Biology Unit 5 Notes

Gene Expression.

Totipotent Cells are undifferentiated cells, such as embryonic stem cells, that are not yet defined in their function. In animals, stem cells are totipotent. Plants have far more types of totipotent cells (Think of how you can make cuttings of plants, and grow an entirely new plant, given the right conditions?)

Cells loose totipotency, as, with age, different genes are swtiched on/off. When certain genes are switched of, they are not translated to produce polypeptides, meaning cells only have specific genes, the proteins produced serving only to aid their function.

Totipotent cells can be used to treat human disorders such as Parkinson's Disease, Alzheimers, Osteoarthritis, MS... all my growing new tissues from stem cells, and growing a culture of the needed type of cell after speciailisation. (That is TOTALLY spelt wrong.)

Oestrogen: 1. The DNA binding site on a Transcription Factor (the thing that stimulates transcription), can sometimes be inhibited 2. Oestrogen is lipid soluble and passes through the cell surface membrane easily 3. It binds with the receptor of the transcription factor. 4. This changes the same of the whole molecule, including the DNA binding site. 5. The Inhibitor is subsequently, removed. 6. The Transcription factor can now join to the DNA, initiating transcription (production of mRNA from DNA)
SiRNA:
1. An enzymes cuts up a piece of double stranded mRNA. 2. This makes little double stranded fragements, called SiRNA. 3. One strand of the SiRNA binds with a enzyme. 4. The enzyme is brought to the mRNA, due to the free bases of the SiRNA binding to a complimentary region on the mRNA. 5. The enzyme cuts of the mRNA into smaller fragments, seperating the sequence of triplet codons, meaning not all of the amino acids needed for the proteins are coded for, meaning the correct protein cannot be translated, as the amino acid sequence determines the strucutre, and it is not present in full.
Quick recap of oestrogen first - transcription stimulated by transcription factor, which has to bind to a specific region on the DNA. Can be inhibited. Oestrogen dissolves through phospholipid bilayer, as it is lipid soluble. Combines with receptor of transcription factor (complimentary). Changes the shape of DNA binding site, releasing inhibitor. Transcription factor can now join with DNA and stimulate transcription.

SO. The transcription factors can be inhibited. Oestrogen bind to the transcription factor on the receptor. Changes molecule shape, including DNA binding site. Releases inhibitor, and can now bind to DNA.

Righto. :P

So, now on to how SiRNA effects gene expression.

Small interferring RNA are little sections of RNA, double stranded. It prevents gene expression my breaking down mRNA. 1. Enzyme breaks down double stranded chains of mRNA into smaller sections, called SiRNA. 2. One strand of the SiRNA combines with an enzyme. 3. This one strand then pairs with the complimentary section of bases on a single stranded chain of mRNA. 4. The enzyme then cuts the mRNA down into smaller sections.
The effect this has? With a broken chain of the mRNA, there is not the correct sequence of triplet codons, meaning incorrect amino acids are produced/not all of the amino acids necessary are produced - meaning the protein outcome will not have the same teritary structure, and therefore, shape, and possibly will not function in the same way. The gene is not expressed.

How this can be used? Use of SiRNA to block the genes that cause some diseases, or to identifiy the role of particular genes by eliminating them, and study the effects/missing chracteristics.
Regulation of transcription and translation. OESTROGEN 1. Oestrogen is lipid soluble, so it can diffuse through the phospholipid bilayer easily. 2. Oestrogen binds to the receptor molecule on a transcription site.The are complimentary. 3. This binding changes the shape of the transcription factor, causing the inhibitor (of where the DNA goes) to detatch. 4. DNA can join with transcription factor, and transcription is stimulated.
Totipotency and cell specialisation.
What are Totipotent Cells?
Totipotent cells are undifferentiated, non specialised cells. Initially, cells can become any type of cell (muscle, epithelial, etc.). Totipotent cells do not yet have a function.

