Genetics Exam 1

What are the nucleotides in DNA

A G C T

What replaces T is RNA

U

Pyrimidines and how many rings

T C U, 1 ring

Purines and how many rings

G A, 2 rings

RNA sugar backbone

ribose and OH and OH

DNA sugar backbobe

deoxyribose and OH and H

what type of bond holds the phosphate group onto the sugar connecting to the nucleotide?

phosphodiester bond

leading vs lagging strand

5’ to 3’ ; 3’ to 5’

B-DNA

predominant form, right-handed

Z-DNA

less common form, left-handed

supercoiling

twisting the DNA molecule more(positive) or unwinding it(negative)

Chromatin

what we call DNA after supercoiling and protein is included

Euchromatin

less condensed, located on chromosome arms

Heterochromatin

more condensed, located at centromeres (center) and telomeres (end of arm)

DNA is wrapped around 8 proteins called

histones

linker DNA

“beads on a string”, connecting 1 nucleosome to the next

Histones

DNA is negative and Histones are positive so they are attracted to each other

what is negative supercoiling used for

DNA replication, allows to separate the two strands of DNA to relax it which is needed for replication and transcription

DNA gyrase (DNA topoisomerase II)

introduces negative supercoiling in bacteria using energy from ATP, relaxes positive supercoiling

DNA topoisomerase I

relaxes negative supercoiling, helps reduce tension

origins of replication in Eukaryotes

chromosomal sites necessary to initiate DNA replication, more than 1

similarities between bacterial and eukaryotic chromosomes?

both use supercoiling and both contain multiple genes

differences in bacterial and eukaryotic chromosomes?

bacterial is circular and eukaryotic is linear

bacterial has 1 origin of rep while eukaryotic has many

bacterial is smaller than eukaryotic

conservative model of DNA rep

both parental strands stay together after replication

Semi-conservative model of DNA rep

the double stranded DNA contains one parental strand and one daughter strand after replication

dispersive model of DNA replication

parental and daughter DNA segments are interspersed in both strands following replication

which model of DNA rep is the correct one?

semi-conservative model

what does helicase do during replication?

breaks hydrogen bonds between the two strands

what does primase do during replication?

synthesizes and RNA primer

what is the RNA primer in replication?

its a sequence of RNA that is complementary to some DNA

What does DNA polymerase III do during replication?

synthesizes a daughter strand of DNA but needs an OH group on RNA and proofreads

What does DNA polymerase I do during replication?

it removes RNA primer after it does it’s job and it fills it in with DNA

What does DNA ligase do during replication?

covalently links the okazaki fragments together

what are the okazaki fragments?

they are on the lagging strand only and are synthesized in sections.

leading strand

synthesizes toward the replication fork

lagging strand

synthesizes away from the replication fork in segments (okazaki)

Discontinuous Replication

creation of the lagging strand because it’s formed in fragments

Discontinuous replication is a result of which property of DNA?

because DNA is antiparallel, DNA polymerase III can only synthesize in the 5’ to 3’ direction

ter

termination sequences of DNA

protein-tus

binds to the ter sequences, stops the movement of the replication forks

what is a mutation?

a heritable (can be passed down) change in genetic material

point mutation

a change in a single base pair

transition mutation

is a change if a pyrimidine to another pyrimidine or a purine to another purine (a type of point mutation)

transversion mutation

is a change from a pyrimidine to a purine or vice versa (a type of point mutation)

silent mutation

base pair substitutions that do not alter the amino acid sequence of the polypeptide

missense mutation

base pair substitutions in which an animo acid change does occur

if the substituted amino acid has no detectable effect on protein function, it is said to be _____

neutral

nonsense mutation

where a normal codon is changed to a stop codon

frameshift mutation

involves the deletion or addition of a number of nucleotides that is not divisible by three (every 3 nucleotides is an amino acid)

promoter

regulates transcription

forward mutation

changes the wild-type genotype into a new variation. can also be described as a missense mutation

reverse mutation

changes a mutant allele back to the wild-type (correcting/getting rid of mutation)

deleterious mutation

decreases chances of survival, the most extreme are called lethal mutations

beneficial mutations

positive effect, enhances the survival of reproductive success of an organism

suppressor mutations

mutations that counteract the effects of the first mutation

intragenic mutation

suppressor mutation where the second mutant site in within the same gene as the first mutation

