Genetics Chapter 7

1 nm =

1 billionth of a meter, or 10^-9 meters

after the second round of replication in the meselson-stahl experiment, it went from 14N/15N to

14N/14N (all new- after transfer to 14N medium, new strands are made from 14N only) and 14N/15N

A 1:1 mixture of DNA from cells grown in 14N and cells grown in 15N, heated (to disrupt hydrogen bonds) and then cooled (to allow reannealing), contains

14N/14N, 14N/15N, and 15N/15N double helices.

between A and T, there are ___ hydrogen bonds

2

between C and G, there are ___ hydrogen bonds

3

nucleotides complementary to the template strand are added to the ____ end of the new strand by DNA polymerase

3'

in a DNA molecule, an OH group is attached to the _____ carbon

3' carbon

DNA's proofreading ability resides in the ______________ activity of DNA polymerases capable of removing some of the newly laid daughter strand sequence

3'-to-5' exonuclease

The structure of DNA polymerase III is such that it can only add new nucleotides to the _____ end of a primer or growing DNA strand.

3'. This is because the phosphate group at the 5' end of the new strand and the 3' -OH group on the nucleoside triphosphate will not both fit in the active site of the polymerase.

in a DNA molecule, 1-3 phosphates are attached at the ___ carbon

5' carbon

The DNA pol I enzyme possesses two activities that accomplish the removal of RNA nucleotides and their replacement by DNA nucleotides. DNA pol I first uses ________________ to remove the 5'-most nucleotide from the RNA primer. then, the newly open space is filled with the correct DNA nucleotide by ________________

5'-to-3' exonuclease activity, 5'-to-3' polymerase activity

purines

A G

the principal constituent of nuclein was eventually identified as

DNA

the major and minor grooves are regions where

DNA binding proteins can most easily make direct contact with nucleotides along one or both strands of the double helix

What enzyme catalyzes the formation of phosphodiester bonds

DNA ligase

step 3 of replication of the lagging strand

DNA ligase closes the gap between fragments A and B

step 1 of replication of the lagging strand

DNA pol III binds to the 3' end of the most recently produced RNA primer, & adds DNA nucleotides in the 5' to 3' direction until it encounters the previous RNA primer

in e. coli, daughter DNA strands are synthesized at the replication fork by

DNA pol III holoenzyme, the main DNA-synthesizing enzyme

Individual nucleotides are assembled into a polynucleotide chain by the enzyme ____________________

DNA polymerase

DNA ligase has exclusive and very high affinity for

DNA-DNA single-stranded gaps. Its single task is to form a phosphodiester bond between the two DNA nucleotides that joins the two okazaki fragments

In e. coli replication, three enzymes bind at oriC to initiate DNA replication

DnaA, DnaB, DnaC

In the structure of DNA, the 3' carbon should be attached to (2)

a hydrogen and a hydroxyl group

nuclein

a mixture of nucleic acids and proteins

to enhance their movement along template strands, DNA polymerases associate with an auxiliary protein complex known as

a sliding clamp

polymerase chain reaction (PCR) is

an automated version of DNA replication that takes place in a test tube, producing millions of copies of a short targeted segment of DNA from the original DNA molecule

rough pneumococcus strains have a mutant allele of the polysaccharide gene, which causes

an easily broken bacterial capsule, vulnerable to attack by mouse immune system antibodies

origins of DNA replication contain sequences that

attract replication enzymes

in the lagging strand, the daughter strand elongates

away from the replication fork

A 1:1 mixture of DNA from cells grown in 14N and cells grown in 15N contains

both 14N/14N and 15N/15N double helices.

To relieve strain ahead of the replication fork, topoisomerase

breaks a covalent bond in the sugar-phosphate backbone of one of the two parental strands, allowing the DNA to swivel around the corresponding bond in the other strand

topoisomerase function (2)

breaks covalent bonds in the DNA backbone, and binds ahead of the replication fork

DNA helicase function (2)

breaks h-bonds between bases, and binds at the replication fork

how was phage DNA labelled in the Hershey-Chase experiment

by growing it in a medium with radioactive phosphorous

how was phage protein labelled in the Hershey-Chase experiment

by growing it in a medium with radioactive sulfur

incorporation of a dideoxynucleotide triphosphate (ddNTP) by DNA pol into a growing strand is a ______________ event that blocks

chain-terminating event that blocks further strand elongation (absence of an OH at the 3' carbon prevents the ddNTP from forming phosphodiester bonds)

