bio exam 2

-mutation occurs in gene but does not change the protein sequence because it ends up coding for the same amino acid

examples of how a silent mutation occurs

true

when a mutation is propagated to daughter cells it cannot be fixed (T/F)

-DNA ligase

basic mechanism of DNA repair

when there are base mismatches, enzymes catch this and cut out the incorrect nucleotide and replace it with the correct one

how does mismatch repair work

there are DNA nicks in the newly synthesized stand that distinguish it from the parental strand

how does mismatch repair know which strand is the right strand to fix

depurination

guanine or adenine are spontaneously removed from DNA (base loss)

deamination

removal of an amine group from cytosine to produce uracil (base changed) (can occur on other bases as well)

pyrimidine dimers

DNA damage from UV light produce \_______________

pyrimidine dimers

these for when thymine absorbs UV light and reacts to covalently bond to adjacent thymine. Distorts the helix shape

false (homologous recombination is more accurate, there is no loss of nucleotides after repair)

nonhomologous end joining is more accurate than homologous recombination (T/F)

nonhomologous end joining (this mechanism repairs the break but results in a loss of nucleotides after)

to fix double-stranded DNA break, in \_____________________ the cell tries to quickly repair the break before the fragments drift apart. the ends are "cleaned up" by nuclease and the ends are joined by DNA ligase.

homologous recombination (the break is repaired with no loss of nucleotides)

to fix double-stranded DNA break, in \_____________________ the undamaged section of DNA is used a template in which enzymes interlace the damaged and undamaged strands and get them to exchange sequences of nucleotides and fill in the missing gaps

it is an exact duplicate of the other helix

in homologous recombination, the second helix can serve as a template for repair because \______________

true

homologous recombination can only occur if DNA break occurs shortly after DNA has been replicated (i.e. before cell division) (T/F)

3, 5 (make sure to flip it when answering a question because strands are always read 5' to 3'!)

writing a complementary strand via a given template sequence will produce the sequence in a \____' to \____' direction

it's easier to pull the strands apart (A-T only have two hydrogen bonds compared to G-C having three)

why do origins of replication contain an abundance of A-T base pairs

false (eukaryotic chromosomes have multiple origins of replication that act simultaneously, if not it would takes weeks for chromosomes to replicate)

eukaryotic chromosomes only have one origin of replication (T/F)

true (also, replication bubbles get larger and larger and eventually merge at origins of replication)

replication is bidirectional and proceeds from each replication fork (T/F)

true (replication still works by unwinding DNA and proceeding in both directions)

bacteria have a single origin of replication (T/F)

helicase

what enzyme is first at the origin of replication and separates the two strands of DNA

by breaking the hydrogen bonds at each replication fork

how does helicase unwind DNA strands

single strand binding proteins

\____________________ work behind helicase and bind to each strand to prevent the broken hydrogen bonds from re-forming

DNA topoisomerase

\______________ is an enzyme that works in front of helicase. it makes small, reversible cuts in the phosphodiester bonds to release torsional stress

primase

what enzyme makes a short "starter" nucleotide sequence of RNA/RNA primer

uracil, thymine (ribose sugar)

the RNA primer is complementary to the DNA sequence except it uses a \__________ base instead of a \_________ base

primase

what enzyme makes a complementary strand of RNA that DNA polymerase can extend from

true (DNA binds to the primer to start replication)

RNA primer initiates DNA synthesis (T/F)

true

DNA polymerase reads the template strand in the 3' to 5' direction and synthesizes the new strand in the 5' to 3' direction (T/F)

3, 5. 5,3.

DNA is READ __' to __', and GROWS __' to __'

DNA polymerase

\___________________ is the enzyme that catalyzes condensation reactions to add nucleotides through the formation of phosphodiester bonds in DNA replication

3

nucleotides are added to the \____' end of the growing strand

true

DNA polymerase adds nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide (T/F)

hydrolysis, high energy phosphate

the energy for the polymerization reaction comes from the \_____________ of a \___________________ bond in the incoming nucleoside triphosphate

true

only one RNA primer is required on the leading strand (T/F)

in order to synthesize in the 5' to 3' direction, primase adds short sequences of RNA primers and the DNA polymerase extends from this primer until it reaches the previous RNA primer

why are there gaps with no phosphodiester bond linkage between nucleotides of okazaki fragments

nuclease

what enzyme removes RNA primers

DNA repair polymerase

what enzyme fills the gap from RNA primer removal with complementary DNA

DNA ligase

what enzyme seals the gap by forming phosphodiester linkage between the discontinuous strands of DNA

a polymerizing site and an editing site

what are the two active sites of DNA polymerase

true (when the polymerase adds an incorrect nucleotide, the new DNA strand temporarily unpairs from the template strand and the 3' end moves into the editing site of the polymerase to allow the incorrect nucleotide to be removed)

DNA polymerase has proofreading ability (T/F)

nucleus

where does DNA replication occur in eukaryotes

false (there are two identical molecules after replication, semiconservative replication)

at the end of replication there is one identical DNA molecule from the original DNA molecule (T/F)

template

each strand of DNA serves as a \________ for the synthesis of a new complementary strand

replication forks

DNA synthesis occurs at Y-shaped junctions called \_________________

true (the lagging strand is synthesized in pieces while the leading strand is synthesized continuously in one piece)

DNA replication is asymmetrical (T/F)

DNA polymerase

what enzyme catalyzes the addition of nucleotides to the 3' end of a growing strand of DNA using a parental DNA strand as a template

DNA helicase

what enzyme uses the energy of ATP hydrolysis to unwind the DNA double helix ahead of the replication fork

single-strand DNA binding protein

what binds to single-stranded DNA exposed by DNA helicase, preventing base pairs from re-forming before the lagging strand can be replicated

DNA topoisomerase

what enzyme produces transient nicks in the DNA backbone to relieve the tension built up by the unwinding of DNA ahead of the DNA helicase

primase

what enzyme synthesizes RNA primers along the lagging-strand template

DNA ligase

what enzyme uses the energy of ATP hydrolysis to join okazaki fragments made on the lagging-strand template

Without DNA polymerase, no replication can take place at all. RNA primers will be laid down at the origin of replication.

