Biochem Final- SG Questions

While there are only 20 amino acids directly encoded by the genetic code, huge diversity is accomplished. Show how this is possible by mathematically calculating the number of 10-mer peptide using the standard 20 amino acids.

1 x 10^13

Explain why kcat = k2 in MM kinetics

Kcat = Vmax/ET Vmax = k2*ET Therefore, Vmax=k2

One strand of a DNA helix has the sequence 5' GATATC 3'. Write the sequence of its complementary strand in the conventional 5'-3' direction.

5' - GATATC-3'

How does the body prevent chymotrypsin from digesting important human proteins in the body?

- The enzyme is produced as an inactive precursor (zymogen) which must be removed to activate the enzyme

What is the net charge of the following amino acids at pH 7.0? Draw the structure of each as it predominantly exists at pH 7.0. o Histidine o Lysine o Aspartic acid o Serine

0 (partial + charge) +1 -1 0

Match the term with its description. 1. Enzyme A. The least stable reaction intermediate 2. Substrate B. Site on the enzyme where catalysis takes place 3. Cofactor C. K2 or Kcat 4. Turnover number D. Biochemical catalyst 5. Allosteric enzyme E. Standard free energy of reaction 6. Transition State F. Change in enzyme structure upon substrate binding 7. Active Site G. Reactant in an enzyme-catalyzed reaction 8. Induced Fit H. A coenzyme or metal required for catalysis 9. G°' I. Responds to environmental signals

1. D 2. G 3. H 4. C 5. I 6. A 7. B 8. F 9. E

Give a description for the following terms: 1. Base Stacking 2. B-DNA 2. A-DNA 4. Z-DNA

1. Stabilization of the double helix due to van der waals forces 2. The most common form of DNA 3. Form of DNA found under dehydrating conditions 4. A left-handed helix of DNA

Give a description for the following terms: 1. supercoiling 2. histones 3. nucleosomes 4. base pairing

1. Twisting of the axis of a DNA helix into a superhelix 2. Basic proteins that make up half of the molecular weight of a chromosome 3. DNA and associated proteins 4. Hydrogen bonding between A/T and G/C

What are the techniques used to understand protein structure. Describe how they work, and some of the advantages and disadvantages of each technique.

1.) Crystallography - X-rays diffract off of electron clouds, gives an exact atomic position of every atom in the protein. Disadvantage - only a snapshot, shows nothing about dynamics. 2.) NMR - Uses nuclear spin to determine atom connectivity. Tells us about Disadvantage- lower resolution and can only be used on small proteins

Biochemist Erwin Chargaff was the first to note that in double-stranded DNA the [dA]=[T] and [dG]=[dC]. If a particular molecule of dsDNA contains 23% A, what are the proportions of the other three deoxynucleotides?

23% A 27% G 27%C

Calculate the isoelectric point for the following amino acids based on their pKa values. Could any of the amino acids act as an effective buffer at pH 8.0? If so, which one? Does it fit the conditions of a Good's Buffer? Leucine 2.33, 9.74, n/a Lysine 2.16, 9.06, 10.79 Cysteine 1.92, 10.70, 8.18

6.04 9.93 5.05 Yes - Cys, the pKa of the alpha amino group is near 8. It is not a "Good's Buffer" The thiol (SH) side chain is highly reactive.

Calculate the pH of the following substances from the [H+]. o Blood plasma, 39.8 nM o Gastric juice, 15.8 mM o Household ammonia, 3.16 pM o Orange juice, 31.6 mM

7.4 1.8 11.5 1.5

A scientist needs to prepare an acetate buffered solution at pH 5.0. What is the final concentration of acetic acid and sodium acetate she needs in the solution to have a create a final concentration of 25mM?

9.2 mM acetic acid and 15.8 mM acetate

Indicate next to each stamens what an enzyme DO or DON'T. _______ speed achieving equilibrium _______ lower activation energy _______ change equilibrium concentrations _________ catalyze reversible reactions ________ change overall energy

DO DO DON'T DO DON'T

On a ribbon structure of a protein. What would represent an alpha-helix, a beta-sheet and a loop?

