exam 2 cell bio

central dogma

replication → transcription → translation

building blocks of DNA

sugar, phosphate, base = nucleotide

bases of DNA

guanine, adenine, cytosine, thymine

DNA strands run in what direction

antiparallel from 5’ phosphate to 3’ hydroxyl

what bond is in between the strands

H-bonds

how many bonds between A-T

2 bonds

how many bonds between G-C

3 bonds

what does the helix allow the strands to do

allows each strand to be copied during replication

human DNA cells are how long?

2 meters

human cell nucleus is how long in diameter?

5-8 meters

DNA is spaced apart

true

the human genome has

23 pairs of chromosomes

(22 autosomes and 1 pair of sex chromosomes)

each cell has how many chromosomes

46

what is a region of DNA thats responsible for specifying a single protein/RNA molecule

chromosomes

chromosomal phases

G1, G2, S phase, M phase

gap phases where cell grows and makes proteins

G1 and G2 phase

chromosomes are copied (DNA replication)

S-phase (interphase)

during mitosis, growth stops and cell divides

M-phase

context of inter phase:

-long, thin tangled threads of DNA that aren’t easily distinguished in a light microscope

-DNA’s less compact than mitotic chromosomes (allowing access for protein expression and replication)

-chromosomes occupy different territories within the nucleus

-chromosomes are NOT mixed together (like pasta)

context of M phase:

DNA is dense and compact, easily visualized

the amount of DNA is doubled in which phase?

S phase

telomere

end of DNA strand

centromere

not directly in the center but is the center for sister chromatids

dye to identify DNA

Hocchst stain (fluorescent)

Ethidium Bromide (UV)

why are dyes harmful to DNA

they are toxic and risk of cancer

painting chromosomes of different colors

DNA hybridization (FISH)

karyotype

display full set of chromosomes in a cell arranged with respect to size/shape/number

Giesma Stains like which base pairings?

A-T

chromatin

complex of dna and potein, aids in folding/packing, contains DNA repair proteins

nucleosomes

bend-like structure unit made out of short lengthed DNA wrapped around a core of histone proteins

chromatin structure has a high proportion of what?

positive charge amino acids, (lysine and arginine)

what has tails?

histones

what do positive charged amino acids help?

histones binding to negatively charged DNA backbone

Histone H1

pulls nucleosomes together into regular repeating array

DNA packing order

DNA double helix → chromatin string → pack of nucleosomes → chromatin fiber loops → chromosome

labile means

changeable

changes in nucleosome structure affect:

allow and prevention of access to DNA

chromatin remodeling complexes

-use energy of ATP hydrolysis to hange position of DNA wrapped around nucleosomes

-loosen DNA (decondense) or tighten (condense)

-alters DNA accessibility to proteins

What moves tightly → loose DNA?

ATP dependent chromatin remodeling complex

heterochromatin

CLOSED and tightly packed (genes not expressed)

Euchromatin

OPEN and loose (genes expressed)

what is the point of regulation

decondensing chromatin (also affects shape)

if genes are exposed, cells:

turn on gene expression

*and if they arent exposed then gene expression is OFF

our environment can effect our genes

histone modification (epigenetics)

if acetyl group is on tail by itself, it will

increase gene expression

if methyl group is on tail, it will

bunch DNA and close; decrease gene expression

H2AX

marker for DNA damage

What is phosphorylated by ATM kkinase when DNA is damaged

H2AX

surrogate parents…

affect the gene expression of the child

epigenetics are

inherited and helps cells ‘remember’ whether a gene was active in a parent cell

(critical for establishment/maintenence of different cell types, tissues, organs for development growth)

DNA+histone

nucleosome

DNA strands serve as a

template

semi-conservative means

one old strand and one new strand

(original strands remain intact for generations

initiator proteins must

break H-bonds separating short lengths of DNA (A-T regions rich)

where are DNA first opened

replicator origin (ORI)

which base pairs are often found at the replicator origin

A-T

What are in origins?

