Genetic mechs Flashcards
What did Levene correctly and incorrectly determine in DNA structure
DNA rep history
Corr - DNA made from nucltid, structure of nucleotide
Incorr - Tetranucleotide hypothesis (bases form circle, equal ratio of all bases)
What did Chargaff figure out and how did it refute Tetranucleotide hypothesis (levene)
DNA rep history
A pairs with T
G pairs with C
Ratio of A and T does not affect G, C
Ratios can be diff
What was error in pauling triple helix model
DNA rep history
not triple helix
phosphates were located in core of helix
negative O would repel in reality
what was technique used by franklin and wilkins to determine DNA structure
DNA rep history
X ray crystallography - DNA sample crystallized, shoot xrays, measure defraction to find 3d structure
signifigance of watson and cricks base pairing
DNA rep history
finalized structure
inspired by alpha helix protein shape
won prize
found location and angle
conservative vs semi conservative vs dispersive model
DNA rep
conservative - whole parent DNA preserved, complete new copy made
semi cons - correct - half parent, half new in each
dispersive - bits of parent, bits of new in chunks
What were the steps in Meselson and Stahls exp
DNA rep
- grew ecoli in heavy nitrogen (N15)
- transfer ecoli to lighter N14, 1 reproduction, centrifuge
- see 1 band (cant be conservative )
- 1 more replication in N14, centrifiuged
- see 2 bands (cant be dispersive)
Must be semi conservative
What would each DNA rep model look like after the first centrifuge
DNA rep
conservative - 2 band (complete parent , complete new)
semi cons- 1 (2 half/half)
dispersive - 1 (mix of both averages out)
What would each DNA rep model look like after the second centrifuge
DNA rep
cons - 2 (3 new on top, 1 parent bottom)
semi cons - 2 (2 half/half, 2 fully new )
disruptive - 1 (average density)
difference between prokaryote and euk DNA rep init
DNA rep
prok - rep begins at 1 certain point, 1 bubble expands
Euk - rep begins thousands of places at once on dna, bubbles form
What is an Ori
DNA rep
Origin of replication
Special sites on DNA where replication begins
Contains a specific sequence recognized by the replication machinery (enzymes)
Often high in A-T base pairs
Steps and proteins in DNA rep init
DNA rep
initiator protein unwinds the DNA
helicase seperates strands
Single-strand binding proteins (SSBPs) - keeps them apart
Topoisomerase
primase makes primer
Why is priming needed
DNA rep
New nucleotides can only be added to the 3 end
DNAP I vs DNAP III
DNA rep
both found in prok
DNAP III catalyzes elongation, adds nucleotide to existing 3’ end, ntide is hydrolyzed
DNAP I - replaces the RNA primer with DNA
what is the problem wtih rep fork as it relates to anti parallel nature of DNA
DNA rep
due to anti parallel nature of DNA one of the new DNA strand will have 3’ end at fork and the other will have 5’ end at fork
New nucleotides can only be added to 3’ end
but both new DNA strands must be built
diff in steps and enz for leading and lagging strand
DNA rep
leading - primase makes 1 primer,DNAP III builds off it, 1 DNAP used at ori
lagging - primase makes primer, DNAP III builds off it, DNAP I replaces primer, DNA ligase, happens multiple times
what is okazaki fragment
DNA rep
fragments of new DNA on lagging strand
What is leading and lagging strand
leading - synthesized continuously, polymerized in direction of fork
Lagging - synthed in short okazaki fragments, polymerized opposite direction of fork
what is telomere
DNA rep
bunch of useless DNA at end of chromosome
starts with 15000 at cenception
death with 5000
What does topoisomerase do
DNA rep
breaks DNA bonds and reforms them
helps to unwind DNA and lower tension
on either side of bubble
What does helicase do
DNA rep
disrpts H bonds in DNA and seperates DNA to make the fork
in base of fork
What do single stranded binding proteins do (SSBPs)
DNA rep
binds to unwound DNA strands keeps it apart
What is an RNA primer
DNA rep
made by primase so that the DNA has something to attach to
is eventually taken out
WHat is 3’ and 5’ end
DNA rep
Has to to with which carbon is exposed.
