MCB chapt 4

three major macromolecules

DNA-deoxyribonucleic acid, DNA let’s us store info,, need to be able to pass it down , we move through RNA then use MRNA to make diff proteins

RNA-ribonucleic acid

proteins

genome-the full set of genes present in a virus or a cell

all the genetic info in an org

bacteria and archaea are haploid, 2N, don’t have homologous pairs, eukaryotes have two sets so diploid or 3N

genotype: specific set of genes or alleles in a gene or organism

phenotype is a collection of observable characteristics

the Griffith experiment

people use to think protein was where we store DNA

figured this out by 3 key experiments

started with Griffith experiment: he worked with steptococcus pneumonia: smooth strain(pathogenic) and R strain which is non pathogenic

exchange of genetic info he saw from one strain to the other, didn’t know which molecule was doing this

a and b.

injected pathogenic strain into mousey, mousey dies

B we put R strain in and mousey survives

smooth strain has a clause and rough strain does not

capsules in pathogens are able toot be seen by a host

rough strain has no capsule, inject with rough strain, so immune system clears out the infection os mouse survives

panel c: heat killed S strain, so he survives

panel d: mixed heat killed s strain with r strain, mouse thinks he’ll be okay, mouse dies. as heat killed strain is dying, it’s releasing thing into the enviro and r strain take the info and puts it into it’s own genome, taking up smth allowing s strain to be pathogenic

concluded live s strain in the r strain, picked up info allowing it to become a capsule

formal conclusion: some transforming principle allow r strain to pick up info from s strain,

c and d is info being taken up

Avery Macleod McCarty

three susepcts: dan, ran, and protein

wanted to see if they could figure out which one it was

had r cells in a plate nd heat killed s cells, mixed these two together

they removed any r cells from culture so whatever was on the plate wasn’t there and they found s cells, saw that it matched with griffifths work

continued

did 3 experiments wtih 3 test tubes

all of them have r cells, the r cells are mixed with heat killed s cells,

in 1 test tube they added protease(enzyme that degraded protein, RNAce, protein that degrades RNA, then a DNA one, one that degrades DNA

realized when you get rid of DNA you don’t have conversion form S cells to R cells

still lingering doubts so Hershey-Chase experiment

cold spring harbor lab

used bacteriophage, they only contain tow macromoelcule,s protein and DNA

were able to label the macromolecule sin the system

were able to see which macromolecules were associated with bacterial cells

top is phase t-2-infects e.coli used S 35 to label the protein and used P53 to label the DNA

P32 and S35 allow the interaction and then blender to pop off virus

spin the culture down to pellet bacterial cells at the bottom of the tube

which radiojlabel is associated with pellet

we see that we have P32 and S35, thing that went into the cell was radiolabled DNA and thing that laid outside of cell was radio labeled protein

the flow of info meaning central dogma

DNA to RNA to protein

you can either replicate DNA and pass it down carefully to future generations

or you can eventually unlock the info in DNA to make proteins

as we move through process to unlock info we use RNA copy and then used Mrna to knoww which proteins to do together

structure of DNA solved by Rosalind Franklin-took photo 51 of double helical nature of DNA, work was given to James Watson and Francis crick without her knowledge and they did further work on the sturyeuce or DNA

James Watson and francis crick were awarded noble prize and Rosalind Franklin wasn’t

a nucleotide building block of DNA is

deoxyribose attached to a 5 carbon sugar

make up rungs of laser, adenine, guanine, cytosine, and guanine in DNNA

nucleoside: is a base and sugar, no phosphate

sugar phosphate base is nucleotide

string together nucleotides, we get nucleic acid

structure of DNA is helical in nature

we have sugar and phosphate in backbone

hydrogen bond togeher

A and T do 2 pairs

C and T do 3 base pairs

important bc we can pull our DNA apart, it’s easier to do it with a and t bc c and g is heard together more tightly

