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173 Cards in this Set

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  • Back
Why was protein thought to be the genetic material?
DNA is chemically simple and protein chemically complex. Proteins must be genetic material.
What early evidence was there that DNA was the genetic material?
Rat experiment when harmless bacteria transformed into lethal bacteria due to addition of nonliving lethal bacteria.
Why was the genetic material called "Transforming Activity"?
Genetic material has ability to absorb material from environment to transform itself into a new sequence. Also, ability to cahnge nonlethal strand to lethal.
Know the structure of a nucleotide. Know the structure of its three components.
Sugar, Phosphate, and base.
- 5 Carbon sugar in DNA = deoxyribose. In RNA = ribose.
- phosphate = 1, 2, or 3.
-Adenine, Cytosine, Guanine, thymine.
What are the major and minor groove of DNA?
2 strands of DNA wind around each other to form right-handed helix. The coiling of 2 strands create 2 major slits in double helix. widest is major groove and smaller is minor groove.
What is Chromatin? Euchromatin? and Heterochromatin?
C- complex of DNA and protein where genetic material is stored.
E- the more "extended" or "normal" form that is more readily transcribed.
H- highly condensed, non-transcribed region of concentration around the centromere and telomere region.
What are the three levels of chromatin (DNA) structure? What structural features do each of these levels include?
1) Naked DNA
2) Nucleosome
3) 30-nm fiber
What is a histone?
the protein that binds to the DNA and compacts it to form eukaryotic chromosomes. responsible for first and most fundamental level of chromatin packing, the nucleosome.
What are the structural components of a nucleosome?
segment of DNA wound in sequence around 8 histone protein cores. 147 nucleotide paris long.
What are the five classes of histones found in nucleosomes?
H1, H2A, H2B, H3, AND H4.
Which histones are found in the core nucleosomes, and how do they interect?
H2A, H2B H3, & H4. all 4 relatively small w/ high portportion of + a.a.'s. + helps histone bind tightly to - sugar-phosphate backbone of DNA.
How does the DNA interact with the histones in a nucleosome?
DNA rightly wraps around histone core completing 1.7 turns in a left-handed coil. + a.a.'s interact with - sugar-phosphate backbone of DNA.
What is the length of DNA found in a core nucleosome?
147 nucleotide base pairs
What is the 30 nm fiber structure of chromatin?
it is a compact structure of nucleosomes. Structure is organized with the aid of H1, pulls the nucleosome together.
What is the Central Dogma of Molecular Biology? Which are "2-way streets", which are not?
What are the primary structure difference between RNA &DNA?
DNA=deoxyribose, dbl stranded, transcription brings RNA
RNA=ribose, single stranded, translation brings proteins
What is meant by the DNA dbl helix being "anti-parallel"?
the 5'-3' strand are complimentary & go opposite directions as they pair up
why is the dbl-hlical structure of DNA excellent for a mechanism of DNA replication?
allows precision in copying it. each strand can serve as template to specify squence of nucleotides in complementary strand. semi-conservative replication allows for mistakes to be caught.
describe a typical replication origin.
Site on a chromosome where DNA replication begins.
what are the number and compnents of a bacterial origin of replication.
Only one origin, 100 nucleotide pairs, that attract initiator proteins, and that are easy to open.
how are eukaryotic origins of replication organized?
They are spaced out along the DNA to shorten the time needed to copy the entire genome. 10,000 origins of replication for eukaryotic organisms.
describe a replication fork its direction and speed.
Y-shaped junction, bidirectional, moving at a speed ranging from 100 to 1000 nucleotides per second depending on the organism.
what is an asymmetrical replication fork?
where the the leading strand grows continuously whereas the lagging strand is synthesized discontinuously.
What are the differences between the leading and lagging strand during replication?
The lagging strand is synthesized discontinuously, leading strand is continuously.
What does 3'->5' mean? What does 5'->3' mean?
justification of direction. mostly describes polarity.
Describe the chemistry of DNA synthesis?
creating of phosphodiesther bonds between 2 nucleotides, you need enzyme DNA pol, primer, template, substrates.
Discuss DNA replication proofreading.
it checks whether the previous nucleotide is correctly base-paired to the template strand. If not, the polymerase clips off the mis-paired nucleotide and tries again.