2 Y-shaped junctions (replication forks) per origin

replisome ‘machine’ doesnt include what?

initiator proteins

what uses ATP hydrolysis

DNA helicase

DNA polymerase

-only adds nucleotides to the 3’ hydroxyl group (phosphate)

-nucleotides enter reaction as nucleotide triphosphates, which provide energy for polymerization ***phosphoanhydride bond***

- can NEVER add nucleotides to 5’

primase

RNA polymerase that makes a short length of RNA (10 nucleotides in length) [primer]

what do primers provide

a hydroxyl group to start DNA polymerase

leading strand

continuous replication

lagging strand

discontinuous replication

proof reading occurs in

dna polymerase

proof reading:

from 3’ to 5’ (OPPOSITE DIRECTION) to check every NEW strand

a distortion/bump indicates

an error (wrong nucleotide)

• in this case, DNA replication stops and fixes it

why is protein synthesis 5’ to 3’

DNA polymerase has separate sites/domains for proof reading and synthesis

proliferating cell nuclear antigen (PCNA)

enhances DNA synthesis elongation with DNA polymerase

single strand binding protein (SSB or RPA)

binds to single strands to prevent DNA from sticking to itself and keeps strands elongated

topisomerase I

resolves tension and detangle DNA by making single or double stranded breaks in phosphate backbone

(act on topology of DNA)

which phase “nicks” 1 strand and relives torsional stress and repairs it after? [breaks 1 backbone[

topisomerase I

what makes double strand DNA break and detanges DNA molecules?

[breaks 2 backbones]

topisomerase II

camptothecin (topisomerase I) includes

drug antibiotics that kill human cells (cancer therapeutic)

as we age,

telomere gets shorter

RNA primer provides

hydroxyl group

we use the RNA template to elongate sequence ONLY FOR

reproduction, not normal body cells

if errors are not fixed (a bump and no H bond),

the next replication cannot identify the previous error

nick is the term for

newly synthesized strand

depurination

leads to a base loss (can be permanent)

deamination

leads to a base change (can be permanent)

Thymine dimer (sunlight/UV)

-tanning beds (bathe in carcinogens → cancer)

-nail salon gel machines (UV)

» damage leads to thymine dimers

thymine dimers are a type of damage that leads to

mutations → cancer

what is the functional polymer of life

proteins

excision repair csteps

1. nuclease cleaves covalent bonds that join damaged base/nucleotides to rest of strand

   1. repair DNA polymerase binds 3’ hydroxyl end and fills in gap

      1. DNA ligase seals the nick

double strand breaks are very toxic to

the cell and genome

nonhomologous end-joining

fast and easy

-usually alters original DNA by deleting or inserting

-has no template for repair

RESULT: double strand breaks repaired with DELETION of nucleotides (mutation)

homologous recombination repair

precise, slow and difficult

• more complicated and less frequent

  • uses “other” chromosomes as template for “perfect” pair

RESULT: double strand break is ACCURATELY REPAIRED

defective DNA repairs have

similar symptoms (cancer, accelerated aging)

Werner syndrome

accelerated aging

• protein mutation (WRN [helicase] )

  • increased cancer risks and sensitivity

cellular response to DNA damage

points of regulation of signal cascades that determine to shut down the cell or repair it

G1 phase

gene expression occurs

RNA is

unstable and temporary unlike DNA

Uracil instead of Thymine (U-A)

U-A has how many bonds

2 H bonds

mRNA

codes for proteins

is completely functional INDEPENDENTLY

transcription steps

1. open/unwind of small portion of DNA to expose bases

2. template strands used for complementary base pairing

3. proper base added and linked to RNA chain by RNA polymerase

4. transcript’s generated thats complementary to strand of DNA

RNA polymerase II (transcription)

• 5’ to 3’ direction

• doesnt need 3’ hydroxyl group UNLIKE DNA

  • Hybrid DNA/DNA forms transiently causing a ‘window’ to move along DNA

RNA polymerase

forms phosphodiester bond to form backbone (sugar phosphate sugar phosphate)

eukaryote mRNA

carries info for 1 protein unlike prokaryote mRNA

General/Basal transcription factors

• A-T rich because 2 H bonds, easier to break

  1. assemble at the promoter

  2. position RNA polymerase

  3. pull apart the double helix (expose template)

  4. launch RNA polymerase