Which cells in plants and animals are totipotent?
Fertilized egg cells.Embryonic Stem cells. Meristematic Cells in plants.

How do cells loose totipotency and become speicialised?
Cells become specialised because some genes become switched off/left on. This means that not all of the cells code for the same proteins, and therefore, have different constitutions, and have different functions due the the varying frequencies of the avaliable proteins.

How can stem cells treat human disorders?
Stem Cells can treat human disorders as they are undifferentiated. A factor can be used to force the cells to differentiate into particular cells - giving the avaliability to re-grow tissues that have been damaged, either by accidents, or via degenrative disease. For example, nerve cells being produced can combat the prgressions of diseases such as Parkinson's, Alzheimers, MS, and strokes.

The rate of cell division is controlled by two things:

Proto-oncogenes :- stimulate cell division
Tumour Supressor Genes :- slow cell division.

Proto-oncogenes code for GROWTH FACTORS. They attatch to a receptor protein on the cell surface membrane, and 'switch on' the genes for DNA replication via relay proteins.
However, the mutated form of a proto-oncogene is a oncogene. Oncognes could either code for a growth factor that is produced in excessive amounts, or just permanently activate the receptor protein, leaving the DNA constantly switched on for replication.

Cells would divide too quickly/too much, meaning a tumour/cancer would occur.

Tumour supressor genes inhibit cell division. It maintains the rate of cell division, and therefore, prevents the growth of tumours. If the tumour supressor gene mutates, it becomes inactive. Most of these mutated cells die, but a small frequency of cells continue to exist and thrive. Being strutually different to other cells in the body, the mutated cells, if built up, on that small chance, can form a tumour.
A tumour that exists without spreading is almost harmless, called Benign. Malignant tumours are cancer. The tumour spreads throughout the body via the blood, existing and affecting multiple locations.
Mutation: Change in quantity or structure or DNA of an organism.

Nonsense mutation:
The mutation creates a stop codon. I.e. The mutation changing one base. Say the recognised stop codon is AUG. And, currently, your codon is ACG. If the C was swapped for a U, this would now be a stop codon, do the polypeptide chain would stop being produced at that point. Final protein would be different, and nto function the same.

Mis-sense Mutation:
If the codon ends up coding for a different amino acid. Say ACC codes for Alanine, and ACG codes for
Glutamine. If the final C on the initial codon was swapped for a G, the codon would now produce Glutamine, not Alanine.The amino acids determine the tertiary structure - so the shape of the protein is likely to be changed, possibly making it non-fucntional.

Silent Mutation:
The Mutation changes a bases, but the codon still does for the same amino acid as previously. This is due to the genetic code being DEGENERATE.

These are all SUBSTITUTION

Deletion of Bases:
A single base is deleted from the code. Although initially thought to be a mild effect, this usually causes what is known as a frame shift. Meaning - where the one base has been removed, the entire chain left shifts over by one place to the left. This changes all of the codons after that point, so the nearer to the begining of the chain, the worse off it is.

Genetic mutation is RANDOM. Mutagentic factors can affect this however. So, high energy radiation, and chemicals that alters the DNA structure, or interferes with transcription.
Also, little note about splicing: the introns are removed because they would interfere with translation.

Translation: 1. A ribosome attatches to the start codon on the mRNA. 2. tRNA, which has an amino acid on one end, and an anticodon on the other. The anti codon in complimentary to the mRNA and joins with it. 3. Another tRNA joins next to the last, complimentary to the mRNA triplet codon there. 4. By the means of an enzyme, and ATP, the two amino acids on the top of the tRNA's are joined by a peptide bond. 5. The ribosome moves on to the next codon in the sequence of the mRNA - another tRNA joining to it, aligning the amino acids in order for these to also be joined via a peptide bond. 6. This process continues until a stop codon is reached. At this point, there will be a full polypeptide chain formed - the ribosome, mRNA, and final tRNA all detatch.
Unit 1 Recap:
Secondary stucture - the polypeptide is coiled or folded
Tertiary structure - secondary structure is folded
Quaternary structure - different polypeptide chains linking.
In Translation, mRNA's function is to act as a template on which the polypeptide is formed. tRNA acts as a carrier for the amino acid. Without tRNA to carry the amino acid AND attach to the mRNA on opposite sides, the amino acids could not line up.