Nucleotides can only be added to the 3’ end.
What does DNAP I do
DNA rep
replaces the RNA primers with DNA, takes place after the DNAPIII
if DNA nucleotides can only be added to a 3’ end, how does DNAP I add new DNA?
it adds it to the 3’ end of the strand before it
What does DNAPIII do
DNA rep
Adds to the 3’ end of an existing strand
What does DNA ligase do
DNA rep
Binds together the okazaki fragments after they are completely DNA
also used to bind the 2 DNA at ori
uses phosphodiester bonds
Eukaryote vs Prok rep termination
DNA rep
euk - when bubble reach another bubble, when it reaches end of DNA
prok - when it circels around to beginning of bubble
what is the replication problem at the end of linear DNA
DNA rep
There was a primer used to start to make the 5’ end that was removed meaning that the ends do not line up, some of the original DNA was not copied. happens with the lagging strand
what is purpose of telomeres and structure
DNA rep
found at end of euk chromosomes
noncoding
made from repeats of short genetic sequence
protects DNA from being eroded, getting unound
what is senescence
DNA rep
when the cell stops growing or dividing, recognizes that DNA is damaged, will not divide for protection
what is apoptosis
DNA rep
programmed self descructtion
what is the cellular concequence of shortened telomeres
DNA rep
senescence or aptosis
what is telomerase and what does it do
DNA rep
enzyme that adds telomeres to chromosomes
is a ribonucleoprotein
does reverse transcriptase
what is a ribonucleoprotein
DNA rep
protein that contains RNA in it and protein
ex human telomerase contain RNA (AAUCC)
what is reverse transcriptase
DNA rep
When RNA is used to make DNA instead of the other way around
ex. Telomerase uses its internal RNA to make the DNA for the 3’ of chromosmes (makes the longer part longer )
How do telomeres relate to aging
DNA rep
they get shorter as you age
15000 bases at conception
10 000 at birth
5000 at death
How the telomere is completed using telomerase
DNA rep
- binds to 3’ (parent strand)
- extends the parent using its RNA template
- the other complimetnary strand gets primer with primase
- DNAP alpha is used to elongate
- DNA ligase connects the newcomplementary strand with the rest of the complimentary strand
- still end up with the parent strand being longer than the complimentary strand but technically nothing is lost. (eveything needed is copied)
What cells contain telomerase acivity
DNA rep
germ cells and cancer cells
Do eukaryotes use DNAP I and III
DNA rep
No
eukaryotes use ones named with greek letters (15)
prok have 5 DNAP (roman numerals )
DNAP alpha is like DNAP III but for euk
DNAP also seems to make the primer?
DNAP delta is like DNAP I?
why does DNAP alpha make telomeres instead of DNAP III
DNA rep
Telomeres only exist in eukaryotes
the issue only needs to be solved in eukaryotes
DNAP III is used in prokaryotes only and does not need to be able to make telomeres
DNAP alpha is used in eukaryotes only
What is a gene
Transcript
stretch of DNA that is transcribed into RNA
aka transcription unit
What is a promoter and why does it have rich AT regions
Transcript
Where the RNAP first binds
upstream of gene
holds TATA box
holds transcription start point
Rich in AT because they are easier to break apart and start transcription
transcrition initiation in euk vs prok
Transcript
prok - RNAP recognizes promoter, binds, unwinds DNA, starts
euk - pre - initiation complex made (protein factors + anactive RNAP II), RNAP gets phosphorylated at C terminal domain, starts
What is coding strand
Transcript
strand of DNA whos base sequence is identical to the RNA
not the template
What is the sense strand
Transcript
same as the coding strand
it is the one what looks like the RNA
what is the antisense strand
Transcript
the template for the RNA
complimentary to the sense strand
does not mean anything by itself
What is the RNA Transcript
Transcript
WHat initially comes out of transcription before the post processing
primary Transcript
newly synthed RNA
