Chapter 3

Question 1

__ ___ are vital for life. It mediates the interaction between enzymes and their
substrates, between proteins and DNA or RNAs, or other proteins. It is the weak non covalent
bonds that hold the two chains of DNA double helix together.

Answer 1

weak bonds

Question 2

Weak binding forces are effective only when the interaction surfaces are __. This proximity
is possible only when the molecular surfaces have __ __ structures, and the
interacting molecules must have a lock and key relationship.

Answer 2

close, complimentary structures

Question 3

The lock & key requirement means that some molecules hardly ever __because such molecules don’t have the properties of symmetry necessary for __ . On the other hand, many molecules with necessary symmetry to permit this in cells. ___ is the most important example of this. These molecules form hydrogen bonds.
In solid and liquid, one tends to have four
nearest neighbors.

Answer 3

bond to other molecules of the

same kind , self interaction. water,

Question 4

A circular DNA that is __ migrates more slowly than does ___, which are compact and
have a small effective volume, migrate more rapidly d
linear molecules of equal size. S

Answer 4

relaxed or nicked, aupercoiled DNAs

Question 5

If two enzymes generate ___, you can easily ligate the

products from two digestions.

Answer 5

the same sticky ends

Question 6

When comparing two alleles of a gene, what defines the two alleles as distinct alleles?

Answer 6

E

Question 7

Can one gene possess only two alleles?

Answer 7

No, a gene may have more than two alleles, but one can determine relationships among all the alleles I.e. By genetic crosses or mapping

Question 8

T or F, one trait is always determined by one gene

Answer 8

D

Question 9

T or F for a given gene, one can always define the alleles as dominant or recessive.

Answer 9

F. Some alleles display incomplete dominance as with the alleles of snapdragon. There is an intermediate phenotype. Also, a gene may have more than 1 allele and the relationship bt each allel relative to each other has to be determined.

Question 10

A. After true breeding pea plants with yellow seed to true bred plant with green, what phenotype is expected in the F1 gen if yellow are dominant to green?
B. You self cross the F1, give expected phenos for the F2
C. Give expected genotypic ratio of the F2
D. Give the expected ratio of homozygotes to heterozygotes in the F2

Answer 10

A. All pea plants will be yellow and heterozygous for Yy
B. 3 yellow:1 green seed
C. 1 YY :2 Yy :1 yy
D. Two heterozygotes (Yy) : two homozygotes (YY and yy)

Question 11

If Mendel had selected two traits controlled blinked genes, which of his laws would’ve been affected?

Answer 11

Independent assortment

Question 12

Define mutation. How could a very low mutation rate be advantageous over the prevention of all mutations in an organism?

Answer 12

F

Question 13

Chromosomes vs chromatids

Answer 13

S

Question 14

What are the types of bonds possible bt macromolecules?

Answer 14

H bonds, ionic bonds, van der Waals interactions, and high energy bonds.

Question 15

T OR F Enzymes lower the change in Gibbs free energy of a rxn

Answer 15

F. Enzymes lower activation energy of a rxn and ΔG stays the same

Question 16

T or F ionic bonds and H bonds are stronger than van der Waals

Answer 16

Ionic > h bonds > van der Waals

Question 17

T or F at 25°, a 10-fold change in Keq corresponds to a 10-fold change in Gibbs free energy

Answer 17

F. At 25° a ten fold change in Keq corresponds to about a 1.4 fold change in ΔG.

Question 18

Which major cellular process involves the rxns of a nucleoside triphosphate breaking down into a nucleoside monophoaphate + pyrophosphate as well as pyrophosphate breaking down into two phosphates? Why is the change in Gibbs for these rxns significant for these processes?

Answer 18

The ΔG is significant bc it = -7 which is that of a high energy bond, it allows for energy to be released and used to make other bonds such as bonding nucleic acid bases. A negative ΔG indicates a spontaneous rxn.

Question 19

What type of bond is responsible:
The two strands of dsDNA interacting?
The dipeptide bind of two AAs?

Answer 19

Hydrogen bonds bt bases

Covalent peptide bonds

Question 20

Define polar and nonpolar molecules in terms of dipole moments. Do van der Waals interactions occur bt polar or nonpolar molecules?

Answer 20

Polar have dipole moments and nonpolar do not. van der Waals can include polar and nonpolar

Question 21

Calc the value of Keq at 25° C given the change in Gibbs = -12 kcal/mol

Answer 21

Keq = [A][B]/[AB]

Question 22

Given the equation AB+energy = A+B, calc the the [A] at equilibrium if Keq=8.0x10^5 mM, [b]= 2mM and [AB]=0.5mM

Answer 22

A

Question 23

Glutamate + NH3 = glutamine + H2O where ΔG =+3.4 kcal/mol. Would coupling this rxn to ATP hydrolysis allow glutamine formation to be favored? What would be the overall rxn?

Answer 23

Yes, ATP+H2O = ADP + Pi ΔG=-7 kcal/mol

coupling the rxn to ATP hydrolysis gives an overall negative ΔG

Glutamate+NH3+ATP=glutamine+ADP+Pi with ΔG= -3.6 kcal/mol

Question 24

Why are NTPs instead of NDPs used in DNA synthesis?

Answer 24

ADP=AMP+P has ΔG = -6 but the energy of hydrolysis of the average high energy bond is = 7 so it has to be ΔG = -7

Question 25

Explain why researchers wouldn’t find any single H bonds bt tryptophan and one of the DNA bases.
Explain why they found single H bonds bt glutamate and each of the DNA bases.

Answer 25

The side chain of tryptophan does not include a H bond donor or acceptor.
The side chain of glutamate includes a carboxylic acid capable of participating in H bonds.