Transcription, Splicing.
Overview of peptide synthesis: * DNA provides instruction - in the long sequence of bases on the nucleotides. The order of the bases and which bases are present determined the instruction. * Complimentary section of the DNA is formed. This is called pre-mRNA. TRANSCRIPTION * Pre-mRNA is spliced to form mRNA. * mRNA acts as template, where tRNA attaches, lining up amino acids and linking them. TRANSLATION. Forms polypeptides.
Transcription is where a complimentary section of DNA is formed, called pre-mRNA. 1. Firstly, DNA HELICASE breaks the hydrogen bonds on a section of a strand of DNA, exposing the nuclotide bases. 2. RNA POLYERMASE moves along one of the strands (template strand), casuing it's nucleotides to join with free nucleotides in the nucleus. 3. The strand of DNA reforms behind this. This forms a strand of pre-mRNA, and the DNA left reformed. 4. The RNA Polyermase stops attatching bases when it reaches a particluar sequence of bases, arranged as a 'stop code'
Splicing is the transformation of pre-mRNA into mRNA. This is done by removing the introns. Introns are regions of non coding, non functional DNA. Exons are regions of coding DNA (for proteins, enzymes, polypeptides.) After splicing, translation happens.

SO
:- Transcription -> Splicing -> Translation. ^____^

DNA Helicase breaks the hydrogen bonds, RNA polymerase adds free nucleotide, DNA Helicase closes it up 12 bp behind. Strand of pre-mRNA is formed. pre-MRNA is spliced (introns removed). mRNA left over.

The Genetic Code, Polypeptide Synthesis, Gene Mutation. ^-^
The genetic code is the sequence of nitrogenous bases on the mRNA - which codes for amino acids. The main features of the genetic code are: * 1 Amino acid is coded for by three bases on the mRNA (codon) * Few amino acids only have a single codon * The code is degenerate. This means that MOST amino acids can be coded for by multiple codons. * Three codons act as a stop codon * The code is non-overlapping. This means that it is read straight off, each base only read once. * It is universal - the same codon codes for the same amino acid across organisms.

RNA
RNA is a single strand of nucleotides. It has the bases A,C,G, and U. ALL RNA has Uracil instead of Thymine.

There are two types, mRNA, and tRNA. mRNA is LINEAR. It is single stranded. It forms from DNA copying part of one of it's two strands. This then passes out of the nucleous through the nuclear pores. The mRNA associates with ribosomes, allowing it to act as the templates on which proteins are made. tRNA is in a clover leaf shape arrangement. It is made up of about 80 nucleotides. It lines up the animo acids with the mRNA in peptide synthesis. The unpaired bases on the tRNA are complimentary to an amino acid. The anticodon is complimentary to the codon on the mRNA, thus, lining the two up in the right position.

Differences: 1. DNA is a double stranded chain, mRNA + tRNA are single. 2. DNA is large, mRNA is a lot smaller, and tRNA is the smallest, at only 80 bp. 3. DNA is a double helix structure, mRNA is single helix, tRNA is clover shaped. 4. DNA's nucleotide sugar is Deoxyribose. mRNA + tRNA have ribose. 5. DNA has bases C,T,A + G. mRNA + tRNA have U,C,G, and A. 6. DNA is mostly found in the nucleus. mRNA + tRNA are made in the nucleous, but found throughout the cell. 7. The amount of DNA in the cells of a species is the same, this mRNA+tRNA it vareis due to factors such as metabolic activity. 8. DNA is very chemically stable. mRNA is least chemically stalbe, tRNA is slightly more.