Where does Transcript take place
in cell, euk vs prok
Transcript
euk - nucleus
prok - cytoplasm
Where does translation take place
prok vs euk
translation
both take place in cytoplasm
euk - leaves nucleus after transcript
prok - does not have nucleus
How do you know the 3’ end 5’ of DNA based off RNA
Transcript
RNA must be made be made in direction of 3’ end
sense strand is in same direction as RNA
antisense strand / templete - is opp direct of RNA
Transcription termination for euk
4
Transcript
- dephosphorylation of C terminal domain on RNAP II (slows it down)
- AAUAAA gets Transcribed, stalls RNAP II, but continues
- GU rich region, gets transcribed, signals endonuclease to cut
- cut happens after AAUAAA, before GU region on RNA
transcription termination for prok
Transcript
- 2 GC rich regions that are complimentary
- when transcribed form hairpint
- dA region on DNA make U region on RNA, weak bonds
- RNAP stops and is released
How are Transcription termination different euk vs prok
Transcript
prok - uses hairpin method
Euk - uses endonuclease to cut RNA off from RNAP
What are the types of RNAPs used euk vs prok
Transcript
prok - only hase 1 types of RNAP
Euk has 3 types, mainl RNAP II used
What is mRNA
Transcript
messenger RNA
final transcript, what gets translated
leaves neucleus
What are the 3 types of RNA processing do both euk and prok have it
Transcript
capping
polydenylation
splicing
only euk does this
What is capping (what, where, why, when)
Transcript
at 5’ end of new RNA
addition of modified guanine
protection from degredation, helps ribosomes bind
during transription
What is polyadenylation (what, where, why, when)
Transcript
3’ end
addition of many adenine (poly A tail)
protection, facilitation of mRNA export
after Transcription
What is splicing (what, where, why, when)
Transcript
introns
intron is taken out
for alternative splicing, exon shuffling
during and after transcription
components of splicing
Transcript
Splice site (on RNA)- on ends of intron, where snRNPs binds
Spliceosome - contains snRNPs+ other proteins
- snRNP - contains snRNA and protein
What are snRNPs and what do they do
Transcript
Part of splicing, turing RNA into mRNA
small nuclear ribonucleoprotein
is a rybozyme - has RNA is catalyzer, not protein
binds to splice site to get rid of a specific intron
What are the mechinisms of splicing
Transcript
2 snRNP binds to intron ends (snRNA is complimentary to the splice site)
More proteins come in to make spliceosome
introns are cut out
exons are rejoined
How can splicing be recognized in a photo
Transcript
loops formed in the RNA
What are introns and their function
Transcript
interveneing
noncoding sequences in between exons
regulate gene expression through alternative splicing
what function of introns have direct relevence to Transcription
Transcript
introns can are used in alternative splicing
allows one gene to make many diff polypeptides by considering different things as introns
What are the 4 steps in translation initiation
translate
- small unit of ribosome finds and binds to mRNA
- small unit ribosome finds start codon (AUG) along mRNA
- initiator tRNA binds
- large unit of ribosome binds, takes GTP, tRNA in P site
prok vs euk translation initiation (compare 4 steps )
translate
- prok - has shine-Dalgarno seq, helps small ribo find start
euk -small ribo binds - prok - has initiation factors
euk - has kozak sequence before start to help locate - prok - starts with fmet
euk - starts with met - both - large ribo binds
What is shine dalgarno sequence
translate
prok version of 5’ cap
helps ribosome find 5’ end of prok mRNA
what are 2 subunits and 4 binding sites in ribosome
translate
large top subunit, small bottom subunit
has A site, P site, E site, mRNA binding site
What is translation initiation complex
translate
complete ribosome+ initiator tRNA at P site+ mRNA at AUG
What is codon and anticodon
translate
codon - 3 consecutive nucleotides on RNA, codes 1 amino acid
anticod - complimentary sequence to codon on tRNA