sugars and phosphate make up the backbones, are bonded by phosphodiester bonds

strands have directionality

3’hydroxyl on sugar is 3 prime end

a 3’5 prime phosphate is 5’ end of DNa molecule

two strands don't set up on top of each other, they are

focus more on scientific aspects of talk

single stranded molecule that is being used

diff number of hydrogen bonds is easier to pull Aand T’s apart than C and G

antiparallel

3’ phosphate

other end has 3 prime hydroxyl

3 and 5 prime across, never the same

dna offset gives DNA landmarks

major and minor group

peak to peak is major

minor to minor is minor

regulatory elements bind to major and minor

used to regulate transcription, expression, places where diff regulatory elements are is good

right handed or left handed in nature

most dna is right nature, DNA b form

circules arond -clockwise or counter clockwise

bacteria-single circular chromosome, no histone , smallest genome sizes

archaea-single circular chromosome packaged around histone protein

eukarya-packaged around pistone proteins

bc genomes are a bit bigger, we need another layer of packaging

first thing: make folded loops in circular structure

then supercoil that then package it more

dna negatvie-histone positive charge

histone complex in eukarya is bigger than in archaea

optometrist in eukarya, tetramer in archaea

packaging DNA protects it

nuclease getting into DNA will eat it up, protects DNA

semi conservative manner

pull molecule apart first DNA

one parental strain to direct synthesis of a new strand, use one old strand to direct the synthesis of a new strand

conservative-would replicate the whole molecule

dna replication

three phases

initiation, elongation, and termination

highly conserved across all three domains

everyone has an origin recognition, primate, helices, replication enzyme-structures can be dirt,

origin of replication-where replication starts, place

pulling apart DNA

pulls structure at halfway point, called theta structure

replicate around on both ways for origin of recognition

until you reach the tear site-tear site is the opposite of OTC?

synth

need to make sure DNA is accurate, starting in right place, careful

DNA polymerase-enzyme that …

DNA polymerase 3-does catalyzing

asymmetric enzyme

two pore enzymes

beta clame

what sits in the core enzyme, what makes sure it stays there?

DNA polymerase-big and multifunctional, needs a template in 3/ to 5/ direction bc it only synthesizes new sequence in 5 prime to 3 prime direction

needs a primer, short RNA sequence, primer carriers a free 3’ hydroxyl group allows anchor to attach to, and deoxyribonucleotide or nucleotide in general

process of DNA replication

initiation

OriC-where DNA starts to pull apart

OriC-4 non base pair repeats, called DNAA boxes , has three repeats of a 13 base pair AT rich region-called DNAA boxes

DNAA protein or initiator protein binds at the boxes

buildup of DNAA proteins at the boxes, causes a conformational change in the DNA strand

causes the DNa to curve or bend, bending at 13 base pair repeats,

puts strain on the molecule, causing the strands to pull apart

getting our separation underway, DnaB -helicases unwind DNa strand, DnaC-a helices loader, grabs DNa B and brings it to where we have the bend in the DNa strand and Dna gyrase, -a tochoisomerase 1, nick DNa strands, relaxing the tension in the supercoils, letting helices come in and unwind the strands

SSB: after pulling it apart, SSB proteins, preventing the strands from just rewinding back ones ch other and stabilizes DNA to avoid degredation

DNaG-a primase an enzyme that lays down an RNA primer

elongation

two forks,

one strand is able to replicate continuously

other strand can’t replicate continuousy so it does it discontinuousy, lagging strand bc DNA can only synthesize from 5 prime to 3 prime direction and DNA its anti parallel in nature

generate Okazaki fragments, where you have RNA then DNA repeating

DNA synthesis

5 prime to 3 prime direction

lagging strand replicates and then adds RNA primer which creates the Okazaki fragments, 1000 to 2000 bp

at the OriC

DNAA boxes that DNAA protein binds to

two things we don’t want strands to remind back to one another or get nibbled away which is why SSb attaches stabilizes dna and prevent s it form unwinding