Habitat: The place in which an organism lives.

Population: A group of organisms of the same species within a particular habitat.

Community: The total number of different populations within a particular habitat.

Niche: The position of an organism within an ecosystem dependant upon the amount of resources it uses. The more resoures looked into, the more carefully definied the niche of the organism will be.

Ecosystem: The BIOTIC communtity, living in an ABIOTIC environment
The Mitochondria

This is a labelled Mitochondria. Mitochondria are where the link reaction (Matrix), the Krebs cycle (Matrix) and oxidative phosphorlyation (Inner Mitochondrial Membrane) take place.

Glycolysis 1.
Glucose (6 carbon) is made more reactive using 2ATP (Phosphorylation). Phosphate is added to it, as it lowers the activation energy for the reactions that follow. 2.
Each Phosphorylated glucose is split to form 2 Triphosphate molecules (3 carbon). 3.
The Triphosphates are oxidised by the removal of hydrogen to form PYRUVATE, the hydrogen is donated to an NAD co-enzyme, which makes red.NAD
Joining a phosphate to another molecule, e.g. ADP is phosphorlyation.

Substrate Level Phosphorylation: the phosphorylation of ADP + Pi = ATP using energy released from chemical reactions. So, the chemical energy used comes from the substrate, hence the name.

Link Reaction
PYRUVATE is oxidised by removing hydrogen. This is because of the DEHYDROGENASE enzyme.
PYRUVATE is DECARBOXYLATED. Decarboxylation is the removal of Carbon Dioxide (Decarboxylase Enzyme). Since a carbon has been removed, it goes from three carbons to two, an ACETYL group. This joins with a co-enzyme.

The Krebs Cycle

The Acetyl co-enzyme joins with a four carbon acceptor molecule to form a six carbon intermediate. The six carbon intermediate is then decarboxylated, and carbon dioxide is released, making it into a five carbon intermediate. At the same time, it is oxidised, loosing hydrogen. This hydrogen reduces an NAD co-enzyme, forming red.NAD which goes on to the electron transport chain.
The five carbon intermediate is decarboxylated, releasing carbon dioxide and making a four carbon intermediate. Enough energy is released to synthesise ATP by ADP+Pi = ATP. As well as this, the fout carbon intermediate is oxidised, donating a hydrogen to an FAD and 2NAD, reducing them too. The too move on to the electron transport chain. The four carbon acceptor goes back round in the cycle to join with an acetyl again.

Electron Transport Chain

In the electron transport chain, co-enzymes donate their electrons and protons (e- and H+). The electrons enter a chain of carriers, arranged in order of decreasing energy content, releasing energy, until they reach the final electron acceptor, molecular oxygen. Meanwhile, the H+ are actively transported through the ATP synthase enzyme, down a concentration gradient. The kinteic energy produced in the process gives enough energy to synthesis ADP + Pi => ATP. Also, the H+ joins on to the molecular oxygen with the electrons to form WATER.
Respiration 1 - A2
Aerobic => Oxygen
Anaerobic => Turns glucose into lactate (when in animals), and into ethanol and CO2 (when in yeast, etc.)

Oxidation is the: * Gain of Oxygen * Loss of Electrons * Loss of Hydrogen
Reduction is the: * Loss of Oxygen * Gain of Electrons * Gain of Hydrogen
Reducing Agent means the thing that is oxidised, and that caused reduction by being an electron donator.
Oxidising Agent means the thing that is reduced, and that caused oxidation by being an electron acceptor.

Co-enzymes
NAD - Nicotamine Adenine Dinucleotide
FAD - Flavine Adenine Dinucleotide
Co-enzymes are a carrier of hydrogen molecules from one molecule to the other. They work in assistance with dehydrogenase enzymes which catalyse hydrogen removal.