What are the parts of tRNA molecule and what does it look like
translate
is clover shaped in 2d
L shaped in 3d
3’ end holds amino acid
Anticodon is on bottom
describe steps of translation elongation
translate
- codon rec - tRNA with right anticodon enter A site, H bonds form btwn mRNA and antocod, uses GTP eng
- pep bond formation - ribo catalyzes reaction in amino acid in P and A, polypep on tRNA in P site moves to tRNA in A site, polypep is 1 longer
- translocation - tRNA in P moves to E and leaves, tRNA in A moves to P, takes GTP eng, next tRNA can enter
What is direction of reading in translation
translate
ribosome reads from 5’ end to 3’ end of mRNA
Where is the C terminus and N terminus of growing peptide chain
translate
C terminus is where new amino acids are added
N terminus is where the start amino acid it
How is translation terminated
translate
at stop codon no tRNA
release factor binds, adds water instead of amino acid
polypep gets hydrollyzed
ribosome disassebles
How to know 5’ and 3’ end in polyribosome on RNA
also what is polyribosome
translate
polyribo - when 1 mRNA has many ribo translating at once
translation starts at 5’ end
translating towards DNA
closer to DNA = been translating longer
Location of ribosome and the type of protein it produces
translate
free ribo (in cytosol) - makes cytoplasmic proteins (organelles)
bound ribo (right outside right endo plasmic reticulum) - makes secretory proteins (lysosomes, membrane proteins)
Cytosol vs cytoplasm
translate
cytosol - fluid in the cell, organelles are within
cytoplasm - inside of cell, iincludes organelles
both exclude nucleus
what are chaperone proteins for
translate
allows proteins to fold by making proper microenv
used by cytoplasmic proteins
makes hydrophillic env
unfolded protein goes in
chaperone gets capped, changes
folded protein out
What is the process of trafficking secretory proteins
7
translate
- signal seq made at N term
- SRP binds to sig seq, stops translation
- SRP binds to SRP receptor on ER, ribo is docked to outside of ER
- sig seq goes through translocon, into ER lumen, SRP leaves, translation cont
- signal peptidase cuts of sig seq
- translation continues
- translation completes, polypep releases into ER lumen
what is signal sequence
translate
all ribos start off free
If N terminus has signal sequence the ribo will stop and go to ER to continue
first step of secretory proteins
5-30 hydrophobic amino acids
what is stop transfer sequence
translate
part of the peptide that anchors it to the ER membrane, stops it from being fully released into ER lumen
C terminus out, N terminus in ER
what si SRP
translate
Signal recognition particle
recognizes signal sequence and takes the ribosome and everything to ER to continue translation
waht is translocon
translate
like a channel protein
places where the polypep goes through to get into ER
waht is signal peptidase
translate
cuts off the signal sequnce once its in the ER lumen
What is SRP receptor
translate
where the signal recognition particle binds to the ER
found on cytosolic side of ER
cell membrane proteins vs secreted proteins
compare making process
translate
Cell membrane proteins have stop transfer sequence, it keeps them in the ER membrane and eventually sends them to cell memb
proteins that are secreted out do not have transfer seq
organelles in endomembrane system and their roles in protein trafficking
4
translate
Endoplasmic reticulum - folds proteins
Golgi complex - for post translational mods
lysosomes - some proteins become them
vesiclesé - transports the polypep to membrane of cell
page 51 of translate slides
What are the steps in secretory system to ER
translate
- sig seq translated, process slows
- Signal rec protein, comes brings it to SRP receptor
- protein sent through translocon, sig seq stays in translocon
- translation continues into ER, forms loop ish thing
- signal pepdase cuts off sig seq
- polypep released
what are all the post translational mods
4 (ACPF)
translate
addition - phosphate, sugar, lipid groups added
