Chapter 7 Flashcards by evan kang

what is the central dogma of molecular biology

replication (DNA) -> transcription (RNA) -> translation (protein)

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DNA nucleotides contain (3)

1) sugar (deoxyribose)
2) one of the 4 nitrogenous bases
3) 1-3 phosphate groups

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a deoxyribose has _____ carbons? and what is connected to each carbon

5
OH at the 3’
only H at the 2’
nucleotide base at the 1’
1-3 phosphates at the 5’

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what are the 2 classes of DNA nucleotides and how do you differentiate the 4 bases?

1) purines (double ring, AG) and pyrimidines (single ring, TC)
2) G is more decorated than A and T has more O’s than C

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Deoxynucleotide triphosphates act as substrates for _______. How many phosphates are used?

DNA synthesis
2 phosphates

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deoxynucleotide monophosphates are apart of _______

polynucleotide chains

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individual nucleotides are assembled into chains by the enzyme _______

DNA Polymerase

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DNA polymerase catalyzed the formation of a _______ between the 3’ _______ and the 5’ ______ of 2 nucleotides

1) phosphodiester bond
2) OH
3) phosphate group

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each polynucleotide chain has an alternating _______ backbone

sugar-phosphate

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The bases of one strand are complementary to the bases in the corresponding strand. which bases pair with which bases?

A with T and G with C

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the two strands are _______ with respect to their 5’ and 3’ ends

antiparallel

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what happens if the 2 strands of DNA are parallel

the charges on the complementary nucleotides would repel each other

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complementary base pairing pairs one _______ with one _______ (classes of nucleotides)

purine with one pyrimidine

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1) G - C forms how many_____ bonds?
2) A - T forms how many _____ bonds?
Which uses less energy (heat) to make or break bonds

1) 3 H-bonds
2) 2 H bonds
AT uses less

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What causes grooves in the DNA to form?

base pair stacking

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The _______ approximately 12 A wide, alternates with the _______ approximately 6 A wide

major groove
minor groove

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The major and minor grooves are regions where _______ proteins can make direct contact with nucleotides

DNA binding

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explain B form DNA

most common
10.5 bases per turn
bases are perpendicular to long axis

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explain A form DNA

11 bases per turn
bases are not perpendicular to long axis
found in dehydrating conditions (crystallization)

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explain Z form DNA

left-handed helix, zig-zag apperance
12 bases per turn
found at the beginning of gene transcription

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DNA replication is usually _______ proceeding in both directions
bacterial circular chromosomes have _______ origin of replication while Eukaryotic linear chromosomes have _______ origins of replication

bidirectional
single
multiple

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large eukaryotic genomes contain _______ origins of replication seperated by _______ base pairs

thousands
40k-50k

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The human genome contains more than _______ origins

10k

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the enzymes and proteins involved in DNA replication are parts of a large complex aggregations of proteins and enzymes called the _______

replisome

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the origin of replication sequence of E.coli is called _______

ori-c

Ori-c contains about _______bp of AT rich DNA and is devided into _______bp sequences followed by _______ bp sequences

245 (3) 13 (4) 9

explain initiation of replication (3)

1) DnaA binds to the 9 mer sequence and bends the DNA 2) Dna B carried by DnaC 3) Dna B is a helicase and uses atp energy

The unwound DNA strands are kept from reannealing by _______

Single stranded binding protein (SSB)

enzymes called _______ catalyze controlled cleavage and rejoining of DNA that prevents over winding and relieves torsional stress

topoisomerase

What kind of bond does topoisomerase break?

covalent bond

Saccharomyces Cerevisiae (_______) has the most fully characterize origin of replication sequences which are called _______

yeast autonomous replicating sequences (ARS)

RNA primers are needed in replication and are synthesized by a RNA polymerase called _______

primase

In E.coli, daughter DNA strands are synthesized by the _______

DNA Polymerase III holoenzyme

what is bigger, the replisome or the holoenzyme

replisome

One copy of pol III synthesizes a daughter strand continuously in the same direction as the replication fork; this strand is called the _______?

leading strand

This daughter strand is synthesized discontinuously in the opposing direction of the fork and is called the _______? it is composed of segments called _______?

lagging strand Okazaki fragments

DNA polymerase has 2 activities to complete replication, what are they?

1) 5'->3' exonuclease activity 2) 5'->3' polymerase activity

_______ seals the gap between the resulting DNA segments by catalyzing the formation of new phosphodiester bonds between neighboring nucleotides

DNA Ligase

The DNA pol III holoenzyme is made up of what

1) 2 polymerase III core enzymes 2) tau proteins 3) clamp loader 4) sliding clamp (made from 2 proteins)

What does DNA polymerase have that allows it to proofread? what are the 2 active sites

3'->5' exonuclease activity polymerase active site exonuclease active site

The problem with DNA replication because the lagging strand can't be completely replicated is resolved by what repetitive sequence at the end of chromosomes?

telomeres

telomere sequences are synthesized by the ribonucleoprotein _______

telomerase

How does telomerase extend DNA? (4)

1) telomerase binds to DNA using its own RNA template 2) it extends the parental strand a couple of times 3) alpha polymerase binds and synthesizes RNA primers 4) DNA polymerase fills in the missing strand

Most eukaryotic telomeres contain a DNA sequence that forms a knotted fold called the _______

T-loop

the T loop binds the _______ protein complex which protects the telomeres from degradation, but telomere shortening will eventually trigger _______

shelterin apoptosis

the _______ represents the number of cell cycles of a vertebrate cell before the cell succumbs to apoptosis

Hayflick limit

Telomerase _______ is associated with normal aging of cells

inactivity

_______ causes early onset of some features of aging and is the result of a mutation in the RECQL2 gene encoding a _______ for telomerase activity

Werner syndrome helicase

_______ is a disorder associated with the loss of a function of a gene DKC1

dyskeratosis congenita

telomerase is usually turned ____ in somatic cells but _______ reactivation is a common mutation in cancers

off TERT

What is TERT resposible for in telomerase

encoding the reverse transcriptase function

The _______ is an automated version of DNA replication

PCR

PCR requires: - double-stranded _______ - supply of the 4 _______ - heat stable _______ - 2 different single stranded DNA _______ - a _______ solution

1) DNA template 2) nucleotides 3) taq polymerase 4) primers 5) buffer

what are the 3 steps to PCR and at what temperature do they occur at?

1) denaturation (95°C) 2) primer annealing ( 45°C-68°C) 3) primer extension (72°C)

What is special about the dye used in realtime PCR or qPCR

SYBR green is only florescent when bound to DNA

What are the benefits of ddPCR (3)

1) highly quantitative 2) very sensitive 3) very precise

Describe sanger sequencing

dideoxynucleotide DNA sequencing that uses small amounts of ddntp's that lack a 3' OH that will kill the sequence. A bunch of fragments are found and then incorperated together to sequence DNA

Describe Griffith's experiment and how Avery, McCarty, and MacLeod expanded on it

Griffith found a transforming factor between S and r strain bacteria and MMA found that the genetic material for the bacteria was DNA

Describe Hershey and Chase's experiment

Waring blender (radioactive P32 for DNA and S35 for protein)

describe Meselson and Stahl's experiment

conservative, semiconservative, and dispersive using DNA grown in N14 and N15