nucleic acid – polymers specialized for the storage, transmission between generations, and use of genetic information. There are two types, DNA and RNA nucleotides – monomers that compose nucleic acid, consist of a pentose sugar, a phosphate group, and a nitrogen containing base. DNA - – a macromolecule that encodes hereditary information and passes if from generation to generation. RNA and the bonds that stabilize them
Purine - one of two chemical forms that the base of nucleic acid will take, a fused double ring structure (adenine guanine) Pyrimidine – one of two chemical forms that the base of nucleic acid will take, a sex membered single ring structure (cytosine thymine uracil) ATP – adenosine triphosphate, acts as an energy transducer in many biochemical reactions. GTP – guanosine triphosphate, serves as an energy source, especially in protein synthesis, also plays a role in the transfer of information from the environment to cells. cAMP – cyclic adenosine monophosphate, is a special nucleotide in which an additional bond forms between the sugar and phosphate group. Essential in hormones and the nervous system. genome – the complete set of DNA in a living organism, not all information is needed all of the time. Gene – the sequences of DNA that encode specific proteins are transcribed into RNA. phosphodiester linkages – joins the nucleotides, one sugar is connected to a phosphate. Ribozymes – catalytic RNAs, catalyze reactions on their own nucleotides as well as in other celluar substances. Protocells – prebiotic water filled structures, could have been the first cells and made up the membrane. Small molecules can pass through them, nucleic acids inside could replicate. reverse transcriptase. - An enzyme that catalyzes the formation of DNA from an RNA template in reverse transcription.
the DNA double helix – built through hydrogen bonding, two complementary polynucleotides strands pair and twist. the molecular structure of nucleotides – in RNA there is phosphate, ribose (sugar) and a pyridine base or purine base. In DNA there is the same except the sugar is deoxyribose and it is connected to another strand. differences between DNA and RNA – DNA stores information whereas RNA carries out information. RNA is single stranded and has uracil instead of thymine base. base-pairing rules – in both RNA and DNA a purine pairs with a pyrimidine. In RNA it is A&U, C&G, in DNA it is A&T, C&G. Hydrogen bonding on the base, the geometry of the sugar-phosphate, and the molecular sizes of the paired bases. antiparallel nature of DNA – one strand is 5’ to 3’, while the connected strand is 3’ to 5’. DNA can only synthesize in the 5’ to 3’ direction. Information flow in biological systems (central dogma of molecular biology) – from DNA to RNA (transcription) to Proteins (translation). evidence that life may have come from outside of Earth - in 1969 a meteorite landed and scientists carefully tested in and deemed that there were molecules and amino acids on it. Water was found trapped under a martian meteorite. chemical evolution and the experiment of Stanley and Urey, did the Stanley Urey experiment include oxygen? - holds that conditions on primitive earth led to the formation of simple molecules and these molecules led to the formation of life. The experiment did not include oxygen, it instead had gases that may have been present in Earth’s early atmosphere such as hydrogen, ammonia, methane and water vapor. They passed an electric spark to see if new molecules could be formed, they were. conditions in which polymers might have been synthesized – solid mineral surfaces such as clay which sped up the formation of carbon based molecules, hydrothermal vents which have iron and nickel and catalyze in the absence of oxygen, hot pools may have had concentrated monomers. the replicator first hypothesis- genetic material comes first, polymers come together and self-replicate going through changes and ending with metabolism. the metabolism first hypothesis – monomers go through chemical changes first, while a selection of monomers are removed there are further changes and then polymerization of replicator occurs and you have metabolism. evidence that supports the “RNA World” hypothesis – A world with only RNA before DNA, RNA polymers can be formed at a rate 7 million times greater than without, a ribozyme can catalyze the assembly of short RNAs into a longer molecule, peptide linkages is catalyzed by ribozymes, and reverse transcriptase catalyzes the synthesis of DNA from RNA. the importance of the cell membrane to the evolution of living things – It protected the cell from outside environment, allowed things to go on inside and for things to reproduce. evidence that ancient rock contain fossils of cells. – Rocks from 3.5 billion years ago had fossilized cyanobacteria that could perform photosynthesis, it was proved that is was once alive and not just formed by a chemical reaction. Carbon isotopes were found and it was proved that life began around 3.5 billion years ago in small cells.