Alpha helix (looks like a coiled ribbon) B sheet (looks like a flat ribbon) Loop (looks like a string, aka tail)

Imagine you are setting up a reaction and need to maintain the pH at 6.1. Which buffer system should you use? What is the necessary ratio of conjugate base: weak acid required to achieve this pH? If the concentration of buffer should be 100mM, what is the concentration of the weak acid and the conjugate base?

Any buffer with a pKa near 6 (see lecture slide of Good's buffers), one example would be MES buffer, which has a pKa of 6.15 To get a pH of 6.1 using MES, you would need a ratio of conj base to weak acid of 0.9 You would need 53 mM of weak acid and 47 mM of conj. base

Which functional groups are capable of participating in hydrogen bonding?

Any polar functional group. Examples: Hydroxyls, amino, carbonyls, amide, guanadinium, carboxy-amides

What is a reducing sugar?

Any sugar that can be oxidized. Must have a unbonded anomeric carbon.

In the derivation of MM kinetics, several assumptions were made. For each of the assumptions below (i) explain what the assumption means; (ii) how it was useful in the derivation of the MM equation b) Product formation is rate limiting

Assumes that ESP is the rate limiting step, and thus the rate of the whole reaction is given by V = k2 [ES]

In the derivation of MM kinetics, several assumptions were made. For each of the assumptions below (i) explain what the assumption means; (ii) how it was useful in the derivation of the MM equation c) Steady State Assumption

Assumes that the rate of ES formation is the same as ES breakdown, i.e. concentration of ES is at a steady state and not changing during the course of the reaction. This allows us to solve for ES and replace [ES] in the equation given in part (b)

Amino acids and peptides tend to be more soluble in water when they are at extremes of pH, rather than near their isoelectric points. Suggest a reason to explain this phenomenon.

At extreme pH amino acids are fully protonated or deprotonated thus interact better with water

Bacteria produce restriction endonucleases as a defense mechanism against phages. Explain why the enzymes do not cleave the bacteria's genomic DNA?

Bacterial resistance is mediated by a methyltransferase, which methylates the DNA sequence cut by the particular restriction enzyme. The methylated DNA cannot be cleaved by the restriction enzyme.

The cell membrane allows simple diffusion of _________, ________, _________, and __________ across the bilayer. In addition, membrane proteins called ___________ allow a more rapid diffusion of water. This is termed __________ diffusion and is a form of _________ transport. In contrast, _____________ moves molecules against the concentration gradient using energy derived from ATP. An example of a transporter that uses this method is the ______________.

CO2 H2O O2 CO aquaporins facilitated passive transports lactose permease

Explain how the CRISPR-Cas system works as a bacterial immune system.

CRISPRs are short palindromic repeats of DNA that are coded as arrays in the genome. Invading DNA from viruses in incorporated in-between the CRISPR sequences. The repeats plus the part of the invading DNA (called the protospacer) are transcribed to produce crispr RNA (crRNA). The crRNA hydribizes with tracerRNA and the RNA complexes with the Cas9 nuclease. The protospacer hybridizes to the target DNA and directs Cas9 to cleave the invading DNA.

Explain what mutarotation is.

Carbohydrates are in equilibrium between open chain, alpha and beta configurations.

Suggest a reason why cells need a barrier that is impermeable to ions such as Na+, K+, Ca2+ or Mg2+.

Cells need ion gradients to create membrane potentials, which are important for a variety of

How do D-amino acids differ from L-amino acids? Which is the form used in building proteins?

Configuration of the alpha-amino group. The L-form is used in proteins.

At pH 7.0, the amino acid threonine is a zwitterion. What does that mean?

Contains both negative and positive ions

Why is the phenomenon of electronegativity so essential to biochemistry?

Creates polarity The resulting partial negative and positive charge allows the formation of hydrogen bonds, a crucial interaction in biochemistry.

Consider what the following mutations would do to the catalytic mechanism of chymotrypsin. c. The serine in the active site is mutated to cysteine.