DnaG is a primate that synthesizes RNA primer

use DNA polymerase 1 which has exonucleus activity and it removes the RNA and synthesizes new DNA in that areas for us

after synthesizing DNa, you have sections of DNa synthesis, you have holes, need to seal it, do this by DNA ligase

leading strand: put down RNA primer, have a 3 prime end that DNA polymerase uses to hook things onto

replication fork unwinds and DNA continues to synthesize

RNA primer is put down 5 prime to 3 prime, then you throw down another RNA primer until you synthesize a new DNA, throw down a new RNA primer as it’s unwinding until you hit a RNA primer

DNA is running in the opposite direction of where DNA is unwinding

get rid of RNA by using DNA polymerase 1

pops out the nucleotides belonging to RNA hooks onto 3 prime and adds onto 3 prime end, get rid of RNA primer until you bump up to 3 prime end

connect that free 5 prime end to free 3 prime end which is what DNA ligase does

by forming a phophodiester bond

when DNA polymerase 3 hits the tear site

has tusk proteins that sit here

DNA polymerase hits the tusk proteins and it triggers DNA polymerase three to dissassociate with the molecule

they are intertwined

topoisomerase 2 : nicks both DNa strands, cutting them allows us to release the molecules

tophoisomerase 2 seals the end of each molecule

termination

DNa segmenet with an 80 percent C and G content will e stale at higher temps than if you had a higher AT conent

does not denature at higher temps bc

diff of number of covalent bond holding together the C and G’s

higher CG is more temp stable

terminating DNa replication in archaea is easer

eukaryotic choromosoems are liner making it harder to terminate DNA replication

eukaryotes-degrade RNA poolymer, area where DNA strand can be degraded, if did not fix it , every round the chromosome would get shorter and shorter and loosing genetic info

use telomerase, specialized DNA polymerase, carries and RNA template, lines RNA template up with telemetric sequence, by doing this we can use the sequence carried in the telomerase as a template to

by laying down an RNA primer, we can get ourselves a free three prime hydroxyl allowing us to synthesize DNA

get rid of RNA primer, sequence of single strand DNaA, it’s degraded, by extending our strand, we don’t degrade back to anything that is important just the telemetric sequence, extending sequence extends new sequence so when we degrade back in we don’t degrade anything important

replicating is passing DNA down to future generations

do it carefully, with high accuracy

DNA polymerase 3: high fidelity does not make mistakes

have proofreading activity, only activated at the three prime end of the new molecule that is being synthesize, every time it puts in a new nucleotide it checks the integrity between the hydrogen bond of the new bond and old one, strong bond means good, lack of integrity in the hydrogen bond, DNA blank has exonumeric activities, it backs up, pops nucleotide out and replaces it with the correct nucleotide, check integrity of new bond and continues

checks the last nucleotide added making sure that no mistakes were made

use transcription to make RNA copies of the gnes

dictates the Aino acid sequence

have a dna copy of the gene

turns into RNA copies of the gene

eventually codes for polypeptides, also codes for tRNA or rRNA

cistron, gene that codes for a single polypeptide

it’s a linear sequence of polypeptides

has a discrete starting and end point

not overlapping

first thing to unlock info is take DNA copies and make them into RNA

called transcription

RNA polymerase-the most important -transcribes, major enzyme player in transcription

DNA is a double stranded molecule, looks for promoters landmark features that tell RNA polymerase where it’s gna set down and which DNA sequence it will use as a template

transcription general overview

dna polymerase replication

rna polymerase=transcription

going to tell RNA polymerase where it needs to bind

the region sequence does

promoter region-landmark features associated with it, upstream of transcriptional start see

RNA polymerase has directionality associated with it

needs RNA primer that has a free three prime hydroxyl o start hooking nucleotides up to, RNA polymerase does not need this

bacterial promoters

10 sequence-prignal box

TTGATA=conserved sequence

intermediate space is not conserved, around 16-18 pairs

first landmark area is -10 sequence, original box

made up of A’s and T’s-easy to pull strands apart here

ransciptioinal start side is 10 bps’s down stream

RNA VESION WE TALKING ABT

strand that w’ere using=template strand

not using strand=coding strand

leader is transcribed, not translated-find shine dalgarno -initiates transcription

after leading sequence codes for AUG, and stop codon here too

trailer sequence is transcribed but not translated-iused as a regulator sequence, mRNA stability