What is semi conservative DNA replication? Why is this an important feature of DNA replication?
carries out DNA replication, synthesis new DNA, proofreads work and corrects any mis-paired bases.
What are primases used for in replication? What do they synthesize?
Primase is an enzyme that synthesizes the RNA primer from the sequence, polymerase replaces the missing segments, and DNA ligase joins the segments.
How are Okazaki fragments resolved into a continuous lagging strand?
1. Nuclease separates RNA primer from the sequence
2. Polymerase replaces the missing segments
3. DNA ligase joins the segments.
What is a DNA helicase? Discuss the structure of helicases.
huge enzymes with large sub units containing lots of ATP.
How does DNA polymerase move and stay connected to the DNA?
has a sliding clamp that forms a ring around the DNA helix. allows it to move around the template strand without falling off.
Describe how the replication machine is assembled? How does it move?
Helicase, Single-strand binding protein binds to the single stranded DNA. The sliding clamp keeps polymerase attached and allows it to move along the template without falling off. A clamp loader hydrolyzes ATP, enabling the sliding clamp.
Describe a typical telomere?
Telomeres are the ends of eukaryotic chromosomes. Telomerase adds more nucleotides onto the ends in order to conserve the chromosome from degradation after multiple rounds of replication.
What is a "mismatch"?
A mistake in copying DNA.
What is depurination and deamination?
Depurination: the loss of purine bases (A or G) from DNA in the cells of the body.
Deamination: Loss of an amino group from cytosine to produce the base uracil.
What are the three most common types of damage that happen to DNA?
Depurination, Deamination, and UV radiation in sunlight
What are the three basic steps in base excision repair?
1. The damaged cell is recognized and removed.
2. DNA polymerase binds and fills the gap.
3. The break in the backbone at the repaired strand is filled with DNA ligase.
What is homologous recombination?
Genetic exhange between a pair of identical or very similar DNA sequences.
Describe a Holliday junction.
Site where two DNA duplexes cross in homologous recombination.
What is a bacterial transposable element? Why are they called "hopping genes"?
DNA sequence that can change its relative position within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste," which is where the genes "hop" from one chromosome or area of a chromosome to another.
What are the main differences between replication and transcription?
Replication: DNA --> DNA, RNA primer, DNA polymerase
Transcription: DNA --> RNA, DNA promoter, RNA polymerase
What are ribonucleotides? How do they differ from deoxynucleotides?
They are the nucleotides in RNA. They contain the sugar ribose rather than deoxyribose.
Describe a generic RNA polymerase.
The enzyme that carries out transcription. It unwinds the DNA helix. It can start an RNA chain without a primer, but does require attachment to the DNA promoter. No proofreading.
How does bacterial transcription work?
RNA polymerase binds to DNA promoter on the chromosome and makes an RNA molecule from this DNA strand.
Describe a typical bacterial promoter?
start codon
What is a sigma factor?
A subunit of bacterial polymerase that is primarily responsible for recognizing the promoter sequence on DNA to initiate transcription.
What is the main function of a sigma factor?
recruits the RNA polymerase to the promoter -10 to -35 motiff.
RNA polymerase transcribes from both strands. How is the transcript organized and the genetic code interpreted?
RNA polymerase as it reads upstream from 3' to 5' and then polymerases 5' to 3'. it can be recruited from one side to another.
What are the main differences between bacterial and eukaryotic transcription?
Bacteria = transcription occurs in cytoplasm.
Eukaryotes = transcription occurs in cells nucleus.
What is a lariat in RNA splicing?
The lariat is the lasso looking structure of intron that is cut out of the pre-mRNA molecule leaving only the exons to leave the nucleus and be translated.
Describe snRNPs
"Snurps" are small nuclear ribonucleoprotein particles. They form the core of the spliceosome.
Describe a spliceosome.
The large assembly of RNA and protein molecules that splices introns out of pre-mRNA in eukaryotic cells.
Why are there only 20 aminoacyl-tRNA-synthases coupling as many as 48 (humans) different tRNAs?
There are only 20 different amino acids used by the human body.
Describe the molecular composition of a ribosome
Has a large subunit and a small subunit. A large complex made from more than 50 different proteins (ribosomal proteins) and several RNA molecules called ribosomal RNAs (rRNAs)
How does a ribosome select the reading frame?