cleavage - some amino acids removed ex. met
polymerization - 2 or more polypep form whole protein as subunits (hemoglobin)
folding - ex insulin
What are all the ribonucleoproteins studed in this unit
translate
Telomerase, snRNPs, (spliceosome)
ribosomes
What are the 3 chars of genetic code
mute
universal - all living things use same bases
redundant - diff codons code for same amino acid
non - ambiguous - each codon makes specific amino acid
What is wobble hypthesis and why importance
mute
wobble position - third position of codon
base pairing rules are flexible there
promotes redundancy
what is inosine and importance
mute
found in wobble position of tRNA
bonds with C, U, and A
allows multiple codons to make same amino acid
promotes redundancy
spontaneous vs induced mutations
mute
spont - errors from replication, from enzymes
induced - from exposure to metagenic factors
examples of physical mutegen and how
mute
UV light
makes pyrimandine dimers - when they bond next to each other instead of across the ladder
can be fixed, by the body usually
```
Perymadine dimers and what is xeroderma pigmentosum
mute
xeroderma - dry skin
pigmentosum - change in pigmentation
unable to repair damages caused by UV light (problem in NER mech)
leads to early skin cancer, must avoid light
Chemical mutagen example and how it can be used benifially
mute
ethium bromide
intercalating agent - gets caught in the rungs of DNA ladder
mutagen may cause DNAP to stutter and make extra base pair in rep
can be used to for staining and visualizing DNA, it glows
Types of DNA muataions
4
mute
- chromosomal mutations (in meiosis)
- missing base pair
- fused base pair (ex. perimydine dimers)
- mismatch (caused by point mutation), most common type
What is point mutation and its types (2 + subtypes)
mute
one nucleotide or base pair is altered
1. substitution
* transition
* transversion
2.frameshift
* insertion
* deletion
transition vs transversion mutation also what type is it
mute
DNA mutation
point mutation
substitution
transition - purine to purine, perimydine to perimydine
transversion - purin to perimydine, vice versa
when do DNA mutations occur
mute
in DNA replication
during S phase
Chromosomeal mutations can happen in mitosis
insertions vs deletions + special case
what type of point mutation is it
DNA mutation
point mutation
frameshift
insertions - extra base is added
deletions - base is deleted
if multiple of 3 ins/del - no frameshift
Mutation classifications for polypeptide
3
mute
missense
nonsense
silent
what is missense mutation (def, where found, effect )
mute
type of polypeptide mutation
when RNA codes for diff amino acid
funciton may or may not change
ex. sickle cell anemia
what is a nonsense muation (def, found where, effect)
mute
codes for premature stop codon
type of polypeptide mutation classification
can be lethal in embryonic stage
what is a silent mutation (def, found where, effect)
mute
when mutation codes for same amino acid
type of polypep mutation
no change
compare diff DNA mutation effec ton polypep
mute
transition, transloc, - missense, nonsense, can be silent
insert or delete - extensive missense, nonsense, never silent
no frameshift, ins/del: missense, nonsense , never silent
1.
2 ways to repair DNA from mutation
mute
endocuclease- repairs DNA outside of replication
exonuclease - proof read as DNA is rep
exo vs endo nucleas repair
mute
exo - instant, DNAP I, II both use it, hydrolyzes phsphodiester bond and adds new nucleotide
endo - repairs after rep, mech of repair called nucleotide excision repair (NER)
Steps in NER and enzymes used
mute
1 . endonuclease - sees issue, takes off only one side
2. polymerase - fills gap with right nucleotides
3. ligase - seals it, connects new with existing nulecotides on same strand
why is antibiotic resistant pos even though its not good for humans
mute
its relative
its good for the thing that got the mutation, bacteria
if mRNA has 27 codons, how many amino acids in final polypep?
mute
26
the met (start codon) is taken out?