Genome sequence data do not identify any sequence consistent with a replication of origin sequence in multicellular eukaryotes. Thus, it seems likely that DNA is selected for replication in multicellular eukaryotes based on

chromatin modification rather than by the presence of specific DNA sequence

telomere length is a kind of ______________ that keeps track of _________

chronometer, the age of the cell. once the shortening reaches a critical point, the cell is directed into the apoptotic pathway

What term is used to describe the pattern of base pairing between one DNA strand and its partner in a duplex?

complementary

replisomes

complex aggregations of proteins and enzymes that assemble at each replication fork

a nitrogenous (nucleotide) base is attached to the 1' carbon of the deoxyribose molecule by a ___________ bond

covalent

deoxynucleotide monophosphates

dNMPs, where N can refer to any of the 4 nucleotide bases

deoxynucleotide triphosphates

dNTPs, free (reactive) DNA nucleotides that aren't part of a polynucleotide chain and carry a string of 3 phosphate groups at the 5' carbon

____________ & _____________ possess strikingly similar DNA replication machinery that is evolutionarily distinct from the replication machinery in ______________

eukaryotes & archaea, bacteria

when building a new strand, DNA nucleotide triphosphates (dNTPs) are recruited by DNA polymerase, which uses catalytic action to remove two phosphates in order to

form the new phosphodiester bond

DNA polymerase III determines which _______________ is complementary to the base being copied.

free nucleotide triphosphate

DNA replication is bidirectional

it progresses in both directions from the origin of replication

pyrimidines

T C

If a mutation inactivated DNA polymerase I in a strain of E. coli, would the cell be able to replicate its DNA? If so, what kind of abnormalities would you expect to find in the cell?

The cell would be able to replicate its DNA. The mutation will result in newly replicated DNA containing small segments of RNA.

If a strain of E. coli acquired a mutation that inactivated DNA polymerase III function, would the cell be able to replicate its DNA? Why or why not?

The cell would not be able to replicate its DNA because it lacks the enzyme responsible for the bulk of DNA synthesis.

DNA polymerase requires the presence of a primer sequence to provide

a 3'-OH end to which a new DNA nucleotide can be added

consensus sequence

a conserved nucleotide sequence that acts as the binding site for proteins that initiate replication

in circular chromosomes in e. coli, topoisomerase enzymes catalyze

a controlled cleavage and rejoining of DNA to allow supercoiled DNA to relax

DNA undergoes mutation at a low rate that introduces genetic variation and serves as

a foundation for evolutionary change

Mixture of heat-killed s-strain (dead pneumonia-causing) and living r-strain caused

most mice to die. Tests revealed living s-strain bacteria in the dead mice.

holoenzyme is the general term used for

multiprotein complexes in which a core enzyme is associated with additional protein components that complete its structure and lead to its function

Dideoxy sequencing produces a large number of

partial replication products, each terminated by the incorporation of a ddNTP at a different site in the sequence

Which chemical groups of nucleotides react to form the phosphodiester bond?

phosphate & OH groups

What is the name of the bond that joins one nucleotide to another in the DNA strand?

phosphodiester (covalent)

DNA polymerase III catalyzes _____________________ between the 5' phosphate of the incoming nucleotide triphosphate and the 3' hydroxyl group of the last nucleotide added to the strand.

phosphodiester bond formation

single-strand binding protein function (2)

prevents H-bonds between bases, and binds after the replication fork

RNA primers are synthesized by

primase

the ______________ protein functions as the sliding clamp in archaeal and eukaryotic replication, encircling the DNA template strand

proliferating cell nuclear antigen (PCNA) protein

essential difference between DNA & protein that made the Hershey-Chase experiment possible

proteins contain large amounts of sulfur but almost no phosphorous, and DNA contains a large amount of phosphorous but no sulfur

double-ringed nitrogenous base

purine

single-ringed nitrogenous base

pyrimidine

single-stranded binding protein prevents

reannealing (rebinding of the parental strands)

telomeres

repetitive DNA sequences that contain no genetic information, so portions (on the lagging strand, after primer removal) can be safely lost in each replication cycle, without consequence to the organism

oriC

sequence-specific origin of replication in bacteria

As soon as the base pairs separate at the replication fork,

single-strand binding proteins attach to the separated strands and prevent the parental strands from rejoining

In cancer cells, reactivation of telomerase activity appears to

stabilize telomere length, disrupting the normal program of progressive telomere shortening that would lead to apoptosis. The extended life span may allow affected cells to acquire additional mutations associated with cancer

antigen

substance that when introduced into the body stimulates the production of an antibody

telomerase is a ribonucleoprotein that synthesizes

telomeric repeat sequences to maintain telomere length in germ-line and stem cells

DNA polymerase catalyzes the formation of a phosphodiester bond between

the 3' OH group of one nucleotide and the 5' phosphate group of an adjacent molecule

a phosphate attached to the 5' carbon of the bottom sugar should be covalently linked to

the 3' OH group of the top sugar.

