Genetics Unit 3

Why do eukaryotes need multiple origins of replication?

Due to their large size, they need multiple origins so the DNA can be replicated in a reasonable length of time

True or False: all genes encode polypeptides that function as units within proteins

False

A double-stranded region of RNA

Forms a helical structure obeys the AU/GC rule may promote the formation of different structures, such as bulge loops and stem-loops

The correct order of base-pair strength in DNA/RNA (from strongest to weakest) is:

GC > AT > AU

Why is NusA important for rho-independent?

Helps RNA polymerase to pause, which causes transcriptional termination.

What holds DNA strands together?

Hydrogen bonding between base pairs and base stacking

What feature of the -10 sequence makes it easy to unwind?

It is AT rich, which has fewer hydrogen bonds.

Features of DNA double helix?

It obeys the AT/GC rule The DNA strands are antiparallel The structure is stabilized by base stacking

If a mutation changed the start codon to a stop codon, would this mutation affect the length of the RNA?

No because it would not terminate transcription; however, the encoded polypeptide would be shorter

When going from simple to complex, the proper order for DNA is?

Nucleotide DNA strand Double helix Chromosome

The origin of replication in E. Coli contains

an AT-rich region, DnaA box sequences, GATC methylation sites.

Why is primase needed for DNA replication?

primase is needed for DNA replication because DNA polymerase cannot initiate DNA replication on a bare template strand.

What is the functional box of the TATA box?

provides a precise starting point for the transcription of eukaryotic protein-encoding genes.

A nucleic acid molecule that has 20% A, 30% C, 20% G and 30% T is most likely

single-stranded DNA

What DNA sequence is required for ending DNA replication in E. Coli?

ter

Is DNA strand breakage needed for catenane separation?

Yes, so the strands can move relative to each and untangle the catenane.

Which DNA molecule form is left-handed?

Z DNA

The enzyme known as ____ uses _____ and separates the DNA strands at the replication fork.

helicase, ATP

The 5' end of a nucleic acid molecule refers to the ---- group on the 5' carbon of the first nucleotide.

phosphate

Which components of a nucleotide for the backbone of a DNA strand?

Deoxyribose and phosphate

Which of the following initiates the formation of the replication bubble?

DnaA

Arrange proteins in the order in which they participate in DNA replication

DnaA, Primase, DNA polymerase III, and Tus

A large nucleic acid molecule that has 20% A, 30% C, 30% G and 20% U is most likely

Double-stranded RNA

What features of DNA structure enable it to be replicated?

Double-stranded structure, and the base pairing between A and T and G and C.

Ribonucleosides lack a

5' phosphate group

Which of the following DNA molecules is the most thermodynamically stable?

5'GCATCGAGGCCGGCTG 3' 3'CGTAGCTCCGGCCGAC 5'

The bond that covalently links 2 DNA nucleotides is

phosphodiester bond

The double-stranded DNA molecule of the newly discovered Elradicus libanii was found by electron microscopy to have a length of 17 micrometers. How many complete turns of the helix are present in this molecule?

5,000

The double-stranded DNA molecule of a newly discovered Elradicus libanii was found by electron microscopy to have a length of 17 micrometers. How many base pairs are present in this molecule?

50,000

A double-stranded DNA molecule is 5,000 base-pairs long. How many complete turns are present in this molecule?

500

How many times would telomerase have to bind to a different site in the telomere to make a segment of DNA that is 36 nucleotides in length?

6 times (36/6)

In nucleic acids, the nitrogenous base is attached to the ----- carbon of the sugar

1'

A double-stranded DNA molecule is 5,000 base-pairs long. How long is this molecule?

1.7 uM

If R = any purine, Y = any pyrimidine, and N = any nucleotide, what is the probability of finding the sequence 5′ GRANTY 3′ in any molecule of DNA? Assume nucleotides are in equal percentages.

1/256

How many hydrogen bonds would connect the DNA sequence CATG and its complement on the other strand in a double helix?

10

If 35% of the bases in a region of the mouse genome are cytosine, what percentage in that region are adenine?

15%

Chromosome #1 of the newly-discovered organism Kalle rummeniggeous contains 500,000 bp of DNA. How long is this double-helix?

170 micrometers

How many replication forks are formed at the origin?

2 replication forks

In nucleic acids, the difference between deoxyribose and ribose lies at carbon

2'

Deoxyribonucleotides lack a?

2' hydroxyl group

In the B-form of DNA, how wide is the major groove?

22 A

DNA replication always proceeds by adding new bases to the _____ end of an existing strand.

3'

Which of the following nucleotide sequences represents the complement to the DNA strand 5' AGATCCG 3'?

3' TCTAGGC 5'

Is the template strand read in the 5' to 3' or the 3' to 5'?

3' to 5'

In the B-form of DNA, how far apart are two nucleotides?

3.4 A

The percentage of cytosine in a bacterial genome was determined to be 20%. What is the percent of adenine?

30%

A radioactive isotope that can be used to label proteins and NOT nucleic acids is

35S

The basal transcription apparatus is composed of

5 general transcription factors RNA polymerase II A DNA sequence containing a TATA box and transcriptional start site

Nucleotides have a phosphate group attached at the _____ carbon atom of the sugar

5'

Chargaff's analysis of the base composition of DNA is consistent with base pairing between

A and T, G and C

What are the base pairing rules for RNA?

A with U and G with C.

What is the advantage of having the replication machinery in a complex?

Allows the coordination of different enzymes. For example, helicase and primase can work together to make multiple primers for the lagging strand.

What is the difference between an endonuclease and an exonuclease?