pos vs neg gene regulation
+ ex
expression
pos - active form of regulatory protein increases transcription of operon
ex. lac operon
neg - operons are switched off when reg protein is active (repressors )
ex trp operon - uses corepressor
lac operon - repressor starts active
what is operon
expression
a groupd of genes that share a single promoter
code for things with related functions
What are components of operon
expression
promoter - whre RNAP binds for transcription
structural genes - things to be transcribed with RNAP
2 regulatory seq - before the gene includes enhancer, operator, promoter
order is enhancer, promoter, operator, gene, another regulatory seq
monocistronic vs polycistronic
expression
mono - in euks, promoter controls 1 gene
poly - in prok , genes with related funcitons tgt, one promoter for many genes
What is a constitutive gene
expression
regulatory genes/housekeeping genes
always transcribing
upstream of operon
unregulated
What is a repressible gene
expression
Usually on
can be turned off
corepressor activates repressor
usually anabolic
What is an inducible gene
expression
usually off
can be turned on
inducer inactivates repressor
usually catabolic
structural vs regulatory gene
expression
struct - regulated, turned on or off
reg - upstream of operon, always transcribing, codes for regulatory protein
Types of regulatory proteins
expression
all are allosteric
repressor - active form block RNAP, in operator
activator - active form enhances RNAP, in enhancer
What do regulatory proteins and genes to in Lac operon
name of reg prot + type of gene, prot, effector+ name of effector
expression
reg gene - Lacl
type of prot - activator
type of gene - inducible
type of effector - inducer
name of effector - lactose
regulatory proteins are usually active, inducer comes in and inactivates it
catabolic
how is lac operon also example of positive gene reg
expression
for lac to turn on there must be lactose and NO glucose
cAMP get binded to Catabolite activator protein (CAP)
CAP attaches to enhancer wich helps RNAP
What do regulatory proteins and genes to in Trp operon
name of reg prot + type of gene, prot, effector+ name of effector
expression
reg gene - trpR
type of prot - repressor
type of gene - repressible
type of effector - co repressor
name of effector - tryptophan
repressor made by reg gene usually off, when too much tryptophan it activates and represses
anabolic
WHat are the types of effectors
expression
ny molecules that regulates activity of protein
corepressor - activates repressor, stops gene expression
inducer- inactivates repressor, stops it from binding , activates gene expression, activates activator
What does lacZ, lacY, lacA do?
lac operon
expression
catalyzes hydrolysis of lactose in bacteria
1. lacZ -> beta- galactosidase - > turns lactose into galactose + glucose (bact version of lactase)
2. lacY - > permease - > channel protein for lactose into cell
dont need to know
3. lacA - > transacetylase - > adds acetyl group to galactose
activator and repressor vs co repressor and inducer
expression
activator and repressor are regulatory proteins, they bind in enhancer or operator
co repressor and inducer and effectors , they bind in repressor
gene regulation and gene expression types
expression
gene reg - can be neg (repressor) or pos (activator)
gene expression - can be inducible (inducer) or repressible (corepressible)
In positive gene regulation how would a repressible and inducible operon look?
expression
regulatory protein is an activator
repressible - activators usually active, uses corepressors to inactivate (corepressor could be the product)
inducible - activators usually anactive, uses inducers (inducer could be the idk)
what are the 4 levels of DNA packing and size
euk chrom
- nucleosome - 10 nm
- selenoid/chromatin - 30 nm
- looped domain - 300 nm
- metaphase chromosome - 1400 nm
what are the parts of a nucleosome
euk chrom
DNA+ core histones
wrapped twice around 8 histones
looks like beads on a string
what is a histone
euk chrom
protein that DNA coils around to make chromatin
has pos charged R groups that bind to neg DNA groups
can be cores or linker
core histone vs linker histone
euk chrom
core - H2A, H2B, H3, H4 (used in step 1 in octomer )
linker - H1 (used in step 2, brings6 nucleosomes tgt )
when does supercoiling begin
euk chrom
on #2
when it becomes chromatic/ selenoid
how does supercoiling/chromosome condensation regulates gene expression/transcription
euk chrom
chromosome must be incoiled at region to be transcribed
wether coiled or not effects gene expression
what is selenoid structure, what level is it
euk Chrome
2 in DNA coiling
H1 histones aggregate causing 6 nucleosomes to coil together
What are looped domains
euk Chrom
chromatin forms loops using nonhisotne scaffolding
300 nm
3rd step
WHat is metphase chromosome
euk Chrome
4th step in DNA coiling
occurs in mitosis
seens in metaphase
The ability to control whether a gene is actively being transcribed or not
can be structural - supercoiling
molecular - neg feedback enzymes
euchromatin vs heterochromatin
euk chrome
euchromatin - loose parts of chromsomes, can be transcribed
hetero - densley packed region, inactive
When and where does methylation occur
euk chrome
When methyl groups attach to bases (often C)
after S phase
supresses genes
what is acetylation and its effects ?
euk chrome
attachemnt of acetyl group to histones
activates gene expression
loosens DNA packing
