Cell and Molec Exam 2

studied byStudied by 35 People
0.0(0)
Get a hint
hint

RNA

1/93

Tags & Description

Studying Progress

New cards
93
Still learning
0
Almost done
0
Mastered
0
93 Terms
New cards

RNA

DNA makes a template for...

New cards
New cards

interphase

chromosomes replicated into a pair of sister chromatids

New cards
New cards

M phase

when is DNA distinguishable/condensed?

New cards
New cards

G1, S, G2

What phases are in interphase?

New cards
New cards

interphase

What phase are cells in most of the time?

New cards
New cards

DNA synthesis

What is S phase

New cards
New cards

miotic chromosome

chromosome easily visualized because it is in most condensed state

New cards
New cards

centromere

region on chromosome that allows for separation of sister chromatids (usually in the middle)

New cards
New cards

kinetochore

complex of proteins that form at the centromere that attach the chromosome to the mitotic spindle, allowing them to be pulled apart

New cards
New cards

replication origin

location on DNA where replication begins

New cards
New cards

1

How many replication origins do prokaryotes have

New cards
New cards

more than 1

how many replication origins do eukaryotes have?

New cards
New cards

telomere

ends of a chromosome where it contains repeated nucleotide sequences.

New cards
New cards

they get shorter

What happens to the telomeres as cells keep dividing over time?

New cards
New cards

histones and non-histone proteins

two classes of proteins that bind DNA to form the chromosome

New cards
New cards

chromatin

made up of histones, non-histone chromosomal proteins, and nuclear DNA

New cards
New cards

histones

what is responsible for the nucleosome

New cards
New cards

DNA

histones are wrapped in what usually?

New cards
New cards

2 of H2A, H2B, H3, H4

What are histones made up of

New cards
New cards

S phase

When do histones assemble into nucleosomes?

New cards
New cards

dimer

2 proteins come together

New cards
New cards

lysine or arginine

more than 1/5 of amino acids on core histones are...

New cards
New cards

neutralize

The positive charge of the histone does what to the negative charge of the backbone?

New cards
New cards

nucelosome positioning

  1. dependent on presence of tightly bound proteins to DNA

  2. Dependent on ATP-dependent chromatin remodeling complexes

New cards
New cards

H1

linker histone that allows for compacting nucleosomal DNA

New cards
New cards

N terminal histone tails

  1. acetylation of lysines.

  2. mono, di, trimethylation of lysines

  3. phoshphorylation serines

  4. exposed with amino acid and can be modifies with acetylation and methylation

New cards
New cards

acetylation

histone acetyl transferase (HATs) add acetyl groups to lysines

New cards
New cards

methylation

trimethylation of Histone H3 attracts heterochromatin protein HP 1 and contributes to the spread of heterochromatin

New cards
New cards

histone code

covalent modifications that can determine multiple outcomes

New cards
New cards

reader complex

recognizes particular of markings on chromatin which attracts additional proteins (what needs to be added)

New cards
New cards

histone chaperones

variety of proteins that bind histones

  • cooperate with chromatin remodeling complexes

  • remove certain dimers from nucleosome

New cards
New cards

covalently modified

the N terminal tails can be...

New cards
New cards

Acetylation (Histone acetyl transferase)

what is looser association and removes the positive charge on the lysine.

New cards
New cards

methylation (Histone methyl transferase

what condenses the chromatin structure where the DNA cannot be replicated

New cards
New cards

parent

what has more methylation: parent or new strand?

New cards
New cards

euchromatin

looser so that it can be used for DNA replication

New cards
New cards

heterochromatin

tightly condensed chromatin that cannot be used for DNA replication

New cards
New cards

tumor-suppressing gene

what does cancer turn off with methylation?

New cards
New cards

semiconservative

each daughter strand inherits original and one new strand

New cards
New cards

deoxyribonucleoside triphosphate

What is used to add a nucleotide because it can also give energy off?

New cards
New cards

RNA

what is the primase made up of to add to the primer strand?

New cards
New cards

5' to 3' (the leading strand has to be 3' to 5')

what way does DNA polymerase synthesize?

New cards
New cards

okazaki fragments

synthesis in the 5 to 3 direction and then joined together after synthesis

New cards
New cards

10^7

1 mistake is every how many nucleotides?