Cys can act as a nucleophile, so the enzyme may still function.

How was A-DNA first isolated? What does it mean to say that a scientific finding may be an artifact?

Dehydration of DNA to form crystals for X-ray diffraction. Artifact is an experimental result that occurs because of how the sample is treated, and does not represent the actual, native form.

A hydrogen bond is a special case of which intermolecular force?

Dipole-dipole interaction

What is occurring in the "burst phase" of catalysis by chymotrypsin? Why is this more rapid than the slower phase of catalysis?

During the burst phase a tetradehral oxyanion intermediate being formed which rapidly collapses and releases the fist (amino) product of the reaction. This occurs quickly because the intermediate is unstable. The 2nd slower phase involves the release of the much more stable acyl-enzyme intermediate.

The following question is related to the Bohr effect. Explain how the Bohr effect results in hemoglobin effectively delivering O2 to tissues during vigorous exercise.

During vigorous exercise, three things are occurring: (i) there is a large amount of ATP hydrolysis occurs which generate H+, (ii) the active cells are consuming O2 at a higher rate than normal, so need more of it, and (iii) there is an increase in CO2 production which also produces more H+ The presence of H+ causes the affinity of Hb for O2 to be reduced, it will then release O2 from the heme, and the cells will obtain more of the oxygen they need. The Hb also helps, by neutralizing the protons and also picking up CO2 for transport to the lungs where it can be exhaled.

What step in Michealis-Menten kinetics determines the overall rate of the reaction?

ES to P (catalytic step)

Draw what the agarose gel would look like if you digested the plasmid pSU922 with the restriction enzyme EcoRI.

EcoRI cuts the plasmid in 2 places. You would get two fragments, one being slightly larger than the other:

The melting point of oleic acid (18:1, cis9) is 16.3°C whereas elaidic acid (18:1, trans9) has a melting point of 44.8°C. Explain how the differences in structure bring about the difference in melting temperature.

Elaidic acid has a higher melting temperature because it has more carbons (18 vs. 16 in oleic acid), also the trans isomer will raise the melting temp relative to the cis isomer

Consider what the following mutations would do to the catalytic mechanism of chymotrypsin. b. The aspartic acid in the active site is mutated to asparagine.

Enzyme would cease to function. Asn donates a H in H-bonds this would stabilize the wrong tautomer of His. The His immadazole ring would face the wrong direction and be unable to deprotonate the Ser side chain, inactivating the enzyme.

How does the addition of a proline residue affect the formation of an alpha-helix?

Fixed phi-psi angles and lack of rotation unwind the helix

What are histones and how do they assist in DNA packaging?

Histones are positive charged protein which form an octomer. DNA wraps around the proteins, which in turn folds the DNA into chromosomes.

The 3D structure of DNA can be reversibly denatured by heating and cooling. What type(s) of interactions are destabilized by heating? How does the %GC impact the temperature at which denaturation occurs?

Hydrogen bonding and base-stacking both contribute to DNA stability. GC stacks better and has more H-bonds, so increases the temperature at which denaturation occurs

What is the energetic force driving formation of lipid bilayers?

Hydrophobic effect

What is the defining characteristic of lipids? How does this definition differ from that of proteins, nucleic acids and carbohydrates?

Hydrophobicity - this is distinct from the other classes of biological molecules which are largely polar in nature.

What happens in the T to R state transition in hemoglobin? What influence does this change have on the affinity of heme for oxygen? How is this small structural change propagated to other monomers in hemoglobin?

In the T-state, the iron pulled below the plane of pyrrole rings by a His residue on helix. This triggers conformational changes as salt bridges are broken, causing the heme in another monomer to adopt the planar conformation, making it easier to bind oxygen. Once oxygen binds to the second heme, all of the other monomers in the tetramer can adopt the R-state

What is the biggest difference between the ping-pong mechanism and the ordered or random binding mechanisms?

In the ping pong mechanism the enzyme is acting as a carrier, a product is released before the second reaction happens.

Explain how partial hydrogenation of oils can lead to the generation of trans fats.