The initiator tRNA finds the AUG start codon attached to the small ribosomal subunit.
What is a “wobble” position in the genetic code?
Some AAs have more than one tRNA and some tRNAs are constructed so that they require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position. This wobble base-pairing explains why so many of the alternative codons for an AA differ only in their third nucleotide.
What are the main implications of templated replication of DNA molecules?Why is it important to have a semi conservative multiplication of DNA molecules?
DNA template can be used again, so future DNA, RNA, and proteins will always be the same. DNA template. Old copy and new copy and if mistake is in the new copy, then the old can be used to notice it.
In observing the central steps of molecular biology (see Figure above), consider the
similarities between the molecular (biological) computer (mathematical) approaches to deal with information.
DNA = Hard-drive = Long term storage
RNA = Microsoft word program = Takes specific part of Hard-drive (DNA) to make documents (proteins)
What are the main differences between DNA and RNA molecules?
DNA = Deoxyribose sugar (Only has one OH group). Double stranded
RNA = Ribose sugar (Has two OH groups). Single stranded
What are the three major groups of living organisms?
Bacteria, Archaea, Eukaryotes
Which group has been missed in earlier biodiversity studies? Explain why?
Archaea...because they have the least affects on humans.
Define the differences between prokaryotes and eukaryotes.
Prokaryotes = unicellular. Nucleiod rather than nucleus
Eukaryotes = multicellular. Nucleus rather than nucleoid. Bigger. More elaborate. Compose more complex multicellular organisms.
A carbon atom contains six protons and six neutrons.What are its atomic number =
Atomic weight =
How many electrons does it have?
How many additional electrons must it add to fill its outermost shell?
6, 12, 6, 4
What are the differences between a covalent and ionic bond?
Covalent = sharing of electrons between two atoms
Ionic = stealing of electrons from one atom by another
Why are hydrogen bonds formed (describe physical forces and chemical properties) and why are they so important in cell function and structure? Give a detailed and complete description.
Hydrogen bonds are the bonds between a Hydrogen of one compound and an Oxygen, Nitrogen, or Fluorine of another compound. These are strong intermolecular, polar bonds. Water is held together by H bonding. They are weaker than covalent bonds.
Describe a hydrogen bond.
Hydrogen bonds are the bonds between a Hydrogen of one compound and an Oxygen, Nitrogen, or Fluorine of another compound. These are strong intermolecular, polar bonds. Water is held together by H bonding. They are weaker than covalent bonds.
Why are substances such as sugars soluble in water and others such as lipids not?
Sugars are polar, same as water, and will interact with the Hydrogen bonding of the water molecules. Lipids are nonpolar and will not interact with Hydrogen bonds very well because of their long hydrocarbon chains.
Why does an acid donate protons when in water?
Acids have an extra proton. Water has negative side (it's polar), which will take the positive proton.
If non-covalent interactions are so weak in a water environment, how can they possibly be important for holding molecules together in cells?
Lots of weak bonds make a strong bond.
How glucose, mannose and galactose differ from each other?
-Position of the OH groups, whether facing up or down, which carbons they are attached to on the ring.
-Isomers of each other
-Numbering of carbons
If 0.5 mole of glucose weighs 90 g, what is the molecular weight of glucose?
180g/mol (90/.5)
What is the concentration, in grams per liter (g/l), of a 0.25 M solution of glucose?
45 g/l (.25mol/L)(180g/mol)
How many molecules are there in 1 mole of glucose?
Describe the formation (condensation) and disruption (hydrolysis) of a glycosidic bond.
condensation is where water is expelled.
hydrolysis is where water is consumed.
Describe different glycosidic bonds? Try to figure out all the different types of bonding
Position of Carbons (1 and 4; 1 and 6) on sugar
Configuration of bonds (alpha or beta) between sugars
Describe the differences between a linear molecule such as cellulose and a non-linear
molecule such as starch.
Both have only glucose as monomer to make polymer.
Starch is globular, branched (makes up pudding). Alpha 1,4 linkage
Cellulose is fibrous and linear, non-branched (makes up a t-shirt). Beta 1,4 linkage
What is the role of glycerol in triglycerides?
Three carbon backbone where the fatty acids attach.
What are saturated and unsaturated fatty acids?