You can tell which end is the 3' end by the presence of __________, and the 5' end by the presence of ____________

the OH group, the phosphate group

DNA polymerase III is responsible for

the bulk of synthesis on both the leading and lagging strands

If complementary strands were to align in parallel,

the charges of complementary nucleotides would repel, and no hydrogen bonds would form

high-speed cesium chloride (CsCl) density gradient ultracentrifugation

the high speeds exert thousands of gravities of separating force, creating a graded variation in density (a density gradient) throughout the CsCl mixture. The substances migrate until they reach the point in the density gradient where their molecular density is matched by that of the gradient

Antigenic variation

the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters its surface proteins in order to evade a host immune response. It is related to phase variation.

when a replication error occurs,

the mismatched DNA bases of daughter and template are unable to hydrogen bond properly. So, rotation of the daughter strand is induced into the 3'-to-5' exonuclease site. Then several nucleotides are removed before it goes back

base stacking

the offsetting of adjacent base pairs so that their planes are parallel, giving the twist to the double helix

The leading strand is made continuously from a single RNA primer located at

the origin of replication

At each replication fork, helicase moves along _________________, separating the two strands by breaking the hydrogen bonds between the base pairs.

the parental DNA

each antigenic type of pneumococcus (S/R I, II, III, IV) elicits a different immune response from the mouse immune system as a result of

the presence of several genetic differences

results of Hershey-Chase

the radioactive phosphorous (DNA) was in the bacterial pellet after centrifuge. radioactive sulfur (protein) in the phage ghosts remained suspended in the liquid

among different types of cells, the length of the S phase is variable, meaning that

the rate of progression of DNA replication varies among cells of different types

DNA regions containing A-T richness require less energy for their denaturation, because

there are only 2 hydrogen bonds between A & T

why did some scientists argue that protein must be the hereditary material and not DNA

they argued that the "20-letter alphabet" of protein could contain more info that the 4-letter alphabet of DNA

the first primers on the lagging strands are

those closest to the origin of replication

DNA polymerase I functions to (2)

to remove the RNA primer and to fill in the gaps with DNA,

in the leading strand, the daughter strand elongates

toward the replication fork

completion of DNA replication results in the formation of

two identical daughter duplexes, each composed of one parental strand and one daughter strand (semiconservative model)

bacterio(phages) are

viruses that infect bacteria. They're made of a protein shell with a tail segment that attaches to a host bacterial cell and a head segment that contains DNA

There should not be _____ bonds in the structure of DNA.

P−C (phosphate-carbon)

the lagging strand is made in segments, each with its own

RNA primer

what is the consequence of abnormal reactivation of telomerase activity in somatic cells?

aging cells will continue to proliferate, allowing them to escape programmed cell death. This is what happens in many kinds of cancer, where mutations reactivate the expression of TERT.

the 3 steps of PCR

denaturation (so DNA will denature into single strands), primer annealing (attachment of the primers to complementary sequences that bracket the target sequence), and primer extension (DNA synthesis by Taq polymerase)

telomerase activity is virtually nonexistent in

differentiated somatic cells (they have finite life spans anyway)

Notice that after one round of replication, the _____________ & _________________ models predict identical results (14N/15N), whereas the ________________ model predicts different results. (14N/14N and 15N/15N)

dispersive and semiconservative, conservative

dispersive model

each daughter duplex is a mix of parental duplex segments and daughter duplex segments

2 limitations of PCR

needing to know the sequences needed for primers, and that amplification products longer than 10 to 15 kb are difficult to produce (restricting its use to the study of selected DNA segments/ individual genes)

DNA pol I removes and replaces

nucleotides of the RNA primer

step 2 of replication of the lagging strand

once DNA pol III encounters the other RNA primer, it falls off and is replaced by DNA pol I. DNA pol I removes each RNA nucleotide and replaces it with the corresponding DNA nucleotide, from the 5' end of primer A to the 3' end of fragment B. When it encounters the 5' end of fragment A, DNA pol I falls off

In the structure of DNA, there should be _________ bond in the phosphate groups.

one P=O double

conservative model

one daughter duplex contains the two strands of the parental molecule, and the other contains two newly synthesized strands