When NAD picks up Hydrogen,
NAD + 2H+ => NADH2
The NADH2 is the reduced form as it has GAINED Hydrogen.

The stages of Aerobic respiration 1. Glycosis -> Takes place in the CYTOPLASM, Aerobic and Anaerobic. 2. Link Reaction -> Takes place in the Mitochondria (MATRIX), Aerobic. 3. Krebs Cycle -> Takes place in the Mitochondria (MATRIX), Aerobic. 4. Oxidative Phosphorylation -> Takes place in the Mitochondria (INNER MITOCHONDRIAL MEMBRANE), Aerobic.
Energy Supply

ATP => Adenine Triphosphate

Energy supply has two key processes: Photosynthesis and Respiration

Photosynthesis - transfers light energy into chemical energy in organic molecules
CO2+H2O => (with light energy) O2 + C6H12O

Respiration - releases energy from organic molecules, e.g. glucose.
C6H12O + O2 => CO2 + H2O + Energy

We only ever have 5g of ATP in the body at any one time, and use 40kg of it in a single day.

Why do organisms need energy? * Growth and Repair * Muscle Contraction * Active Transport (changes the chape of the protein carrier) * Metabolism * Maintainence of body temperature in birds and mammals. * Movement. * Building up of large molecules.
Why is it an energy carrier?
It is small, soluble, and therefore, easily transported around the body.
ATP is a specialised compound. Reactions are coupled of transferring energy releasing reactions and those that require energy.
Why not just use Glucose?
Glucose is too slow to break down. It breaks down in several stages, and because of this, looses a lot of energy as heat energy. It is wasted.
How does ATP store energy? * The bonds between the phosphate groups are unstable and have a LOW activation energy. * This means the phosphate bonds are easilt broken to release energy. * Usually only the terminal phosphate group is removed. Energy is released in small usable amounts when ATP is hydrolysed to ADP + Pi
ATP is RE-synthesised from ADP + Pi by Phosphorylation, which is a condensation reaction. * ATP is broken down in a single reaction, rapidly releasing energy to cell reactions, unlike glucose which, as previously said, needs to be broken down by a long series of reactions. * ATP releases smaller more useable quantities of energies than Glucose does. (Plus heat is released with Glucose.)
Summary: Advantage of ATP as an energy carrier (Universal) 1. It is an immediate source of energy (small reaction.) 2. The phosphate bonds are unstable, have a low activation energy and are easily broken. 3. ATP is a small molecule, and is highly soluble, meaning it is easily transported anywhere in the body.
Predators are animals that hunt and kill, then eat their prey.

In a predator-prey graph, there are two things to remember: 1. Predators numbers are always less then it's prey. 2. A little while after the preys populations increase, the predators does too.
As the prey population declines, there is increased competition between predators for they remaining prey. Eventually, their numbers begin to fall. When a predator population declines, prey population builds up. Predators have more food, so their population then rises again.
Interspecific- When competition arises between two different species.
Intraspecific- When competition arises between the same species.

Plants compete for: Light, water, nutrients, growth space.

Interspecific Competition: * Where two populations initially occupy the same niche, one will normally have a competitive advantage over the other. * The population of this species will gradually INCREASE in size while the other will decrease. This is known as the 'comeptitve exclusion' principle.
'Competitive Advantage' is a better term to use then 'Dominant'. Avoid dominant.
Niche + Competition -> * Do they feed in different areas/levels? (E.g. feed in water, whereas other feeds from shrubs. Or Feeding on the sea bed, as opposed to the water surface.) * Where do they nest/settle? (Trees, bushes, ponds, underwater, underground.)
Plants stuff. ^_^
Via cohesion tension, how does a plant take up water? Water molecules are COHESIVE. This means that they form hydrogen bonds between molecules, and they stick together, forming a chain. This is an unbreakable chain up the xylem to the mesophyll, and, as water evaporates from the mesohpyll on the leaf surface, more water is drawn up, due to the aforementioned cohesive properties.