Incomplete hydrogenation of the cis double bond will produce the trans isomer.

Consider the implications of an enzyme that has higher affinity for substrate than for the transition state. Would this be an effective enzyme?

It would not be. High affinity for substrate would create an energy well, which would effectively increase the amount of energy required to reach the transition state.

We often say that the KM reflects the affinity of an enzyme for its substrate; however, this is a simplification of what is truly observed. Describe a situation where the KM value is equal to the dissociation constant (KD) of the enzyme for substrate. Now describe one where KD is lower than KM.

KD = k-1/k1 KM = k-1 + k2/k1 KM = KD if k2 is many magnitudes of order smaller than k-1 KD will be lower than KM if k2 is similar in magnitude to k-1

Provide an explanation of what KM and Vmax are, and also provide a mathematical definition.

KM - Expression of all the rate constants and an approximation for enzyme affinity for substrate. KM = k-1 + k2/k1 Vmax - the maximum catalytic rate at a given enzyme concentration Vmax = k2 [ET]

What feature of mucins is responsible for their gel-like properties? Which post- translational modification gives rise to this feature?

Massive layer of extracellular carbohydrate. Glycosylation

You are part of a team of biochemists that uses molecular biology techniques to modify the interface region between the α/β chains in Hemoglobin. The mutant exist only as dimers of α/β (no more tetramers). Would you expect this protein to bind oxygen more weakly, or more tightly? Explain your answer.

More tightly. An inability to form tetramers would limit the cooperativity of these variants, and the binding curve would become hyperbolic. Also the BPG binding site would be disrupted. Oxygen binding would be tighter because the default state in the absence of bound BPG is the R-state.

Explain why the curve for myoglobin is hyperbolic while that of hemoglobin is sigmoidal. Explain why the shape of the hemoglobin curve effectively delivers oxygen from the lungs to the tissues

Myoglobin is a monomer, and so exhibits saturation kinetics and a hyperbolic binding curve. Hemoglobin is a tetramer and exhibits cooperativity. The binding of one O2 to one monomer makes it easier for the other monomers in the tetramer to bind O2. Hence the sigmoidal curve. In the lungs O2 is at a high pressure, and hemoglobin binds with high affinity (right hand side of the curve). In tissues, the O2 pressure is much lower, and hemoglobin has a much lower affinity for O2 (left hand side of the curve), and thus releases O2 into the tissues that need it.

What are the physiological functions of myoglobin and hemoglobin? Explain why the affinity of each protein for oxygen is logical.

Myoglobin is for oxygen storage, while Hemoglobin is for oxygen transport. Since Myglobin is for storage it must have high affinity for oxygen. Since Hemoglobin is for transport, and must bind and release oxygen, it must have a lower overall affinity for oxygen.

Draw the peptide described using the single letter code as C-H-E-M-I-S-T-R-Y as it exists at pH 7.5. What is the net charge of this peptide?

Net charge = 0

How do enzymes compare to non-biological catalysts? List at least two differences.

Non-biological catalysts ted to be small molecular weight, inorganic materials, which enzymes are large molecular weight, protein catalysts. Enzymes are generally much better at rate acceleration than non-biological catalysts, and are generally much more specific.

Why is it important to get omega-3 fats in your diet?

Not all Omega-3 fats are cannot be made by human cells and thus must be acquired through dietary intake. They important components in cell membranes as well as a variety of other important biological functions.

What are the three elementary components that make up a nucleotide? Which are hydrophilic and which are more hydrophobic?

Nucleobase, phosphate(s) and a sugar (ribose or deoxy ribose). The base is hydrophobic and the phosphates/sugar are hydrophilic.

What is meant by saturation or unsaturation when referring to oils and fats?

Oils are liquid at room temp, while fats are generally (semi) solid. This is controlled by the melting temperature of the fatty acids in the triglyceride molecules. Saturated fatty acids have higher melting temperatures, and thus tend to be found in fats. Unsaturated fatty acids (cis isomer) have lower melting temperatures and are found in oils.

