Cell and Molec Exam 2

RNA

DNA makes a template for...

interphase

chromosomes replicated into a pair of sister chromatids

M phase

when is DNA distinguishable/condensed?

G1, S, G2

What phases are in interphase?

interphase

What phase are cells in most of the time?

DNA synthesis

What is S phase

miotic chromosome

chromosome easily visualized because it is in most condensed state

centromere

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

kinetochore

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

replication origin

location on DNA where replication begins

1

How many replication origins do prokaryotes have

more than 1

how many replication origins do eukaryotes have?

telomere

ends of a chromosome where it contains repeated nucleotide sequences.

they get shorter

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

histones and non-histone proteins

two classes of proteins that bind DNA to form the chromosome

chromatin

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

histones

what is responsible for the nucleosome

DNA

histones are wrapped in what usually?

2 of H2A, H2B, H3, H4

What are histones made up of

S phase

When do histones assemble into nucleosomes?

dimer

2 proteins come together

lysine or arginine

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

neutralize

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

nucelosome positioning

1. dependent on presence of tightly bound proteins to DNA
2. Dependent on ATP-dependent chromatin remodeling complexes

H1

linker histone that allows for compacting nucleosomal DNA

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

acetylation

histone acetyl transferase (HATs) add acetyl groups to lysines

methylation

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

histone code

covalent modifications that can determine multiple outcomes

reader complex

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

histone chaperones

variety of proteins that bind histones
- cooperate with chromatin remodeling complexes
- remove certain dimers from nucleosome

covalently modified

the N terminal tails can be...

Acetylation (Histone acetyl transferase)

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

methylation (Histone methyl transferase

what condenses the chromatin structure where the DNA cannot be replicated

parent

what has more methylation: parent or new strand?

euchromatin

looser so that it can be used for DNA replication

heterochromatin

tightly condensed chromatin that cannot be used for DNA replication

tumor-suppressing gene

what does cancer turn off with methylation?

semiconservative

each daughter strand inherits original and one new strand

deoxyribonucleoside triphosphate

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

RNA

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

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

what way does DNA polymerase synthesize?

okazaki fragments

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

10^7

1 mistake is every how many nucleotides?

DNA polymerase

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

exonucleolytic proofreading

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

DNA helicase

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

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

DNA polymerase I

what takes off RNA primer?

RNA primer

what is synthesized by DNA primase?

DNA ligase

joins the DNA fragment ends in the lagging strand

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

clamp loader

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

DNA polymerase

primer is essential for what?

DNA

okazaki fragments are made up of what?

origin recognition complex (ORC)

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

protein kinase

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

telomerase

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

telomeres

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

DNA topoisomerases

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

topoisomerase I

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

topoisomerase II

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

strand directed mismatch repair

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

create permanent mutation

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

nicks/ single strand breaks

newly synthesized lagging strand DNA contains....

after DNA replication

when does the repair of DNA occur?

MutS and MutL

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

DNA glycosylase

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

AP endonuclease and phosphodiesterase

enzymes tat recognize the blank space in a DNA strand

nucleotide excision repair

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

ionizing radiation, replication errors, oxidizing agents, radicals

how can double strand breaks occur on DNA?

nonhomologous end joining (NHEJ)

-broken ends are rejoined by DNA ligation (lose portions of chromosome)
- loss of nucleotides
-quick and dirty solution

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

yes

does homologous recombination lose diversity?

ATM/ATR kinase protein

transducing DNA damage signals to checkpoint control proteins

kinase

phosphorylates

phosphatase

de-phosphorylates

kinase and phosphatase

what two enzymes help regulate the cell cycle

G1

what is between M and S?

G2

what is between S and M?

gap phases (G1 and G2)

allows time for growth of the cell

G0

resting state of no replication

microscopy

- can use DNA binding fluorescent dyes: reveals condensation of chromosomes in mitosis
- antibodies against microtubules

artificial thymidine analog

- can incorporate into DNA during DNA replication

flow cytometer

- rapid analysis of a alrge number of cells
- measures DNA content in a cell population and sorts the data

late in G1

start/restriction point
- is environmental favorable?

G2/M transition

- controls system triggers early mitotic events that lead to chromosome alignment on the mitotic spindle in metaphase.
- is all DNA replicated?
- is environment favorable?

metaphase/anaphase transition

- control system stimulates sister-chromatid separation leading to completion of mitosis and cytokinesis
- are all chromosomes attached to the spindle?

cyclin dependent kinase (CDK)

-members of a family of kinases
- rise and fall throughout the progression of the cell cycle
- cyclical changes in phosphorylation of intracellular proteins

cyclin protein

CDK regulator
- CDK is dependent on this
- made and destroyed though the cell cycle

G1-S cyclins

activates CDKs late in G1
- levels fall in S phase

S cyclin

- binds CDKS after progression through start
- stimulate chromosome duplication
- remain elevated until mitosis

M cyclin

- activates CDKS that stimulate into mitosis at G2/M transition
- fall in mid-mitosis usually around metaphase/anaphase