How does water enter a root hait cell? Water potential is high in the soil, and the water potential in the root hair cell is low, due to the sugars, amino acids, and ions dissolved in it. This creates a waer potential gradient and water moves in by osmosis.

Root cortex - The simplastic pathway means going through the cells. The root hair cell will now have high water pressure, whereas the first cellin the cortex will have low. This means water will move in via osmosis. Then, the next cell will have a lower water potenital then the one the water had just moved into. So water will move into this one via osmosis. This will continue, and whilst this is happening, the water potential of the first few cells has lessened after the water moves on to the cell after, meaning more water can move in.
The Apoplastic way involves moving through the cell wall of the root cortex cells. Due to the cohesive properties of water, it gets pulled along in a unbroken steam, with little resistence, due to the mesh like structure of cellulose having water filled gaps.

Endodermis - Xylem. The water travelling the apoplastic pathway can no longer continue in that pathway, due to the casparian strip, which is waterproof, and so joins the Symplastic pathway, to continue through the endodermis. Endodermal cells actively transport minerals into the xylem, lowering it's water potential, and causing a water
Oxygen Disassociation Curves. (:
Aerobic respiration => Glucose => ATP released.

Haemoglobin => Pigement
It enable the bodt to carry round lots of oxygen.

Haemoglobin may vary. Each polypeptide chain (four of them) associates with one haem group, which contains a ferrous Fe2+ ion. This can readily bond to oxygen. It picks up four oxygen molecules.

Haemoglobin without oxygen is blue. Haemoglobin with oxygen is red.

The oxygens leave one at once, not all off of one haemoglobin, and then the next. The first oxygen molecules on all goes, and then the second.

The more oxygen avaliable, the higher the percent saturation with oxygen.

Haemoglobin is in three environments: Tissues, Lungs, Blood Vessels.

In the Tissues and the Lungs, the blood is contained within capillaries that have small pores, meaning the percent saturation can change. In the blood vessels, such as arteries, veins, it cannot change as they are not porus.

Associates with oxygen in the lungs.
Dissociates with oxygen in the tissues.

If there's a high partial pressure (lungs), any drop in it has a small effect in percent saturation, however, if there's a low PP, (tissues) any drop in it has a large effect on percent saturation.

If the curve shifts to the LEFT, there is a greater affinity for oxygen.
If the curve shifts to the RIGHT there is a lower affinity for oxygen.

High affinity => More readily associates with oxygen
Low affinity=> More readily dissociates with oxygen

Oxygen Disassociation Curves. (:
Aerobic respiration => Glucose => ATP released.

Haemoglobin => Pigement
It enable the bodt to carry round lots of oxygen.

Haemoglobin may vary. Each polypeptide chain (four of them) associates with one haem group, which contains a ferrous Fe2+ ion. This can readily bond to oxygen. It picks up four oxygen molecules.

Haemoglobin without oxygen is blue. Haemoglobin with oxygen is red.

The oxygens leave one at once, not all off of one haemoglobin, and then the next. The first oxygen molecules on all goes, and then the second.

The more oxygen avaliable, the higher the percent saturation with oxygen.

Haemoglobin is in three environments: Tissues, Lungs, Blood Vessels.

In the Tissues and the Lungs, the blood is contained within capillaries that have small pores, meaning the percent saturation can change. In the blood vessels, such as arteries, veins, it cannot change as they are not porus.

Associates with oxygen in the lungs.
Dissociates with oxygen in the tissues.

If there's a high partial pressure (lungs), any drop in it has a small effect in percent saturation, however, if there's a low PP, (tissues) any drop in it has a large effect on percent saturation.

If the curve shifts to the LEFT, there is a greater affinity for oxygen.
If the curve shifts to the RIGHT there is a lower affinity for oxygen.

High affinity => More readily associates with oxygen
Low affinity=> More readily dissociates with oxygen