exam 4

How many phosphoester (phosphate ester) and phosphoanhydride bonds are in adenosine and adenosine diphosphate (ADP)?

*phospohodiester*: adenosine: 0 ADP: 1 *phosphoanhydride*: adenosine: 0 ADP: 1

are associated with DNA structure:

- pyrimidines in the anti conformation - Z-DNA - G tetraplexes

mRNA

-It carries genetic information to the ribosomes. -It is formed by transcription. -It can be of varying lengths.

phrases that accurately describe properties of the most common form of the DNA double helix:

-The phosphodiester bonds between nucleotide residues run in opposite directions in the two strands. -A helical turn consists of about 10 base pairs. -DNA contains equal amounts of adenine and thymine, and equal amounts of cytosine and guanine.

properties of the most common form of the DNA double helix

-The phosphodiester bonds between nucleotide residues run in opposite directions in the two strands. -The sugar-phosphate backbone is in contact with water, whereas the nitrogenous bases are in the interior of the double helix. -A helical turn consists of about 10 base pairs.

bases in DNA:

-They have vertical stacking interactions. -They absorb UV light. -They hydrogen bond between two, three, or four complementary DNA strands.

pyrimidines

-contain one heterocyclic ring -contain only two ring nitrogens

purines

-contain two heterocyclic rings -contain four ring nitrogens

James Watson and Francis Crick used the X-ray diffraction image taken by Rosalind Franklin shown below to deduce structural properties of B-form DNA. What findings did Watson and Crick make from this image?

-shaped like a helix -has a consistent diameter -includes 10 base pairs per repeat

Calculate the weight in grams of a double-helical DNA molecule stretching from the Earth to the Moon (320,000 km). Assume that the DNA double helix weighs 1 × 10-18 g per 1,000 nucleotide pairs, and that each base pair extends 3.4 Å .

.00094

If a negatively supercoiled (ΔLk = -32) closed circular DNA of 2520 bp is relaxed by one catalytic cycle by a type II topoisomerase, what is the resulting Lk?

210

DNA polymerase moves down a DNA strand in the _________ direction and thus replicates the new strand of DNA in the _____________ direction.

3' to 5'; 5' to 3'

It can contain the pyrimidine uracil.

RNA

This contains the sugar ribose.

RNA

Translation

RNA -> protein

rRNA

Ribosomal RNA forms part of a ribosome, which serves as the site of protein synthesis.

When reading a chromatogram, what is indicative of a mutation in the sequence you are studying?

a double peak in the same position of two different nucleotides

What is the resulting bond that is formed from a nucleophilic attack during DNA polymerase reactions, and which molecules are involved?

a phosphodiester bond between the OH group of the pentose ring on the last nucleotide added to the growing strand and the alpha phosphate of the newly added nucleotide

Regulatory sequences do not include __________.

a signal for termination of DNA repair

Which of the following single-stranded DNA sequences is most likely to form a stem-loop structure? a. AGGAGCACTGGCTCCT b. ATAAGATGGGAGCATG c. GCAGGGACTCCGACGT d. ACTTCTTCTCCGCTGC

a. AGGAGCACTGGCTCCT

Which nucleoside is the one most commonly found as part of coenzymes?

adenosine

nucleosides

are the combination of a monosaccharide and a base. Nucleosides are produced when a base binds to carbon 1 (C1) of a monosaccharide. The monosaccharide may be ribose or deoxyribose. The base may be a purine or a pyrimidine. Nucleosides do not contain a phosphate group. Nucleotides contain a monosaccharide, a purine or pyrimidine base, and a phosphate group.

Which method is not associated with DNA sequencing? a. Sanger sequencing b. Maxam and Watson sequencing c. pyrosequencing d.electrophoresis

b. Maxam and Watson sequencing

In which way can nucleotides not be involved in signaling? a. extracellular ATP binding to its receptor b. cyclic dGMP as a second messenger c. as precursors for synthesizing second messengers d. extracellular ADP binding to its receptor

b. cyclic dGMP as a second messenger

The sugars are connected with a 3\'-5\' phosphodiester link.

both RNA and DNA

can contain the purine adenine.

both RNA and DNA

Which statement regarding chromosomes is false? a. They contain telomeres in eukaryotes. b. They contain centromeres in eukaryotes. c. They are circular in prokaryotes. d. They are all of natural origin.

c. They are circular in prokaryotes.

Which of the following is not a pyrimidine base? a. cytosine b. uracil c. adenosine d. thymine

c. adenosine

Which of the following is not part of a deoxyribonucleotide? a. deoxyribose b. phosphate c. ribose d. nitrogenous base

c. ribose

Supercoiling __________.

can be thought of as the coiling of the central axis of a DNA double helix upon itself.

Type II topoisomerases __________.

can decatenate catenated circular DNA molecules

Triplex DNA

can form between two pyrimidine-rich strands and one purine-rich strand. This form of DNA results from *Hoogsteen base pairing*. Hoogsteen pairing is non-Watson-Crick pairing, in that the bases form different hydrogen bond arrangements that enable a third strand to base pair with a double helix.

both nucleoides and nucleosides

contain a base, which may be a purine or a pyrimidine, and a monosaccharide, which may be ribose or deoxyribose. Both nucleosides and nucleotides are components of RNA and DNA.