An endonuclease can cleave within a strand, whereas an exonuclease digests a strand, one nucleotide at a time, starting at one end.

In the lagging strand, DNA is made in the direction _______ the replication fork and is as made _______

Away from, Okazaki fragments

The form of DNA found in living cells is

B DNA

Differences between B DNA and Z DNA?

B DNA is right-handed, and the backbone is helical, whereas Z DNA is a left-handed helix and the backbone appears to zigzag slightly. Z DNA has the bases tilted, whereas B DNA is perpendicular. B DNA = 10 base pairs; Z DNA = 12 base pairs

For a double-stranded DNA which of the following base ratios ALWAYS equals 1?

C/G

Does oxygen in the newly made ester bond come from the phosphate or from the sugar?

Comes from the sugar

What types of bonds hold nucleotides together in a RNA strand?

Covalent bonds

Which of the following bases has a single heterocyclic ring structure?

Cytosine and thymine

Key difference between DNA and RNA?

DNA has deoxyribose and thymine RNA has ribose and uracil

DNA polymerase in eukaryotes does not

DNA polymerase a synthesizes a short RNA-DNA primer, e and loop do not synthesize most of the leading and lagging strands lesion-replicating DNA pol do not replicate over damaged DNA

Suppose a new species of bacterium is discovered. It contains a form of DNA pol III that can add new nucleotides to either the 5' end or the 3' end of an existing strand. All other properties of the enzyme remain unchanged. How would DNA replication in these bacteria differ from normal replication?

Okazaki fragments would no longer be required for replication

Which of the following is a rapid-aging disorder?

Progeria

Which of the following base sequences is used during transcription?

Promoter and terminator

Difference between RNA and DNA?

RNA is generally shorter than DNA RNA is usually single-stranded whereas DNA is double-stranded RNA contains ribose whereas DNA contains deoxyribose RNA contains uracil whereas DNA contains thymine

Which RNA polymerase in eukaryotes is responsible for the transcription of genes that encodes proteins?

RNA polymerase II

To synthesize DNA, what does telomerase use as a template?

RNA that is a component of telomerase

Why is it necessary for portions of sigma-factor proteins to fit into the major groove?

So it can recognize a base sequence of a promoter

Which of the three mechanisms for splicing is most common in eukaryotes?

Splicing via spliceosomes

What are the functions of the AT-region and DnaA boxes?

The DnaA boxes are recognized by the DnaA protein, which binds to them and causes the DNA to unwind at the AT-rich region

Describe the differences between the synthesis of the leading and lagging strands

The leading strand is made as one, long continuous strand in the same direction that the replication fork is moving. The lagging strand is made as Okazaki fragments in the direction away from the replication fork.

What would be the consequences if a mutation removed the rut site from this RNA molecule?

The mutation would prevent rho-dependent termination of transcription.

Why is there a need to produce Okazaki fragments on the lagging strand, but not on the leading strand of DNA?

The two parental strands of DNA are antiparallel and DNA polymerase makes DNA in the 5' to 3' direction only.

With regard to transcriptional termination in eukaryotes, which model suggests that RNA polymerase is physically removed from the DNA?

Torpedo model

Which base is only found in RNA?

Uracil

What is not found in DNA?

Uracil and Ribose

What does the term consensus sequence mean?

When comparing a group of related sequences, the consensus sequence is the most common base found at each location within that sequence.

In a DNA strand, a phosphate connects to a 3' carbon atom in one deoxyribose to

a 5' carbon in an adjacent deoxyribose

To make a new DNA strand, which of the following is necessary?

a template strand and nucleotides

The proofreading function of DNA polymerase involves the recognition of a ______ and the removal of a short segment of DNA in the _____ direction

base mismatch, 3' to 5'

An enhancer is a _____ that ______ the rate of the transcription

cis-acting, increases

When DNA is ________________ hydrogen bonds are broken.

denatured

In eukaryotes, RNA primers are primarily removed by

flap endonuclease

Which of the following bases has a double heterocyclic ring structure?

guanine

A groove in the DNA refers to

indentations where the atoms of the bases are in contact with the surrounding water

Sigma factor is needed during which stages of transcription?

initiation

The 3 stages of transcription are

initiation, elongation, and termination

DNA polymerase III is a processive enzyme, which means that

it does not dissociate from the growing strand after it has attached a nucleotide to the 3' end

Which of the following statements about Z-DNA is FALSE?

its strands are not antiparallel

With regard to a promoter, a transcriptional start site is

located at the +1 position, and is where the first base is used as a template for transcription.

A site in a chromosome where DNA replication begins is

origin of replication

A uracil-rich sequence occurs at the end of the RNA in

p-independent

The complementarity of DNA strands is based on

the AT/GC rule

Evidence or approaches that lead to the discovery of the DNA double helix include

the determination of structures using ball-and-stick models the X-ray diffraction data of Franklin the base composition data of Chargaff

In eukaryotes, DNA replication is initiated at an origin of replication by

the origin recognition complex

Why is carboxyl terminal domain (CTD) phosphorylation functionally important?

the phosphorylation of CTD allows RNA polymerase to proceed to the elongation phase of transcription

The model that correctly describes the process of DNA replication is

the semi conservative model

The DNA double helix resembles the structure of a spiral staircase. Which DNA component is analogous to the spiral staircase's side rails?

the sugar-phosphate backbone

A Meselson-Stahl experiment is performed on DNA isolated from an alien. How many bands would be expected to form after THREE generations assuming a CONSERVATIVE mode of DNA replication?

two bands; one heavy and one light