cell bio exam 2

monomer of DNA

nucleic acid

what direction does DNA go in

5’→ 3’

runs antiparallel and are complimentary

bacteria

single stranded

circular DNA molecule

no nucleus (all prokaryotes)

eukaryotes

long

double stranded

DNA is packed into chromosomes

how many pairs of chromosomes do humans have?

23 pairs

43 individual

23rd set is the sex chromosome

what are the 4 phases of the cell cycle?

G1

S phase - DNA replication

G2

Mitosis- Cell divides

what does interphase look like?

has long thin tangled threads of DNA

cannot see clearly w/ a light microscope

where the cell is preparing to duplicate

includes G1, S, and G2 phases

G1 phase

cell grows physically larger

copies organelles

makes the molecular building blocks it will need in later steps

S phase

cell synthesizes a complete copy of the DNA in its nucleus

duplicates a microtubule-organizing structure called the centrosome

centrosomes help separate DNA during M phase

G2 phase

the cell grows more

makes proteins and organelles

begins to reorganize its contents in preparation for mitosis

phase ends when mitosis begins.

M phase

cell divides its copied DNA and cytoplasm to make two new cells

involves two processes: mitosis and cytokinesis

cytokineses in animals needs cleavage furrow to split, plants needs cell plate

mitotic chromosome

the “X” shape

only happens during division

interphase nucleolus

contains dense DNA for ribosomal RNA

centromere

where 2-sister chromatids connect after replication

telomere

ends of chromosome

replication origins

duplication on DNA begins here

there can be multiple of them on the chromosome

dye to identify DNA

Hoechst stain: attaches directly to DNA

way to identify human chromosomes

FISH (DNA hybridization)

“painting” chromosomes a dif color

karyotype

displays full set of chromosomes labeled with numbers

A-T banding

shows A-T rich regions

is a specific banding pattern for each chromosome

red knobs are genes that code for large ribosomal RNA

translocations

can lead to cancer

shown by karyotypes

how does all the DNA fit into the cell?

chromatin aids w/ folding and packing

contains DNA repair proteins

nucleosome

beadlike structural unit composed of a short length of DNA wrapped around 8 histone molecules to form chromatin

histones are positively charged and DNA backbone is negative

in interphase the chromatin are tightly packed

when they are unpacked they are nucleosomes

how is the chromatin structure?

structure is labile or constantly changing and flexible

chromatin remodeling complexes

use ATP hydrolysis to change position of DNA wrapped around nucleosomes

can loosen or tighten DNA

if DNA is too tightly coiled what happens?

it can turn off the expression

heterochromatin

closed

tightly packed

highly condensed form of interphase chromatin

euchromatin

open

more extended

what does a cell use to communicate opening and closing of DNA?

histone tails which can make reversible modifications

epigenetics

modifications on the DNA can happen from the environment

can be inherited as well

acetylation

open, increase gene expression

methylation

close, decrease gene expression

epigenetic inheritance

ability to inherit chromatin structure helps cells “remember” whether a gene was active in the parent cell

how long does copying the human genome take? how many mistakes?

8 hours

only one or two mistakes!

what acts as a template for its own duplication?

DNA

one side is template and one is complementary strand

5’ → 3’

semi-conservative

DNA replication is this

1 old strand and 1 new strand

where is DNA first opened?

origin of replication is where DNA is first opened

eukaryotes have many origins

bacteria has 1 origin

where are A-T rich regions typically found?

at the origins of replication bc they are easier to break apart

replisome

has all the proteins needed for copying the DNA

DNA helicase

separates and opens DNA strands so proteins and enzymes have access to genetic material

uses ATP hydrolysis to do open double helix

DNA polymerase

synthesizes new DNA using an old strand as a template only in 5’→3’

primase

a RNA polymerase that generates a short length of RNA or a primer

provides base-paired 3’ OH end as a starting point for DNA polymerase

nuclease

breaks apart the RNA primer

repair polymerase

replaces RNA w/ DNA

DNA ligase

acts as a “glue”

joins 5’ phosphate of new DNA to 3’ hydroxyl end of the next

what happens when DNA polymerase makes a mistake

the proofreading subunit corrects it bc mistakes can cause distortion

single stranded binding protein

binds to single-stranded DNA and keeps the strand straight

what do topoisomerase I and II do?

resolve tension and tangled DNA

topo 1 is for single stranded, makes a “nick”

topo 2 is for double stranded coiling, breaks and untangles

telomerase

reaches end of DNA where there is a gap due to RNA primers

extends the strand and allows another primer and DNA polymerase synthesizes

mutation

permanent change in the DNA

many mutations can lead to cancer

how does mismatch repair work?

the DNA mismatch repair proteins bind and remove the strand and DNA polymerase and ligase come and fix it

only happens if DNA polymerase doesn’t catch its own mistake

what are the types of base damage?

depurination- leads to a base loss in guanine and adenine

deamination- leads to a base change in cytosine, uracil, and thymine

what does UV radiation cause in thymine?

thymine dimers- where two thymines covalently attach to each other instead of their corresponding base pairs

excision repair

base nucleotide and single strand repair work this way

nuclease cleaves covalent bonds that join damaged base, repair DNA polymerase fills in gap from 3’ hydroxyl, DNA ligase seals nick

what are the two types of double stranded break repairs?