Unsaturated have at least one double bond, saturated don't because they have as many Hydrogens as possible.
Describe the basic structure of fatty acids and a phospholipid.
Fatty acid = Hydrophilic carboxylic acid head with one hydrophobic hydrocarbon tail.
Phospholipid = Hydrophilic head with polar group, phosphate, and glycerol along with two hydrophobic fatty acid tails.
Why do phospholipids spontaneously form lipid bilayers when dissolved in water?
Hydrophobic portion goes away from the water and hydrophilic portion goes toward the water. Two phospholipid layers can readily combine tail-to-tail in water to make a phospholipid sandwich, or lipid bilayer, which forms the structural basis of all cell membranes.
Describe a micelle.
Small sphere made of one layer of phospholipid, where hydrophobic hydrocarbon chains are in the middle and hydrophilic heads face the surrounding water.
Place each of the 20 amino acids into one of the following groups: acidic, basic, uncharged polar, and non-polar
Basic HAL = Basic Histidine, Arginine, Lysine. At Basic (Army training program), Arg His Ly! = Hydrophilic
Acidic GlAsp = Glutamic acid, Aspartic acid = Hydrophilic
Nonpolar= I saw Lucy methodically probe and phen alan and then val trip glycine, not cool, not polar
Nonpolar= Isoleucine Methionine Proline Phenylalanine Alanine Valine Tryptophan Glycine = Nonpolar = Hydrophobic
Uncharged Polar = Everything else = Hydrophilic
Describe a peptide bond.
Covalent linkage between two adjacent amino acids in a protein chain
Describe the basic building blocks of nucleotides. Which components remain constant and
which are the ones that are variable?
Two types of nucleotides: DNA and RNA. Nucleotides are made up of phosphate group (constant), sugar (variable from deoxyribose in DNA to ribose in RNA, but otherwise are constant), and bases (variable from A, G, C, T, and U).
The nucleotide ATP is a building block for the synthesis of DNA. What other function does ATP perform in cells? Why?
ATP provides energy for many reactions, like enzymes. Rupture of the three phosphate bonds releases large amounts of useful energy. The terminal phosphate group in particular is frequently split off by hydrolysis.
What are the chemical differences between DNA and RNA?
DNA = has deoxyribose sugar (which has one less Oxygen, an -H group where the ribose has an -OH group)
RNA = has ribose sugar
Both DNA and RNA are synthesized by covalently linking a nucleotide triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together?
Hydrogen bonds
Draw the general structure of an amino acid.
H2N - C - COOH
What are the four weak non-covalent interactions that determine the conformation of a
hydrogen bonds, electrostatic attractions, hydrophobic interaction, and van der Waals
What are the major properties that distinguish different amino acids from one another? What roles do these differences play in the structure and function of proteins?
Sidechains. Some are nonpolar (hydrophobic) and tend to cluster in the interior of the folded protein. Polar side chains tend to arrange themselves near the outside of the folded protein, where they can from hydrogen bonds with water and with other polar molecules. When re-naturing, the prosthetic group is in a different place.
When proteins denature and renatured, some fully recover its original conformation and function, and others often partially renature and remain functionally inactive. Why is this happening?
The 3D structure is determined by the order of the amino acids in the chain. If the denaturing only disrupts the non-covalent forces, then the protein will renature back to its original form. If the covalent bonds are disrupted, then denaturing will be complete.
What is a molecular chaperone? Why are they important in the crowded cytoplasm?
Molecular chaperones are special proteins that assist in protein folding. Chaperones bind to partly folded chains and help them to fold along the most energetically favorable pathway.
Chaperones are vital in the crowded conditions of the cytoplasm, because they prevent newly synthesized protein chains from associating with the wrong partners. Nevertheless, the final three-dimensional shape of the protein is still specified by its amino acid sequence; chaperones merely make the folding process more efficient and reliable.
Protein structure is dictated by the amino acid sequence. Should a protein, in which the order of all amino acids is reversed, (ABC->CBA) have the same structure as the original protein?
No. Polarity in English is left to right. Polarity in protein is N- to C-termini. Thus, the N terminus would be on C for the 2nd but on A for the first.
Explain how is it possible that living cells contain such an enormously diverse, but structurally stable, set of proteins? How is function and specificity determined in proteins?