the cell theory – the first unifying principle of biology that has three components (see concepts) light microscopy – can be used to visualize living cells but do not have as great of a resolution. resolution – a magnified object must be sharp or clear, the minimum distance two objects can be apart and still be seen as two objects. magnification - when the apparent size of an object in increased scanning electron microscopy – directs electrons to the surface of the sample where they cause other electrons to be emitted. Electrons are then viewed on a screen. transmission electron microscopy – a beam of electrons is focused on the object by magnets, appears darker if electrons are absorbed. If electrons pass through they are detected on a fluorescent screen. (plasma) membrane – very thin structure forms the outer surface of every cell and has the same thickness and molecular structure in all cells Cytoplasm – the loose material enclosed inside of the cell membrane, holds all of the other structures in a cell. Consists of cytosol and suspended particles. Cytosol – consists mostly of water, that contains dissolved ions and soluble macromolecules. Is in the cytoplasm. Organelle – the membranous compartments of eukaryotic cells, each has a specific role in its particular cell. Some make products while other take in energy and convert it into another form. Nucleus – contains most of the cells genetic material (DNA), the replication and the first steps in expressing genetic information take place here. Transcription is turned on or off, nucleolus is located here. Nucleoid – place in the prokaryotic cells where the DNA is located. nuclear membrane (envelope) – the nucleus is surrounded by two membranes which form this, this structure separates the genetic material from the cytoplasm. Functionally it separates DNA transcription from translation (in the cytoplasm). Regulates information coming in. nuclear lamina – at the interior periphery, the chromatin is attached to a protein meshwork, formed by the polymerization of proteins called lamins into long thin structures called intermediate filaments. Maintains the shape of the nucleus. nuclear matrix – within the nucleoplasm, a network of structural proteins that help organize the chromatin. nucleolus – a region within the nucleus where ribosomes begin to assemble from RNA and proteins. Chromosome – Chromatin occurs in the form of exceedingly long thin threads, these are chromosomes. chromatin – DNA inside the nucleus is combined with proteins to form this fibrous complex. nuclear pore- surrounded by eight protein complexes, protein fibrils on the nuclear side form a basketlike structure. They allow the NLS to enter or not. nuclear localization signal – The sequence of amino acids that allow larger molecules to come in through the nucleus pores, is a part of the protein. If the NLS is removed, the protein stays in the cytoplasm, if it is added the protein moves into the nucleus. Some viruses have them. Nucleoplasm – surrounding the chromatin are water and dissolved substances endomembrane system – takes up much volume in eukaryotic cells, an interconnected system of membrane enclosed compartments that are sometimes flattened into sheets and other times have shapes. Includes the plasma membrane, nuclear envelope, endoplasmic reticulum, golgi apparatus, and lysosome (from the golgi). rough endoplasmic reticulum (RER) – many ribosomes are attatched to the outer surface of the membrane, are involved in protein synthesis actively. Transports proteins, proteins can be chemically modified, shipped to cellular destinations, membrane bound proteins are made in the RER. ribosome – complexes of RNA and protein, only seen in an electron microscope. Sites for protein synthesis. transcription
smooth endoplasmic reticulum (SER) – lacks ribosomes, and is more tubular. Is responsible for chemical modification of small molecules taken in by the cell, site for glycogen degradation, synthesis of LIPS AND STEROIDS. Cisternae – has three distinct regions, are flattened membrane sacs. Membrane enclosed vesicles lumen – the interior compartment of the ER is separate and distinct from the surrounding cytoplasm. golgi apparatus (cis and trans)- compartments in which some proteins are synthesized by the ribosomes and packaged/sent to appropriate locations. Flattened membrane sacs called cisternae and small membrane enclosed vesicles. Receives ribosomes, concentrates and packages proteins before they are sent out, adds some carbohydrates. Cis region lies closest to the