biochem exam 5 part 1

Define replicate

to make an exact copy

does replication happen slow or fast?

fast faster in prokaryotes than eukaryotes

Eukaryotes package some of their _____ in mitochondria and chloroplasts, while in prokaryotes it flows ________

DNA, freely

DNA is replicated -__________ and semi-discontinuous

semi-conservatively

What does semi-conservative replication mean?

Each new DNA molecule consists of one parent strand and one newly replicated strand

Semi-discontinuous:

The leading strand is synthesized continuously ___' to ___', while the lagging strand is synthesized discontinuously by ___________ fragment formation

5' to 3', okazaki

What did the Meselson-Stahl experiment prove?

That DNA replication is semi-conservative

Replication starts at the ______________

Origin of replication

True/False: Replication is considered bidirectional

True

Define bidirectional replication

Both strands are replicated simultaneously in opposite directions

Replication Fork

A Y-shaped region where the parental strands are being unwound and new strands are being synthesized

RNA primers on the replication fork is the binding site for _____ _________ to initiate replication

DNA polymerase

DNA polymerases have __' to __' exonuclease activity called _________, except for DNA pol ___ and ____.

3' to 5', proofreading, alpha, beta

What is proofreading?

corrects mis-incorporated nucleotides on the new DNA strand

exonuclease vs endonuclease

Exonuclease cuts at ends and endonuclease cuts in middle

DNA Pol I and Pol epsilon also have __' to __' exonuclease activity

5' to 3'

What is Nick translation?

When DNase 1 make a single-stranded nick in the DNA, and DNA Pol I adds and removes dNTPS 5' to 3' . New fragments are sealed in with ligase.

How many hydrogen bonds for A-T?

2 hydrogen bonds

How many hydrogen bonds for G-C?

3 hydrogen bonds

For replication to happen, the bases that come in will need to H bond pair to make sure they are the correct match for the compliment strand. A ____________ bond is formed by the 3' OH attack of the ______ of the dNTP. _______ positions the electrons for the attack to occur.

phosphodiester, phosphate, magnesium

DNA replication is thermodynamically favorable due to what 4 reasons?

dNTPs PPi is released Base stacking H bond formation

Eukaryotic DNA Polymerases

alpha, beta, gamma, delta epsilon

DNA Pol alpha

primes both strands

DNA Pol beta

DNA repair

DNA Pol gamma

mitochondrial DNA synthesis

DNA Pol delta (very processive)

replicates and elongates lagging strand

DNA Pol epsilon (very processive)

replicates and elongates leading strand

Define processivity

the number of nucleotides added before polymerase dissociates

DNA Pol I, II, III are all

prokaryotic DNA polymerases

DNA Pol I

replaces RNA primer with DNA

DNA Pol II

DNA repair

DNA Pol III

primary replication enzyme

Eukaryotic replication occurs in the

nucleus

prokaryotic replication occurs in the

cytoplasm

how many origins of replication do eukaryotes have

more than 1

how many origins of replication do prokaryotes have

1

DNA replication steps

initiation, elongation, termination

DNA replication

1. Initiation at the Ori

2. DNA A binds to help unwind DNA

3. ssDNA-binding proteins keep the separated strands extended

4. Helicase cuts the strands at the replication fork

5. Primase makes RNA primers 5' to 3'

Topoisomerases relieve supercoiling (Gyrase in prokaryotes)

Topoisomerase I

cuts 1 strand of DNA to relieve supercoiling

Topoisomerase II

cuts both strands of DNA to relieve supercoiling

Okazaki fragments are form on which strand?

Lagging strand

Synthesis of okazaki fragments

As DNA Pol III makes a new section, waiting for helicase to unwind DNA.... primase adds new RNA primers allowing DNA Pol I to bind and replace primers with DNA.

This creates okazaki fragments. Ligase seals everything with a phosphodiester bond

DNA Pol III has 2 reactive centers called cores, each with a ____ ___ on it

beta clamp

B-Clamp

A protein complex that encircles the DNA and keeps DNA pol III attached during DNA replication.

Define mutation

a permanent change in nucleotide sequence

Define point mutation

permanent change of a single nucleotide

How are mutations both good and bad?

Mutations are good because they provide a mechanism for evolution, but are also bad because mutations cause diseases

Protecting ______ cell DNA protects the individual

somatic

Protecting ______ cell DNA protects the species

germline

Depurination

spontaneous hydrolysis of B-N-glycosidic bonds due to heat fluctuations resulting in the loss of a purine base from a nucleotide

Deamination

the removal of an amino group from an amino acid

Ex. Adenine to hypoxanthine

Pyrimidine dimers are caused by

uv exposure

2 categories of point mutations

transition: a purine to a purine or pyrim to pyrim transversion: purine to pyrim and vice versa

Consequences of point mutations include what 2 mutations?

missense, nonsense

missense mutation

a change in a single amino acid

nonsense mutation

a change in a codon that encodes an amino acid to encode a stop codon instead

frameshift mutation

insertion or deletion of 1 or 2 nucleotides

DNA photolyase system

repair of pyrimidine dimers by absorbing blue light photons, in prokaryotes FADH cofactor

O6Methylguanine methyltransferase is considered what kind of enzyme

suicide enzyme

Base Excision Repair

corrects an error in a single base by cleaving glycosidic bonds, in prokaryotes

4 steps of base excision repair

1. DNA glycosylase cleaves glycosidic bond

2. AP endonuclease cleaves phosphodiester bond

3. DNA Pol I does nick translation

4. DNA Ligase stitches it all back together

Nucleotide Excision Repair

An exonuclease cleaves phosphodiester bond to replace damaged segments of DNA, in prokaryotes

Mismatch Repair

corrects mismatches in bases caused by polymerase stutter, in prokaryotes

How can you differentiate between a newly synthesized strand and the old strand?

For a short period after replication, the new strand is not methylated while the template strand is

MutL-MutS complex

prokaryotic mismatch repair protein that recognizes mismatch

Translesion DNA synthesis

A lot of proteins and polymerases have to help repair because there is so much damage

Recombinational DNA repair

using recombination to repair double stranded breaks

Mutations in MSH2 and MLH1 cause what cancer?

colorectal cancer

mutations in BRCA cause what cancer?

breast and ovarian cancer

Xeroderma pigmentosum is a condition that prevents the repair of thymidine dimers, needing people to stay in complete darkness. A mutation in what repair mechanism causes this?

nucleotide excision repair

DNA recombination

Happens during meiosis

• Chromatids of 2 homologous chromosomes cross over

• The homologous chromosomes exchange genetic material

Conjugation (mating) in prokaryotes

a portion of the chromosome from a donor cell is transferred to a recipient cell

transducing phage in prokaryotes

when a bacterial DNA is packaged into a phage particle and introduced into a new host cell

transformation

environmental dna is taken up by bacterium