intergenic mutation

suppressor mutation where the second mutant site is in a different gene from the first mutation

position effect

changes in chromosome structure that affect gene expression, a gene may be left intact but its expression may be altered due to it’s new location

spontaneous mutation

naturally arise, result from abnormalities in cellular/biological processes

induced mutations

caused by environmental agents like radiation or chemicals

mutagens

agents that are known to alter DNA structure, radiation and chemicals etc…

spontaneous mutations can arise by 3 different types of chemical change:

depurination, deamination, and tautomeric shift

depurination

involves the removal of a purine from the DNA

deamination

involves the removal of an amino group from the cytosine base— now you have a uracil

tautomeric shift

involves a temporary shift in base structure, can occur in all 4 bases found in DNA

reactive oxygen species (ROS)

oxidative stress can cause humans to release these, hydrogen peroxide, superoxide, and hydroxyl radical

the body tries to block buildups of ROs through antioxidants and certain enzymes

Trinucleotide repeats (TNRE)

several human genetic diseases are caused by this unusual for of mutation

Ex: CAG CAG CAG

what are the 3 main types of chemical mutagens

base modifiers, intercalating agents, base analogues

what are some physical mutagens

ionizing radiation (x-rays and gamma rays)

non ionizing radiation (uv light)

What is the first line of defense for DNA repair?

DNA polymerase

Alkyltransferase

removes the methyl group from a methylated base to a regular base

Nucleotide Excision Repair (NER)

removes DNA damage induced by UV light which produces a thymine dimer (TT)

photolyase

cuts out the damaged region of DNA out of the bubble that the UV light created, DNA polymerase replaces the cut out DNA and ligase seals the backbone

Base Excision Repair (BER)

eliminates non-helix distorting changes, deamination converts a cytosine to uracil, uracil is detected and removed by DNA-N glycosylase

DNA N Glycosylase

removes the detected uracil from DNA backbone during BER

mismatch repair

eliminates mismatched base pairs, cuts them out and is replaced by DNA polymerase and sealed by ligase

double stranded breaks

breakage of chromosomes due to x-rays, gamma rays, chemical mutagens, there are 10-100 breaks per cell per day

homologous recombination repair (HRR)

uses sister chromatid to make exact copy

nonhomologous recombination end joining (NREJ)

lost information, brings what pieces we have together

translesion synthesis

when DNA is too far damaged, translesion DNA polymerase forces synthesis

gene

unit of storage, DNA that produces a functional product

Transcription

synthesizing RNA from DNA template

central dogma

DNA—RNA—Protein

what is the 3 step process of transcription

initiation, elongation, termination

initiation in bacteria

promoter region containing the TTGACA box (-35bp), TATAA box (-10bp) from start site

promotes recognition for transcription factors

transcription factors

proteins that control the rate of transcription

elongation is bacteria

elongation begins when sigma factor is released

Rho-dependent termination (P)

1. P protein binds to rut site in RNA and moves towards 3’ end (similar to helicase)

2. RNA polymerase transcribes a region that forms a stem-loop and then proceeds to terminator

3. P protein catches up to the open complex and separates the RNA-DNA hybrid due to pause from stem loop

what does the stem loop do in Rho-dependent termination

causes the RNA polymerase to pause in the GC rich region of a stem loop

Rho-independent termination

rut site doesn’t exist, still have stem loop, hits an A-U rich region (weak bonds) and RNA polymerase ends up falling off and termination occurs

RNA polymerase I in eukaryotes

transcribes genes for rRNA

RNA polymerase II in eukaryotes

synthesis of mRNA

RNA polymerase III

transcribes all tRNA genes

differences in transcription in bacteria and eukaryotes

bacteria has 1 RNA polymerase while eukaryotes has 3

bacteria has transcription factors (beta, alpha, sigma and eukaryotes don’t

bacteria transcription happens in cytoplasm while in eukaryotes it happens in nucleus

cic-acting element in eukaryotes

has an effect on a particular gene

trans-acting elements in eukaryotes

binds to cis-acting elements

basal transcription

an area where there is a low amount of transcription happening

Translation

mRNA provides info to synthesize amino acids into polypeptides

genetic code

mRNA sequences are read in groups of 3 nucleotides called codons

sense codons

sequence of 3 bases that codes for an amino acid