nucleus, medial is in between and the trans region is closest to the plasma membrane. mitochondria – power plat, energy is stored in carbohydrates and fatty acids and converted into a form more useful for the cell (ATP) . Cellular respiration occurs here. mitochondrial matrix – the space enclosed by the inner membrane, contains many enzymes, ribosomes and DNA. mitochondrial intermembrane space – the primary barrie between the cytosol and mitochondrial enzymes. cristae – the folds in mitochondria tend to be quite irregular and create shelf like structures. Chloroplasts – contain the green pigment chlorophyll and are the sites for photosynthesis. Is surrounded by two membranes. plastids – present only in plant cells and certain protists, can divide autonomously. There are several types. Thylakoids - what makes up the granum, flat closely packed circular compartments, most abundant lipids in the biosphere. Stroma – the fluid in which the grana are suspended, contains ribosomes and DNA used to synthesize proteins. granum – each chloroplast stack, consist of a series of flat, closely packed, circular compartments. Chromoplast – another type of plastid, make and store red, yellow, and orange pigments, especially in flowers and fruits. Amyloplast – a leucoplast that stores starch.
leucoplast – storage organelles that do not contain pigments. Vacuoles – found in many cells but mainly plant and protest cells, storage, structure, reproductions and digestion. vesicles – when the cell reproduces the nuclear envelope breaks down into small droplets containing pore complexes. The envelope reforms after the replicated DNA has been distributed to the daughter cells. primary lysosomes – originate from the primary lysosomes. Contain digestive enzymes and are the sites where macromolecules, proteins polysaccharides nucleic acids and lipids are hydrolyzed into their monomers. Sites for the breakdown of food, taken up by phagocytosis. Generated by the golgi, secondary lysosomes – The combination of a primary lysosome and a phagosome, digestion occurs here, small molecules generated by digestion diffuse into the cytoplasm. Peroxisomes – accumulate toxic peroxides such as hydrogen peroxide. Glyoxysome – similar to peroxisomes, found only in plants. Stored lipids are converted into carbohydrates for transport. lysosomal diseases – Tay-Sachs, occur when lysosomes fail to digest internal components. phagocytosis – How materials get into a cell,, a pocket forms in the plasma membrane then deepens and encloses material from outside the cell. Becomes a small vesicle called a phagosome. Phagosome – occurs after phagocytosis, contains food or other material, fuses with a primary lysosome to create a secondary lysosome where digestion occurs. Autophagy – the programmed destruction of cells or cell components, the lysosome breaks down its own material. cytoskeleton – composed of several types of protein (actin) based filaments,has both structural and functional roles. No membrane so not an organelle. Microtubules – long hollow unbranded cylinders, form a rigid internal skeleton for some cells, act as a framework. Tubulin – a protein that assembles microtubules.
Microfilaments – can exist as single filaments, in bundles, or in networks. Help the entire cell or parts to move, determine and stabilize cell shape. Actin – assemble the microfilaments, has plus and minus ends. Myosin – the motor protein, works with actin for muscle contractions. intermediate filaments – though ropelike proteins assemblages, do not re-form. Anchor cell structures in place, they resist tension. keratin
motor proteins – specialized molecules that use cellular energy to change their shape and move. dynein
flagella - how some prokaryotic cells swim, look like tiny corkscrews. Made of a protein called flagellin. The motor protein spins this like a propeller and is anchored to the plasma membrane. cilia, centrioles, basal bodies, gap junctions, tight junctions, desmosomes, cell walls plasmodesmata
extracellular matrix – no membrane but has structural and functional roles. Collagen
symbiosis – relationship between to different organisms, both organisms benefit from the situation. endosymbiosis theory
flagellin – how some prokaryotic cells swim, look like tiny corkscrews. Made of a protein called flagellin. The motor protein spins this like a propeller and is anchored to the plasma membrane. THE PROTEIN that makes flagella. Pili – structures made of protein that are hair like and project from the surfaces of some bacterial cells, used for adherence.