non-homologous end joining- alters original DNA by deletions or insertions, is fast and easy to do

homologous recombination repair- is more complicated and less frequent but is precise, slow and difficult to do

what is a popular disease that defective DNA repair will lead to?

cancer is the main one

werner syndrome

aging 2x as fast as a normal person

BRCA ½ defects

tumor suppressor proteins

what tells DNA when there’s damage?

cell signaling and ATM kinase which senses damage and amplifies the signal to the cell

structure of RNA

single stranded most of the time

has a ribose sugar

AUGC (AU connected by 2 H-bonds same as AT)

unstable and temporary

has an OH group

messenger RNA (mRNA)

codes for proteins

ribosomal RNA (rRNA)

forms the core of the ribosomes structure and catalyzes protein synthesis

microRNAs (miRNAs)

regulates gene expression

transfer RNA (tRNA)

adaptors between mRNA and amino acids during protein synthesis

transcription

DNA → RNA

opening and unwinding small portion of DNA to expose bases

template strand used for complementary base pairing

correct base is added and linked to RNA chain by RNA polymerase

RNA polymerase II

makes RNA

no primer sequence is needed

no proofreading

makes mistakes but it’s okay because it’s temporary

promoter

is the start sequence on the DNA

terminator

stop sequence on the DNA

how many RNA polymerase do eukaryotes have?

3- RNA poly I, II, III and they need accessory proteins

RNA polymerase II

all protein coding genes, miRNA genes, and other non-coding RNAs

general transcription factors (GTFS)

basal transcription factors; needed for transcription to occur

eukaryotic GTFS (5)

TFIIA and B help bind TBP (TATA binding protein) to the TATA box

TFIID is a complex that contains TBP

TFIIE helps melt or break bonds

TFIIH has helicase activity to unwind DNA

transcription initiation complex

general transcription factors + RNA polymerase II

order of the GTFs will vary based on the promoter or point of regulation

release of RNA polymerase II from the DNA needs dephosphorylation

RNA capping and polydenylation

done before the mRNA moves to the cytoplasm

poly-A tail is a series of Adenines at the 3’ end

5’ cap is specially altered nucleotide end to 5’ end of mRNA

eukaryotic mRNA contains non-coding regions

introns- non coding intervening sequences so they never code for amino acids

exons- expressed sequences code for the proteins

UTR- untranslated regions are important for gene expression

splicing

removal of introns

spliceosome

RNA splicing carried out by RNA molecules

snRNPs form the core of it and carry out RNA splicing

removes introns from pre-RNA to create mature mRNA

how are introns removed?

special sequences are recognized by snRNPs which cleave the RNA at exon-intron borders and covalently link the exon sequences together

alternative splicing

greater protein diversity

exons from the same gene are joined in different combinations, leading to different, but related, mRNA transcripts

increases the coding potential of the human genome bc there are more options of proteins that can be made

where are mature mRNAs transported to, to be translated?

cytoplasm

what marks the mature mRNA that allows recognition that they have been spliced?

poly A tail and 5’ cap

once recognized it moves on out of the nucleus

the start codon

AUG or methionine

how many reading frames is RNA translated into protein?

3 reading frames based on where it starts, but only one encodes the actual message

what process are ribosomes responsible for?

translation and making proteins by reading the order of amino acids and linking them together

what sites and subunits are made up of the ribosome?

A, P, E

large and small ribosomal subunit

what do the 3 sites in the ribsome do?

A site- accepts new tRNA

P site- at the peptide site, takes amino acids off the 2 RNAs to add to the polypeptide chain

E- ribosome exits and tRNA leaves

where on the tRNA is the mRNA code?

3’ end holds the amino acid

what recognizes the amino acid sequence on the mRNA?

anticodons

what covalently couples amino acids to the acceptor arm of the tRNA?

aminoacyl tRNA synthetase

produces a high energy bond between tRNA and amino acid

this charge is used later to link amino acid to the polypeptide chain

where do the ribosomes first start translating?

at the AUG closest to the 5’ end of mRNA

what are the stop codons?

UAA, UAG, UGA

release factors bind to stop codon (protein that allows for the termination by recognizing the stop codon)

do not code for any amino acids

polyribosome

more protein molecules can be made in a given time

what do antibiotics and other drugs block?

protein synthesis

differentiation

process by which a non-specialized cell becomes specialized (can perform specific tasks)

cloning

can take only one cell from cow and experiment to make a calf

that one cell contained all the info to clone

housekeeping proteins

common to all cells

differential gene expression

allows for variation in size, shape, behavior, and function of differentiated cells

cells can change gene expression in response to env. using signaling cascades- phosphorylation turns proteins on/off

3 main points where gene expression is regulated?

transcriptional control: when a given gene is transcribed and how often

mRNA degradation control: selectively degrade certain mRNA molecules

protein degradation control: selectively activating/inactivating proteins

transcriptional control

controlling when a gene is transcribed and how much

starts w chromatin remodeling to open up the gene, histones attach to tails- happens before eukaryotic transcription