Suppose you are studying an ion channel protein, would you expect to find polar amino acids on the inside of the protein or the outside of the protein? Why?

On the inside. The center of the ion channel would need to be polar in order to move ions through the membrane. The outer amino acids embedded in the membrane would be non-polar.

Consider the following peptides: Ala-Cys-Asp-Glu-Phe and Phe-Glu-Asp-Cys-Ala. How do they differ?

Opposite directions N to C terminus

Consider what the following mutations would do to the catalytic mechanism of chymotrypsin. a. The specificity pocket remains hydrophobic, but becomes more shallow.

Specificity would change towards smaller hydrophobic amino acids eg. Ala, Val,

The peptide bond is said to exhibit resonance. Explain what resonance means in terms of the peptide bond, and what the significance of resonance is for protein structure.

Partial double bond character means no rotation.

One of the original structures proposed for DNA had all of the phosphate groups positioned at the center of a long fiber. Give a reason why this proposal was rejected.

Phosphates are hydrophilic, thus unlikely to form the core of the molecule, also the negative charges on the phosphates would repel each other.

Explain the statement that DNA is much more stable to hydrolysis than RNA. Is there any benefit to using RNA for some functions rather than DNA?

RNA has a 2'OH group on the ribose sugar (DNA does not). The -H can be deprotonated under basic conditions producing an oxyanion nucleophile. This nucleophile attacks the electrophilic phosphodiester bond, breaking it, releasing the nucleotide. This is why RNA is less stable. This is a benefit for the function of RNA in transcript, as the RNA molecule must be rapidly degraded and turned-over during gene expression.

Consider the overall shape of a glycerophospholipid, versus a single fatty acid salt. Snake venom contains the enzyme phospholipase A2. The action of phospholipase A2 cleaves the fatty acid tail from the position 2 of a phospholipid structure. Considering the shapes above, discuss the structural ramifications of this reaction on a cell membrane.

Removal of the fatty acid would alter the structure of the membrane, damaging the cell.

What is the catalytic triad? In simple terms what is the role of each amino acid of the triad in chymotrypsin?

Ser-Asp-His - three amino acids crucial for the catalytic cycle of chymotrypsin Ser - Is the nucleophile that participates in covalent catalysis His - Is a base and then an acid. It creates the nucleophile and is carrying out General Acid/nase catalysis Asp - Stabilizes the correct tautomer of His by hydrogen bonding and shifts the pKa of His so it can be an effective base. Also provides energy through formation of a low barrier hydrogen bond.

Why is RNA more susceptible to mutation than DNA? What are the implications?

Since RNA is temporary, the consequences of RNA mutation are far less dire than that of DNA mutation.

How are soaps prepared?

Soaps are prepared by boiling animals fats in a strong base like NaOH. This hydrolizes the triglycerides producing.

2. Why are GC and AT the only base pairs that can occur in the double-stranded DNA helix?

Stable hydrogen bonding occurs only between GC (3 bonds) and AT pairs (2 bonds) mostly because two purines are too large to fit inside the double helix, and two pyrimidines are too small to form base pair.

4. Describe how the polymerase chain reaction works and results in exponential amplification of DNA. What steps are involved, what temperatures are required, and what components are needed for the reaction to occur.

Steps - Denaturation (~95 C), Annealing (~55 C), Extension (~72 C) Components - DNA template, DNA primers, Taq polymerase, ddNTPs, buffer containing Mg2+,

Consider the structure of cholesterol. How is it structurally similar to other membrane lipids? How is it different?

Structurally similar in that it is highly hydrophobic, but different in that it does not contain fatty acids, but rather is composed of fused rings Membranes that contain cholesterol tend to be less fluid at higher temperatures, and this functions to stabilize the state of the membrane. Also in the presence of cholesterol, the effects of temperature on membrane fluidity are less dramatic (linear rather than sigmoidal relationship), suggesting that cholesterol acts as a buffer to maintain the correct fluidity over a wider range of temperatures.

What is Taq polymerase? Where was it isolated and from which organism? Why is it crucial for the polymerase chain reaction?