Enormous amount of amino acids and combinations of them.
What common feature of alpha helices and beta sheets makes them universal building
blocks for proteins?
Hydrogen bonds are independent of side chain parts, come from backbone of aa.
Why do you suppose that only L-amino acids and not a random mixture of L- and D- amino
acids are used to make proteins?
If body recognized D-aa instead of L-aa, then that'd be fine, but the mix between L and D messes up the aa chain.
Explain the coiled coil protein structure
Sometimes two (or three) alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This structure forms when the alpha helices have most of their nonpolar (hydrophobic) side chains on one side, so that they can twist around each other with these side chains facing inward--minimizing their contact with the aqueous cytosol.
What do we mean by primary, secondary, tertiary and quaternary structure of proteins?
Primary = sequence of aa
Secondary = alpha helices and beta-pleated sheets
Tertiary = The full, three-dimensional conformation formed by an entire polypeptide chain--including the alpha helices, beta sheets, random coils, and any other loops and forlds that form between the N- and C-termini.
Quaternary = a complex of more than one polypeptide chain.
Why are the membrane-spanning regions of transmembrane proteins frequently alphahelical?
Maybe b/c...Sidechains attached to the alphahelix are nonpolar, same as the inside of the membrane is nonpolar.
Describe the structural and functional properties of a cellular enzyme?
Enzymes are proteins that bind to one or more ligands, called substrates, and convert them into chemically modified products. Enzymes are catalysts that speed up reactions without being changed themselves.
Given that proteins act as molecular machines explain why conformational changes are so
important in protein function.
Each protein's conformation endows it with a unique function based on its chemical properties. This union of structure, chemistry, and activity gives proteins the extraordinary ability to orchestrate the dynamic processes that occur in living cells. Changes to conformation change the chemistry which change the capability of the protein to carry out its original function.
How does the structure of a protein determine how it will function?
The structure is made up by the specific amino acids, alpha helices, beta sheets, intramolecular, and covalent bonds, which each are specific for a particular protein, which means only specific ligands can bind to the protein, thus the protein has specific functions.
What defines binding and catalytic site?
aa can help bind the ligands to the enzyme (this is the binding site) and some of these aa also participate in actually catalyzing the reaction (catalytic site). Binding site is where the ligand joins the protein. Catalytic site is where the enzyme breaks down the molecule.
How can enzyme activity be regulated?
Not enough substrate, not enough material for reactions.
More enzymes, more reactions.
Substrate level can hit a maximum due to only a certain amount of enzymes available for the substrates to bind to at one time.
Higher temperature, higher rate of enzyme activity. But if temperature goes too high, then protein will denature and decrease enzyme activity or eliminate it.
How does lysozyme catalyze the hydrolysis of the glycosydic bond?
The reaction catalyzed by lysozyme is a hydrolysis: the enzyme adds a molecule of water to a single bond between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break.
Based on the energy requirement shown above, describe the course of an enzymatic reaction.
Enzymes lower the activation energy without changing the course, reactants, products, or itself in the reaction.
What are the differences of micelles and lipid bilayers?
Micelles are spheres made of one layer of phospholipids where the hydrophobic tails are in the middle of the sphere and the hydrophilic heads are on the periphery. Lipid bilayers have two layers of phospholipids where the heads face the aqueous cytosol and the outside world. Phospholipids create barriers between the inside and outside of the cell.
Describe the types of lipid movements that occur at lipid bilayers. Explain the type of movement that happens less often too.
Hydrophobic molecules can pass through the lipid bilayers because they have similar charges to hydrophobic tails, but hydrophilic molecules can't pass through the chains unless they are extremely small. Proteins embedded in the membrane help pass the molecules too big or of too dissimilar charge; many of these proteins are channels for such molecules. There is diffusion, facilitated diffusion, primary and secondary active transport.
What is the role of cholesterol in membrane bilayers?
Because cholesterol molecules are short and rigid, they fill the spaces between neighboring phospholipid molecules left by the kinks in their unsaturated hydrocarbdon tails. In this way, cholesterol tends to stiffen the bilayer, making it more rigid and less permeable.
How are proteins anchored or attached to membranes? Discuss at least three different modes.