Experimental techniques used to study cells (fractionation, microscopy) the differences between prokaryotic and eukaryotic cells – prokaryotic cells do not have membrane enclosed internal compartments, are single celled, eukaryotic cells have DNA in the nucleus and there is also a mitochondria. reason cells are small – cells must maintain a large surface area-to-volume ratio in order to function, volume increases faster than surface areas. Things inside the cell must be able to move quickly and therefore need a smaller volume. surface area to area ratio – as an object increases in volume, its surface area also increases but not at the same rate, the volume determines the amount of chemical activity and the surface area determines the amount of substances that can enter in from the outside environment. the cell theory – Cells are the fundamental units of life, all living organisms are composed of cells, all cells come from preexisting cells. the relative sizes of biological organisms/molecules (eukaryotic cells, prokaryotic cells, organelles, viruses, DNA molecules) – light microscopes can detect most cells, but not viruses. A frog egg can be detected by the naked eye. the advantage of light microscopy over electron microscopy – can view living cells and see their components more clearly. the advantage of electron microscopy over light microscopy – better resolution, permits details of many subcellular structures to be seen, a beam of light is focused and electrons can be seen. functions of the plasma membrane -separates the interior of a cell from outside environments, is a feature in ALL cells. Composed of a phospholipid bilayer, proteins and other molecules are embedded in the lipids. Is an oily fluid that can change shape, is selectively permeable, allows for a constant internal environment (homeostasis), communicates with adjacent cells, proteins bind and adhere to other cells. the general structure and function of each eukaryotic organelle discussed – See definitions. Can you identify these organelle? – see page 86/87
the movement of proteins through the endomembrane system – start in the nucleus, move to the envelope and transport to the RER, a vacuole will transport it to the golgi where it is processed and sent out to various places. where do transcription and translation take place
the structure and functions of cytoskeleton components discussed motor proteins
functions of the extracellular matrix
functions of the plant cell wall
how did the nuclear membrane and internal membranes arise ? motion of flagella and cilia
demonstration of cytoskeletal functions
Support for the endosymbiosis theory
general structure of prokaryotic cells.
Definitions: Energy, Potential energy, kinetic energy, metabolism, anabolism, catabolism, The First Law of Thermodynamics, the Second Law of Thermodynamics, enthalpy, free energy, entropy, metabolic pathway, endergonic, exergonic, chemical equilibrium, ATP, catalyst, enzyme, ribozyme, activation energy, transition state intermediates, reactants (substrates), active site, enzyme-substrate complex, competitive inhibitor, non-competitive inhibitor, reversible inhibitor, non-reversible inhibitors, allosteric regulation, coenzyme, cofactor, prosthetic group, intermediates, end products, effector molecules (activators and inhibitors), commitment step in metabolic pathway, isozyme.
Concepts: Endergonic versus exergonic reactions and the free energy change of each, oxidation/reduction reactions, the role of ATP in biochemical energetic, the formation of ATP (exergonic or endergonic), the hydrolysis of ATP (endergonic or exergonic), ATP and energy coupling, the features of enzymes, what mechanisms do enzymes use to catalyze a reaction?, how do enzymes affect activation energy?, do enzymes affect the final equilibrium and ∆G?, the Induced-Fit model of enzyme function, enzyme saturation, control of enzyme activity, effect of environmental conditions on enzyme activity, enzyme denaturation, metabolic pathways and how they function, feedback inhibition.