Taq polymerase is a thermo stable DNA polymerase isolated from the bacteria Thermus aquaticus. The enzyme is crucial for PCR because it does not denature and lose function in the denaturation step of PCR.

The following question is related to the Bohr effect. Briefly describe the molecular mechanism behind the Bohr effect.

The T-state is stabilized by salt bridges, including some by Histidine residues. If the side chain is protonated the interactions form, and the T-state is held together. If the side chain deprotonates, there is not more charge, so the T-state is destabilized. The presence of a large concentration of protons, favors protonation of histidine residues, and hence favors the T-state.

Define the following terms: o Buffering capacity o Titration o Acid strength o Hydrophilic o Conjugate base o Equivalence point o pKa

The amount of strong acid/base a buffer can absorb A experiment to determine the equivalence point The relative amount an acid dissociates into ions Soluble in water A base that can be converted into an acid by a proton transfer reaction. The equivalence point is titration where the amount of titrant added is enough to completely neutralize the analyte. logKa

We've learned that the distribution of phospholipids within membranes is not uniform. What feature of membranes might prevent the random diffusion of the phospholipid classes which would allow uniformity?

The inability of lipids to move across leaflets and lipid rafts help to maintain heterogeneity.

Why is it necessary for cell membranes to have proteins that help transport molecules?

The membrane is a hydrophobic barrier. Only non-polar molecules, water, and gasses can pass through it directly through diffusion.

Consider the overall shape of a glycerophospholipid, versus a single fatty acid salt. How do the shapes help to predict the structures that these molecules will form in an aqueous environment?

The narrower shape of a single fatty acid lends itself to a spherical self-assembly (micelle), whereas the cylindrical shape of the phospholipid results in self-assembly into a more linear bilayer.

Briefly outline one of two strategies for recreating extinct species.

The passenger pigeon is using CRISPR based Genome editing technologies. Sequence the passenger pigeon genome See how it is different from existing pigeon species Use CRISPR technology to change existing pigeon DNA to be passenger pigeon DNA The other approach would be somatic nuclear transfer (see you lecture notes)

What is the explanation for the effect of the pH changes on the conformation of poly(Glu) and poly(Lys)?

The unfolding of an alpha-helix can be monitored by specific rotation. (poly(Glu)) is alpha-helical at pH 3, but there is a large decrease in the specific rotation at pH 7. poly(Lys) where the peptide is alpha- helical at pH 10, but unwinds at PH 7

What is the effect of a catalyst on the standard free energy of a reaction?

There is no effect, the standard free energy of a reaction remains unchanged by catalysis.

Name at least one amino acid that contains the features listed below in its side chain: o A hydroxyl group o A thiol group o A chiral carbon o An amine group o An amide group o An aromatic ring o A branched alkyl group o o A carboxylic acid group

Thr Cys Thr Lys Gln Phe Val Glu

What is the difference between the behavior of carrier and channel proteins?

Transporters use energy and alter conformations to move molecules across the membrane, channels are pores through the membrane.

Of the classes of lipids that we've studied, one is not present in membranes. Which type is this and why would it not be a good membrane component?

Triglycerides are not present in the membrane. They contain 3 fatty acids, and are more hydrophobic than phospholipids. They would be unable to forma bilayer because they lack a large polar headgroup to interact with the solvent faces of the membrane.

In the following peptide, which are the polar amino acids, which are the aromatic amino acids, and which are the charged amino acids. Trp-Phe-Asp-Ile-Ala-Ser-His-Gly-Leu-Glu

Trp-Phe Asp-His-Glu Asp-Ser-His-Glu

What is the relationship between pKa and the useful range of a buffer?

Useful buffer range is +/- 1 pH unit of the pKa value

Under what conditions is KM an approximation of KD?

When k2 is much smaller than k-1

If you mix equal volumes of 0.1M NaOH with 0.2M acetic acid, is the resulting solution a buffer? Why or why not? Given that the pKa of acetic acid is 4.76, what is the pH of the resulting solution?