1. Transmembrane proteins have both hydrophobic and hydrophilic regions. Their hydrophobic regions lie in the interior of the bilayer, nestled against the hydrophobic tails of the lipid molecules. Their hydrophilic regions are exposed to the aqueous environment on either side of the membrane.
2. Other membrane proteins are located entirely in the cytosol, associated with the inner leaflet of the lipid bilayer by an amphipathic alpha helix exposed on the surface of the protein.
3. Some proteins lie entirely outside the bilayer, on one side or the other, attached to the membrane only by one or more covalently attached lipid groups
How different are membrane bilayer lipids? How are these components arranged?
Lipids can move and rotate within the layer, but don't switch layers, and you can have different sets of lipids, one looking to the inside and another to the outside.
What defines a transmembrane domain in proteins? How many amino acids and what type of amino acids are needed to form a transmembrane domain? ***
Transmembrane proteins go from one side of membrane to the other. At least 20 aa are needed. Nonpolar side chains on aa.
Why are plants green.
Green is reflected from the plant because of the chlorophyll pigment which absorb a majority of the photons for the excitation of the electrons in the ETC. Other colors are primarily absorbed by the plant cells. Green is detected by the cone cells in the eye.
Why plants have two photo systems (II and I)?
Electrons need to be going down the ETC constantly, and thus the membrane of the thylakoids need photons to continue the excitation of the electrons.
Describe the Calvin cycle.
Light independent. Inside chloroplasts. Forms glucose from CO2, recycling ATP and NADPH.
Draw the picture: 3 CO2 going in, boxes forming a circle with one of them being rubisco, and then NADPH, ATP, and glucose being the product.
Unlike mitochondria, chloroplasts do not have a transporter that allows them to export ATP to the cytosol. How then does the rest of the cell get the ATP it needs to survive?
Plant cells also have mitochondria.
What are the roles of ubiquinone and cytochrome c.
Pass electrons from one complex (protein) to the next.
Describe the differences between cytochrome b-c1 and cytochrome oxidase complex.
Both help pass protons through the membrane by passing electrons down the ETC. Cytochrome b-c1 passes the electrons to a cytochrome c molecule. Cytochrome oxidase complex passes electrons to Oxygen, which helps convert 1/2O2 and 2H's to water.
How many ATP molecules are produced by the complete oxidation of one molecule of glucose? Take into account ATP molecules that have been invested early in the process and the ATP molecules produced during glycolysis, the TCA cycle and oxidative phosphorylation.
2 from glycolysis. 2 from TCA. 34 from ETC = 38 ATP, at the very most.
In glycolysis, why do you think is it that the glucose molecule is activated by two phosphates – at the expense of 2 ATP molecules per mole, in a process designed to extract energy (catabolism)?
In order to begin the reaction, the energy of activation must be overcome, this requires energy input, in the form of breaking the phosphate bond in ATP. After the energy of activation is overcome, then the glucose molecule can be catabolized which brings further production of ATP from the energy in the glucose bonds.
In the absence of oxygen, cells consume glucose at high steady rate. When oxygen is added glucose consumption decreases precipitously and is then maintained at the lower rate. Why is glucose consumed at high rate in the absence of oxygen and at low rate in its presence?
Without oxygen, animal cells only produce ATP (their main source of energy) through glycolysis, which only makes 2 net ATP from every glucose, thus cells must use a lot of glucose to make enough ATP. With oxygen, animal cells will use glycolysis but also the ETC to produce ATP, which produces a net near 34 ATP, thus they don't need to use as much glucose.
The figure above illustrates the coupling of a favorable reaction to drive and unfavorable one. Describe how this concept works in cells using an example one of the common activated carrier molecules.
The unfavorable reaction of glucose combining to form glycogen requires the favorable reaction of ATP to ADP and P as the energy released from the break down of ATP provides the necessary energy to combine two glucose molecules together (exceeding the needed activation energy).
Describe briefly the three stages of cellular metabolism that lead from food to waste products in animal cells.
Glycolysis = breaking down glucose to pyruvate, producing some ATP and NADH
[then pyruvate to acetyl Co-A and CO2 (waste)]
Krebs cycle = further break down of the acetyl Co-A into CO2 (waste) and producing NADH and FADH2 and ATP
ETC = Produces much ATP from NADH and FADH2, ADP and P, and much water from O2 and NADH and FADH2.