DNA can undergo many types of modifications. One of these is methylation. Which base(s) is(are) methylated more often in human DNA?

cytosine

DNA can undergo many types of modifications. One of these is methylation. In bacteria, which two bases undergo methylation more often?

cytosine and adenine

The process of separating strands of a DNA double helix is known as _______.

denaturation

What reaction catalyzed by DNA polymerase uses water?

exonuclease proofreading activity

DNA renaturation experiments are useful strategies to estimate the

genetic relatedness between two species.

mirror repeats

have symmetry within a strand such that folding the sequence back on itself superimposes the bases. Mirror repeats do not have complementary sequences within the strand, and therefore cannot form hairpin or cruciform structures.

inverted repeats

have two-fold symmetry such that folding the double-stranded sequence back on itself and onto the other strand (horizontally and vertically in the sequence below) superimposes the bases. Two segments read the same in opposite directions. Inverted repeats have a complementary sequence within the strand. Inverted repeats can form *cruciform* structures when both strands are involved, or *hairpin* structures when only one strand is involved.

Energy for DNA polymerization during replication is derived from _____.

hydrolysis of a high-energy phosphate bond within the incorporating nucleotide.

Topoisomerases __________.

interconvert topological isomers of DNA

A G tetraplex (or quadruplex)

is a right-handed helix that consists of four DNA strands, each of which contains a large number of guanosine residues involved in Hoogsteen hydrogen bonds.

palindrome

is a sequence that reads the same forwards or backwards.

A gene...

is all the DNA that encodes the sequence of some protein or RNA product

DNA in the nuclei of interphase cells __________.

is in a form known as chromatin

Z-DNA

may exist in short stretches in prokaryotes and eukaryotes. An oligonucleotide with alternating purine and pyrimidine bases is more likely to form Z-DNA.

A strand of DNA or RNA _______.

might be an oligonucleotide.

A mutation to the exonuclease domain of DNA polymerase would most likely result in _____.

more mutations in DNA replicated by this polymerase.

Bases are attached to sugars in an α N-glycosidic linkage.

neither RNA nor DNA

In terms of base composition, the %A = %G.

neither RNA nor DNA

Mutations in DNA can result from _______.

oxidation of deoxyribose.

Type I topoisomerases __________.

pass one strand of a DNA double helix through a transient break in its complementary strand

What chemical reaction is prevented by the incorporation of ddNTPs into the sequencing reaction?

phosphodiester bond formation

In its simplest form, polymerase chain reaction _______.

requires two oligonucleotide primers.

Electrophoresis separates DNA based on:

size and charge

The major problem associated with intracellular packing of DNA is __________.

the fact that the total length of DNA in a cell is many times longer than the dimensions of the cell

RNA can have enzymatic activity.

true

RNA can have secondary structure.

true

This contains the pyrimidine thymine.

DNA

Replication

DNA -> DNA

Transcription

DNA -> RNA

Nucleosomes consist of __________.

DNA and histones

Hydrolysis of ATP to ADP and phosphate releases about 14 kJ/mol of free energy.

FALSE

Hydrolysis of the α, β and β, γ phosphoester bonds of a nucleotide is used as a source of chemical energy.

FALSE

Sanger sequencing can only be used on DNA for which the sequence is unknown.

FALSE

dATP is the most common source of chemical energy in cells.

FALSE

Describe the bonds that form when a nucleotide is incorprated into the growing DNA strand.

Hydrogen bonds with the complementary nucleotide on the template strand, and a phosphodiester bond with the pentose of the last incorporated nucleotid

In the heterozygous BRCA2 mutation of the simulation, which of the following statements is TRUE regarding the Sanger sequencing method detection of the mutation?

In the sequencing reaction, the fragment identifying the mutation and the fragment identifying the wild type base at that position would be the same length.

mRNA definition

Messenger RNA is produced from a strand of DNA during transcription and carries the genetic information from the nucleus to the cytoplasm. The sequence of nucleotide bases of an mRNA molecule is complementary to the sequence of nucleotide bases in DNA. Each series of three mRNA bases is a codon which codes for a specific amino acid.

nucleotide

Nucleotides are produced when the carbon 5 (C5\') hydroxyl group of a nucleoside reacts with hydrogen phosphate to form a phosphate ester. To differentiate nucleotides from nucleosides in naming, nucleotides are called the name of the nucleoside of which it is made plus 5\'-monophosphate. Adenosine 5\'-monophosphate is a nucleotide which contains the nucleoside adenosine. Nucleotides are the monomers of nucleic acids.

What would happen if unlabeled dNTPs were not added to the sequencing reaction?

Only the first nucleotide in the sequence would be determined.

What is the purpose of DNA polymerase?

To replicate a template DNA strand and proofread the replicating strand.

tRNA

Transfer RNA carries amino acids to the site of protein synthesis. Transfer RNA has anticodons complementary to the mRNA codons. The anticodon binds tRNA to mRNA during transcription. The 3\' end of the tRNA molecule is bound to the amino acid appropriate for the mRNA codon.

It has a major groove and a minor groove.

DNA

The structure of the ddNTP pentose sugar ring is most similar to the pentose sugar ring of:

DNA

complementary

C-G A-T

It can form a right- or left-handed double helix.

DNA

It can form cruciform structures.

DNA

It contains equal amounts of purines and pyrimidines.

DNA

CTP hydrolysis can be a source of chemical energy.

TRUE

RNA can code for polypeptide chains.

TRUE

B-DNA

The Watson-Crick structure is the B form of DNA. The majority of DNA under physiological conditions is B-DNA.