Yes it would be. Adding 0.1 M NaOH would make the solution be 0.1M acetic acid and 0.1M acetate. pH = 4.76

The hormones oxytocin and vasopressin are 9-mer peptides than differ in the identity of only two residues, yet have very different functions. In contrast, the primary structure of insulin varies the identity of four amino acids in different species but maintains the same function. Offer an explanation that resolves this contradiction in the role of primary sequence.

a difference in sequence does not always indicate a change in function

7. Like proteins nucleic acid molecules are also raveled and packed into three dimensional shapes. Describe the interactions that leads to each level of structure and give an example of a nucleic acid polymer that exemplifies the feature. a. 1° b. 2° c. 3°

a. phosphodiester bonds b. hydrogen bonds and hydrophobic base stacking c. electrostatic interactions between histones and DNA

Label the acid and conjugate base in each pair of molecules below. H2PO4 -and HPO4 2- CH3CH2COOH and CH3CH2COO- HCO3- and H2CO3

acid, base acid, base base, acid

What is the difference between a aldose and a ketose?

aldose - aldehyde; Ketose -- Ketone

Which of the following statements are true? a. All membrane proteins are bound to the interior of the membrane. b. Both proteins and lipids undergo transverse diffusion from the inner to outer leaflets. c. Some proteins and lipids undergo lateral diffusion along the surface of the membrane. d. Carbohydrates are found covalently attached to molecules on the outside of the membrane. e. The term 'mosaic' describes a highly-ordered region of the membrane rich in cholesterol and sphingolipids.

c. Some proteins and lipids undergo lateral diffusion along the surface of the membrane. d. Carbohydrates are found covalently attached to molecules on the outside of the membrane.

In an alpha-helix, the shape is a ______ . The hydrogen bonds in an alpha helix are ________ to the axis of the helix, and the amino acid side chains are pointing _____ from the helix. In an alpha-helix a backbone carbonyl is hydrogen bonded to the amide nitrogen of another amino acid that is ______ amino acids away in the sequence. The amino acids in a beta-sheet are in a fully_______ conformation. The hydrogen bonds in beta-sheet are _______ to the direction of the peptide backbone and the side chains alternate ______ and ________ the plane of the sheet.

coil parallel away 4 extended perpendicular up, down

Each DNA strand is built from ______ by the formation of a ______ bond, catalyzed by DNA ____, between the 3'_____ of one nucleotide and the 5' _______of the next. The result of this directional growth of the strand is that the one end of the strand has a free 5' _______ and the other a free 3' ________ group. These are designated as the 5' and 3' ends of the strand. DNA typically exists in as a double-stranded ______, in which the strands run ___________ to each other. Through base pairing, one can predict that if one strand read 5'-AGTCT-3', the opposite strand will read 5'-_______-3'.

nucleotides phosphodiester polymerase OH phosphate phosphate hydroxyl helix anti-parallel AGACT

In the derivation of MM kinetics, several assumptions were made. For each of the assumptions below (i) explain what the assumption means; (ii) how it was useful in the derivation of the MM equation a) Only initial rates are measured

only the initial rate is measured. This means that Product formation will be negligible, so the back reaction (P ES) can be ignored. Also leads to the Steady State Assumption

Considering the peptide sequence below, calculate its net charge at pH 2 and pH 8. Met-Asn-Val-Tyr-Lys-Tyr-Arg-Pro-His-Cys-Thr

pH 2 net charge: +4 pH 8 net charge: +2

Why does the pH change by one unit if the hydrogen ion concentration changes by a factor of ten?

pH = -log[H+] --- log scale, so a change of 1 unit is a 10 fold change in concentration

The following question is related to the Bohr effect. How does pH affect the affinity of myglobin and hemoglobin for oxygen?

pH does not affect myoglobin, but does cause a decrease in the affinity of hemoglobin for oxygen.

Which of the following two peptides is more likely to from an alpha-helix and why? a) LKAENDEAARAMSEA b) CRAGGFPWDQPGTSN

peptide a (smaller side chain, no prolines, no glycines)