New cards
New cards

DNA polymerase

what enzyme proofreads before the new nucleotide is added? (correct nucleotides are energetically favorable)

New cards
New cards

exonucleolytic proofreading

What occurs when incorrect nucleotide is added that has difficulty extending off improperly based paired 3 OH end?

New cards
New cards

DNA helicase

opens the replication fork hydrolyze ATP when bound to single strands of DNA

New cards
New cards

single stranded binding proteins (SSBs)

binds tightly and expose single strand DN without covering the bases; aid helicases by stabilizing the unwound single strand conformation; mainly used in the lagging strand

New cards
New cards

DNA polymerase I

what takes off RNA primer?

New cards
New cards

RNA primer

what is synthesized by DNA primase?

New cards
New cards

DNA ligase

joins the DNA fragment ends in the lagging strand

New cards
New cards

PCNA sliding clamp

keeps DNA polymerase firmly on DNA when moving but releases as soon as the polymerase runs into double stranded DNA; a ring around DNA polymerase

New cards
New cards

clamp loader

protein complex responsible for assembly of the clamp, requires ATP hydrolysis

New cards
New cards

DNA polymerase

primer is essential for what?

New cards
New cards

DNA

okazaki fragments are made up of what?

New cards
New cards

origin recognition complex (ORC)

multisubunit initiator of protein that binds to a minimal DNA sequence required for directing DNA replication initiation

New cards
New cards

protein kinase

phosphorylate helicases that activates replication but when phoshphorylates ORC it is not able to accept new helicase

New cards
New cards

telomerase

replicates the ends of chromosomes; stabilizes the end of the chromosome

New cards
New cards

telomeres

contain tandem repeats of short sequences (GGGTTA) and at the end of the chromosome

New cards
New cards

DNA topoisomerases

put nicks to release tension in the DNA and then puts them back together; prevents tangling during replication

New cards
New cards

topoisomerase I

produces transient single strand breaks; break allows two sections of DNA helix on either side of the nick to rotate freely

New cards
New cards

topoisomerase II

associates with both strands at the same time; forms covalent linkage to both strands of the DNA HELIX AT THE SAME TIME

New cards
New cards

strand directed mismatch repair

detects the potential for distortion in the DNA helix from the misfit between non-complementary base pairs

New cards
New cards

create permanent mutation

what would happen if there was a change in a nucleotide in the template strand?

New cards
New cards

nicks/ single strand breaks

newly synthesized lagging strand DNA contains....

New cards
New cards

after DNA replication

when does the repair of DNA occur?

New cards
New cards

MutS and MutL

what two proteins scan DNA to detect nicks in the new strand?

New cards
New cards

DNA glycosylase

recognizes a specific type of altered base DNA and catalyze its hydrolytic removal

New cards
New cards

AP endonuclease and phosphodiesterase

enzymes tat recognize the blank space in a DNA strand

New cards
New cards

nucleotide excision repair

can repair damage cause by large change in the structure of DNA double helix

New cards
New cards

ionizing radiation, replication errors, oxidizing agents, radicals

how can double strand breaks occur on DNA?

New cards
New cards

nonhomologous end joining (NHEJ)

-broken ends are rejoined by DNA ligation (lose portions of chromosome)

  • loss of nucleotides -quick and dirty solution

New cards
New cards

homologous recombination

  • exchange of DNA strands between a pair of homologous duplex DNA sequences

  • can repair double stranded breaks accurately without loss or alternation of nucleotides at site of repair

  • looks at other chromosome, scan to recognize what portion is missing or similar

New cards
New cards

yes

does homologous recombination lose diversity?

New cards
New cards

ATM/ATR kinase protein

transducing DNA damage signals to checkpoint control proteins

New cards
New cards

kinase

phosphorylates

New cards
New cards

phosphatase

de-phosphorylates

New cards
New cards

kinase and phosphatase

what two enzymes help regulate the cell cycle

New cards
New cards

G1

what is between M and S?

New cards
New cards

G2

what is between S and M?

New cards
New cards

gap phases (G1 and G2)

allows time for growth of the cell

New cards
New cards

G0

resting state of no replication

New cards
New cards

microscopy

  • can use DNA binding fluorescent dyes: reveals condensation of chromosomes in mitosis

  • antibodies against microtubules

New cards
New cards

artificial thymidine analog

  • can incorporate into DNA during DNA replication

New cards