Oxidation of glucose to CO2 and H2O in cells happens in a stepwise mode as compared with direct burning of sugar. Why do you think cells employ this stepwise oxidation approach?
Burning releases heat rather than a usable energy source like ATP, as it does in a stepwise mode.
In the reaction 2 Na + Cl2 --> 2 Na+ + 2Cl- , what is being oxidized and what is being reduced? How can you tell?
Na is being oxidized, because it loses electrons.
Cl2 is being reduced, because it gains electrons.
Animals and plants use oxidation to extract energy from food molecules. Explain how.
The NADH and FADH2 made directly or indirectly from glucose (food) molecules are then oxidized to NAD+ and FAD++ as they pass their protons into the inner mitochondrial space of the mitochondria, where the protons are then used to power ATP pumps.
Distinguish between catabolic and anabolic pathways of metabolism, and indicate in a general way, how such pathways are linked to one another in cells?
Catabolism is break down of large molecules to smaller ones, like glucose breaking down to pyruvate, which breaks down to CO2 and acetyl Co-A...ultimately leading to energy in the form of ATP, which powers many of the cell's functions.
Anabolism is the build up of larger molecules from smaller ones, like amino acids adding to another through peptide bonds to form a protein, which the cells use for structure and function.
Explain active transport of proteins entering through nuclear pores.
GTP hydrolysis drives nuclear transport in the appropriate direction. Nuclear pore proteins operate this molecular gate at an amazing speed, pumping macromolecules in both directions through each pore.
Provide functionally complete descriptions for three distinct modes of active transport.
1. ATP-driven pumps couple uphill transport to the hydrolysis of ATP (Breaking down of ATP into ADP and inorganic P provides energy to transport molecules)
2. Light-driven pumps, which are found mainly in bacterial cells, couple uphill transport an input of energy from light.
3. Coupled transporters couple the uphill transport of one solute across the membrane to the downhill transport of another.
Why does the nucleus consist of an envelope instead of a membrane?
Nuclear envelope consists of two concentic membranes. The inner nuclear membrane contains proteins that act as binding sites for the chromosomes and provide anchorage for the nuclear lamina, a finely woven meshwork of protein filaments that lines the inner face of this membrane and provides a structural support for the nuclear envelope. The composition of the outer nuclear membrane closely resembles the membrane of the ER, with which it is continuous.
How does an electrochemical gradient interfere with the rate of passive transport?
K+ can go like H+, but Cl- can't, because of different charge. The ions must be on the correct side of the membrane for gradient to work and for passive transport to go.
What are the differences between channel and carrier proteins?
Channel proteins discriminate mainly on the basis of size and electric charge: if a channel is open, an ion or a molecule that is small enough and carries the appropriate charge can slip through, as through a narrow trapdoor.
Carrier proteins allow passage only to those molecules or ions that fit into a binding site on the proteins; they then transfer these molecules across the membrane one at a time by changing their own conformation, acting more like a turnstile than an open door..
Describe the types of molecules that diffuse through membranes without any specific aid. Thinking on the molecules Na+, O2, H2O, K+ and CO2, order them based on their ability to permeate the membrane – from very fast to very slow.
Small, hydrophobic molecules (like O2, CO2, N2) and small uncharged polar (like water, glycerol, ethanol) can go through lipid membrane without any specific aid because they are small.
Large uncharged polar (aa, glucose, nucleotides) or ions (H+, Na+, K+) can't go through lipid membrane because they are either too big or too charged.
Fastest: O2, CO2, H20, Na+, K+ Slowest
Describe the protein spectrin – focus on the domains and how they function in human blood cells.
The main component of red blood cells' cortices is the protein spectrin-- a long, thing, flexible rod. Spectrin forms a meshwork that provides support for the plasma membrane and maintains the cell's shape. The spectrin meshwork is connected to the membrane through intracellular attachment proteins that link the spectrin to specific transmembrane proteins. Spectrin has an anchor and a structure domain. p378
What is the function of H1 in 30nm fiber structure?
H1 is linker histone that helps pull nucleosomes together in 30 nm fiber.
Why is the respiratory chain organized in the sequence NADH dehydrohengase, cytochrome b-c1, and cytochrome oxidase?
For redox ptential
Is cancer hereditary? Explain.
