, and most of the reason is because of the environment, what if we had an environment that stayed constant, we could predict that the organisms would still be a lot alike A coelacanth is a real live fish that lives today, and we have fossils of this species from 18 million years ago, which are exactly the same as today. Its fins are almost limb like, it cant move on the land, but it does have limb like. And they thoguth it was a fossil, but in the early 1920’s a fisherman caught it, they found out it is the Coelacanth, almost like finding a trex, there a populations living in the very deep oceans in the indian ocean, and the environment is much the same as it used to be. No eveolutanary change, when environment stays constant, there has to be variation as well for evolution to take place.

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