BIOG275 - Exam 3

Covers DNA history, DNA structure, chromosome structure, DNA replication, and mutations

nuclein

now known as DNA, discovered by Fredrich Miescher

Hershey and Chase experiment

radioactively labeled bacteriophages (³⁵S and ³²P) to determine that the transforming principle is DNA

nucleotide

made up of a sugar, base, and phosphate group

nucleoside

made up of a sugar and a base

purine

double ring structure, includes A and G

pyrimidine

single ring structure, includes C and T

complementary base pairing

A binds to T, C binds to G

antiparallel

strands that are parallel and run in opposite directions (one 5’ → 3’, other 3’ → 5’)

DNA shape

double helix

double helix variety types

B form, A form, and Z form

B form

spirals to the right, a full turn every 34A, each b.p. is 3.4A apart, is the only natural variation

A form

same as B form but is more tightly wound

Z form

same as B form but instead spirals to the left

3 forms of RNA

rRNA (ribosomal), mRNA (messenger), tRNA (transfer)

RNA

single stranded molecule complementary to DNA

topoisomerase

enzyme that relieves strain/tension on DNA due to its supercoiling

polytene

when a chromosome multiplies without mitosis, the chromosome is very thick and only found in somatic cells

p arm

the shorter chromosomal arm

q arm

the longer chromosomal arm

nucleosome

DNA wrapped around a histone core, 200 b.p. total

scaffold

formed by remaining nonhistone proteins

condensins

condense for mitosis

euchromatin

loosely coiled and lightly stained, genes can easily be accessed

heterochromatin

tightly wound, include centromere and telomeres, form a barr body, genes are not easily accessible

satellite DNA

highly repetitive DNA sequences, flank the centromere

middle repetitive sequences

tandem repeats, are associated with transposed sequences

transposed sequences

sequences that can move, “jump” around

telomere

located on the ends of chromosomes, don’t have genes, act as protective caps

VNTRs

“mini satellites” with 15-100 b.p. and are the basis for fingerprinting

STRs (short tandem repeats)

“micro satellites”made of 2-5 nucleotides repeated 5-50x, act as molecule markers

SINEs

short, < 500 b.p. are 13% of the genome, Alu family transcribed, 1.5mil x dispersed

LINEs

long, 6 kb llong, 850k times in genome, 21% of genome, Ll family, include retrotransposons

noncoding regions

make up about 50% of all DNA, do not code for genes

functional human genes

only about 2% of DNA

pseudogenes

very mutated duplicated gene copies, not functional

conservative

old b.p. pair with old b.p. and new b.p. pair with new b.p.

semiconservative

one old pairs with one new

dispersive

old and new are randomly dispersed

the proven replication mechanism

semiconservative replication

DNA helicase

an enzyme that “unzips” the strands of DNA

replication fork

separation between strands

DNA helicase summons what other enzyme?

primase

primase

an enzyme that makes an RNA primer

prokaryotic replication characteristics

have only one origin of replication, end at the “ter” region (termination)

gyrase

enzyme that relieves supercoiling

DNA polymerase I

removes the RNA primer

leading strand

follows the replication fork, is continuous, builds 5’ →3’

lagging strand

moves opposite of the replication form, is discontinuous, must use okazaki fragments to buil

DNA ligase

join fragments of DNA together

okazaki fragments

discontinuous replication of very short DNA strands

shelterin

keep the 5’ gap safe in eukaryotic DNA replication

telomerase

extend the telomere sequence

single stranded binding proteins (SSBP)

hold strands apart during DNA replication

origin replication complex

marks the DNA origins in eukaryotes, only occurs in G1

heteroduplex

made of 1 old strand and 1 homologous strand

branch migration

the cross bridge in a heteroduplex moves down the chromosome, forms a holliday junctino

mutation

inheritable change in the nucleotide sequence of DNA

forward mutation

makes a novel allele

reverse mutation

when an allele reverts back to the wild type

neutral mutation

mutation in a noncoding region

point mutation

mutation in a sequence

missense mutation

mutation where the incorrect amino acid is added

nonsense mutation

mutation that stops a sequence early

silent mutation

mutation where the DNA changes, but the outcome remains unchanged

base substitution

base change mutations

transition mutation

a base change w/in the same group (purine → purine, pyrimidine → pyrimidine)

transversion mutation

a base change from one group to another (purine → pyrimidine, pyrimidine → purine)

amorphic

a mutation that causes a complete loss of function

dominant negative mutation

impact how a protein functions

frameshift

change how a sequence is read (insertion/deletion)

spontaneous mutation

a mutation that occurs randomly

induced mutation

a mutation that is caused by the environment or a certain stimuli

___________ mutations are rare

spontaneous

single nucleotide polymorphisms (SNPs)

single differences in generations

DNA replications occur less than once every ____

10⁹ b.p.

tautomeric shift

the random temporary flip of a molecule

tautomeric shifts causes…

a different configuration, point mutations

replication slippage

loop that forms in the template strand, occurs when nucleotides are missed or inserted

transposable mutations

cause frameshifts and disrupt regulatory regions and potential recombination between transposons

mutagen

chemical change that causes a mutation

base analogs

mimic natural bases, but do not pair normally

alkylating agents

donates alkyl groups which changes the base pairing

intercalating agents

insert between regular bases

adduct forming agents

covalently bind to DNA, change DNA’s structure

UV light causes…

2 thymine bind to make a thymine dimer, forming a bubble shape

photoreactivation

the use of photo lyase to repair mutations using UV, only occurs in prokaryotes

ionizing radiation

create free radicals, very high energy and high in damage, alter bases

mismatch repair (MMR)

repair base mismatch or small insertions/deletions, only occurs in prokaryotes

how MMR occurs

use the methylated strand: nicks backbone → removes incorrect base → fills the gap

postreplication repair

a form of homologous recombination repair, occurs if DNA isn’t fully replicated

base excision repair

removed altered U bases

how base excision repair occurs

endonucleases remove nucleotides to form a gap → glycosylases remove U → polymerases and ligase fill in the break

nonhomologous end joining

fix breaks formed in G1, typically can cause small deletions and sometimes translocation

SOS system

emergency error-prone DNA polymerase is created, creates new DNA w/ mismatches, only occurs in prokaryotes

AMES test

assesses mutagenicity, looks for reverse mutations

double strand break repair

5’ ends digest and make an overhang, displaces the sister chromatid, internal strand pairs w/ complement, ligase seals gap and creates heteroduplex region