What would happen during the DNA replication process if DNA polymerase were missing?

DNA ligase links the DNA fragments that are produced on the lagging strand. In the absence of ligase, the newly replicated DNA strands will remain as fragments, but no nucleotides will be missing.

What would happen during the DNA replication process if DNA ligase were missing?

Without DNA helicase, the DNA polymerase will stall because it cannot separate the strands of the template DNA ahead of it. Little or no new DNA will be synthesized.

What would happen during the DNA replication process if DNA helicase were missing?

In the absence of primase, RNA primers cannot begin on either the leading or the lagging strand. DNA replication therefore cannot begin.

What would happen during the DNA replication process if primase were missing?

False. Identical DNA polymerase molecules catalyze DNA synthesis on the leading and lagging strands of a bacterial replication fork. The replication fork is asymmetrical because the lagging strand is synthesized in pieces that are then stitched together.

Is this statement correct? A replication fork is asymmetrical because it contains two DNA polymerase molecules that are structurally distinct.

False. Only the RNA primers are removed by an RNA nuclease; Okazaki fragments are pieces of newly synthesized DNA on the lagging strand that are eventually joined together by DNA ligase.

Is this statement correct? Okazaki fragments are removed by a nuclease that degrades RNA.

new nucleotide that fixes incorrect nucleotide doesn't have high-energy bond from triphosphate to drive reaction

why can DNA not be proofread if synthesized 3' to 5'

true

DNA polymerase can only elongate from free 3' hydroxyl group (T/F)

creates buffer zones called telomeres at the ends of chromosomes, when the ends are eaten up over time (due to the end gap from removed RNA primer on lagging strand) the internal chromosomes regions containing genes can be protected for some time

how does telomerase help the end replication problem

false (telomerase is active primarily only during development and in stem cells)

telomerase is active during one's entire life (T/F)

true

telomerase uses RNA bases (T/F)

telomere

a region of repetitive DNA sequences at the end of a chromosome

telomerase

an enzyme in cells that helps keep them alive by adding DNA to telomeres

telomerase

RNA-dependent DNA polymerase that synthesizes telomeric DNA sequences

DNA polymerase

enzymes that create DNA molecules by assembling nucleotides

storage, transmission, and use of genetic information

main functions of nucleic acids

nucleotides

what are the subunits of nucleic acids

nitrogenous base, 5 carbon sugar, phosphate group

components of a nucleotide

5, 3

DNA and RNA are written from \___' to \___'

3, 5

nucleotides are added to the \____' end of the chain, not the \___' end

OH group (carbon 3 spot)

to add a nucleotide, the phosphate group of the new nucleotide attaches to the \______ of the last nucleotide in the chain

true

nucleic acids have polarity (T/F)

-nitrogenous bases are hydrophobic and cluster inside the helix (repulsive forces)

how is the DNA double helix held together and stabilized

adenine and guanine

purines in DNA

cytosine, thymine

pyrimidines in DNA

-adenine and thymine

pair the bases in DNA

false (purines pair with pyrimidines)

in base pairing, purines pair with purines and pyrimidines pair with pyrimidines (T/F)

2

adenine and thymine form \_____ hydrogen bonds

3

cytosine and thymine form \_____ hydrogen bonds

true (bases are on the inside)

sugar-phosphate backbone is on the outside of the double helix structure (T/F)

true

DNA is double-stranded and twists into a double helix (anti-parallel) held together by hydrogen bonds (T/F)

false (the structure is energetically favorable because the bases are hydrophobic and the sugar-phosphate backbone is hydrophilic)

DNA structure is energetically unfavorable (T/F)

it would alter the width of the DNA

why would pairing a purine with a purine or pyrimidine with a pyrimidine be energetically unfavorable

purine

has two rings

pyrimidine

has one ring

10

there are \____ base pairs per complete turn of the DNA double helix

nucleotides

information is encoded in the order of \___________

chromosome

a threadlike structure of nucleic acids and proteins found in the nucleus, carrying genetic information in the form of genes

genome

total genetic information carried in an organism's chromosomes

23

how many pairs of chromosomes do you have (somatic cells)

true

one chromosome in a pair is inherited from the mother, the other one from the father (T/F)

false (they carry the same genes but differ in their sequence, this leads to unique traits)

inherited chromosomes carry the same genes and same nucleotide sequence (T/F)

nucleosome

length of DNA coiled around a core of histones

histone

DNA is wrapped around a protein called a \________ (reduced DNA length by 1/3!)

8

nucleosomes contain DNA wrapped around a protein core of \____ histone molecules

chromosome vs. chromatin

coiled DNA vs uncoiled DNA

positively charged amino acids of histones bind tightly to the negatively charged sugar-phosphate backbone of DNA

why do histones bind well to DNA

true

an individual nucleosome contains 8 histone proteins with 2 molecules of each histone H2A, H2B, H3, and H4 along with double-stranded DNA 147 nucleotide pairs long (T/F)

chromatin/chromatin fiber

nucleosomes are packed on top of one another in a condensed structure to make\__________