Yes, genetic instability can cause mutations.
How do cancers arise?
from violations of the basic rules of social cell behavior.
How tumors evolve?
by repeating rounds of mutation and proliferation.
Why are cancer cells genetically unstable?
increase the mutation rate.
Describe an oncogene and its corresponding proto-oncogene?
an oncogene is a mutant gene that is a result of a single mutation event in proto-oncogene, creating the oncogene.
Define three stages of the cell cycle?
G-1, interval between M-phase & S-phase.
G-2, interval between S-phase and M-phase.
S-phase, cell replicates of nuclear DNA.
What are cyclin-dependent kinases (Cdks)?
the kinases of the cell control system.
What are the cell cycle checkpoints?
they ensure that key processes in the cycle occur in the proper order.
Describe the steps of M-CDKs activation.
it must be phosphorylated @ 1 site and dephophorylation @ 2 other.
Why are M-Cdk and S-Cdk regulated by sequential cyclin activation in addition to multiple phosphorylation and dephophorylation steps?
each one phosphorlates a different set of target proteins in the cell. as a result each type of complex triggers a different transition step in the cycle.
Describe how S-Cdk controls initiation of DNA replication?
S-Cdk triggers origin firing by causing the assembly of the protein complexes that initiate DNA synthesis.
Define caspases, how are they synthesized and activated?
family of proteases, activated by causing the assembly of the protein complexes that initiate DNA synthesis
Describe an intracellular "stimulus" that induces apoptosis
proteolytic cascade one molecule activates many more molecules of caspase, one cleaves nuclear lamin and one cleaves cytosolic protein
Describe one type of targeted (programmed) cell death?
BAX, member of the BcL2 family of intracellular protiens that can trigger apoptosis be releasing cytochrome c from mitrochondria
Describe one of the simplest genetic mechanisms, which allow daughter cells to "remember" what kind of cell they are supposed to be.
Through + feedback loop where a key gene regulatory protein activates transcription of its own gene in addition to other cell-type specific genes.
Describe how gene activation can occur at a distance of up to several thousand base pairs in eukaryotic promoters?
by the use of enhancer-binding proteins.
Why is eukaryotic RNA polymerase II phosphorylated?
so it can go from initiating to elongating.
Why does eukaryotic RNA polymerase II require general transcription factors to initiate transcription?
Eukaryotic promoters build a protein complex around the TATA box and there it is where RNA polymerase is recruited to. Distant regulatory elements also interact with these proteins in order to activate or repress transcription.
Describe the dual nature of the regulatory switch that controls the lactose operon in E. coli.
The fact that lactose is only used when glucose is not present makes this a dual choice promoter. Lactose is mediated by a repressor and absence of glucose is mediated by an inducer, cyclic AMP.
Describe the regulatory switch of the operon that manufactures tryptophan in E. cole.
tryptophan low=genes are on, mRNA is transcribed.
tryptophan high=genes are off, no mRNA is transcribed.
what is an operon?
where genes are transcribed and regulated individually
What are "regulatory DNA sequences" found in operons?
regulatory proteins that switch the gene on or off
what are structural genes?
what are gene regulatory protein?
-a gene that codes for any RNA or protein product other than regulatory proteins
-special proteins that regulate transcription
What does "negatively-acting" mean? what is the outcome of a repressor?
through (-) acting, repressor suppresses transcription
What does "positively-acting" mean? What is the outcome of an activator?
through (+) acting activator stimulate transcription
what is "constitutive expressing' of a gene?
gene that is transcribed continuously
What is an inducer? what is a repressor?
-molecule that starts gene expression
-a protein that binds to specific regulatory region of DNA to prevent transcription of an adjacent genes
Be able to draw the short form nomenclature of a nucleic acid molecule.
Why is the presence of uracil in DNA bad?
Damination and deprotination has occurred which makes mutations and causes errors.
What is the recognition or strand specificity problem in DNA repair, how have cells solved this problem?
problem is which strand has wrong nucleotide in it, cell solved this with okzaki fragments by noticing these nicks.
How is translation initiated in eukaryotes?
use of start codons. AUG
How is translation initiated in bacteria?
ribosome binding sequences up to 6 nucleotides long are located upstream of AUG.
How is translation terminated?
stop codons.
What does "p" in pH stand for?