terminator sequence-

prokaryotic=continuace squence, whole sequence is coding sequence

eukaryotes=discontinuous, we have axons express regions and introns, intervening sequence. exons then intron, exons then intron-expressed with non express

must take away introns and then put them together=called splicing, mix and match diff axons

codes for tRNA and rRNA

genes coding for rRNA or tRNA are transcribed as a long rprecurosr and get cut up and put back together to make diff sequences

transcription process

making mRNA

differences of mRNA and dRNA

the sugar-DNA-2 deoxyribose, RNA-ribose

DNA has a hydorgoen and ribose on 2 carbon is hydroxyl

everyone has guanine, cytosine and adenine, diff =thymine-methyl group in DNA and uracil in RNA-hydrogen attached

RNA=single stranded, DNA is double stranded

bases in molecule can base pair with one another in RNA

transcription

RNA polymerase-scans DNA molecule, look for promoter and sit down there and pull apart there and Polymerase helps unwind DNA further-summary

5’ to 3’ direction still

i

RNA initiation and elongation

promoter Reigion

if yk any of these three strands, you can figure out coding and template, vice versa

DNA coding strand-not using as template, it’s the same sequence as mRNA strand, any place that we would have T we would have a U

DNA template strand is complimentary to DNA coding strnad

5 polypeptide is code and sigma factor

sigma figures out where promotor region

core enzyme has catalytic activity allowing us to generate the new mRNA sequence

sigma binds to core enzyme-scans DNA strand for promoter region and complex binds here , we have localized unwinding at the prime box

disassociates from R polymerase leaving core enzyme behind

core enzyme uses template DNA strand to synthesize mRNA molecule

number of diff sigma factors hanging out in the cell-most frequent is 6-70, house keeping sigma factor-when binding to core enzyme it takes I to core region to make everything that the cell needs

other sigma factors binding to core enzyme too in response to enviro in the cell,t take it to slightly diff promotor

peach-toasty conditions it does not want to be in like hot enviro it makes heat shot proteins, blank binds to core protein, take it to promoter to make. certain enzyme

after unwinding produces transcription bubble, 160-20 base pairs

region of unkindness where RNA polymerase is working on DNA strand

unwinding forward and rewinding behind

in order for RNA pol to work it needs template DNA strand and rNTP’s, ribonucleotide triphosphate, bases to string nucleotides together

don’t need a fee three prime hydroxyl group

once it hits terminator sequence in bacteria: two types in bacteria=2 types

Rho-independent termination-does not use Rho protein to help terminate, we use structural signals within the mRNA, to help mRNA understand when to disassociate

halobromic allows us to base pair together

having appropriate sequence for stem structure, appropriate A for uA hybrid, stem of the cell is heavy and pulls down on MRNA strand, physically disassociate the mRNA strand to DNA strand. using stem movement, pulling them apart triggers RNA to disassociate from DNA

eukarya=3

rho dependent-bacteria

transcribing DNA to RNA

we get rut site-binding site for Rho protein, Rho starts moving along mRNA sequence-towards 3 prime end, trying to catch u p t o RNA polymerase, RNA polymerase pauses once hitting the terminator allowing Rho to catch up, it encodes a helices, allows us to unwind MRNA and DNA strands, unwinding triggers RNA polymerase to disassociate from DNA molecule, as Rho is scooting down it uses hydrolization of ATP to do this

eukarya:

eukarya: 1 of each similar to Rho dependent and independent, other is unique

eukarya has 3 diff RNA polymerase to transcribe diff things, RNA polymerase 1, terminate of RNA polymerase 1=rho dependent, RNA polymerase 3 transcribes TRNA and small RNA molecule-looks like rho independent

RNA polymerase 2-deos the bulk of protein transcription genes, cleaved by a specific endonuclease, as it cleaves RNA polymerase 2, it triggers RNA polymerase to dissociate from the DNA strand

mRNA mole generated in prokaryotes is ready to go

not the case for eukaryotes bc gene sequence regions has axons and introns, we have intervening sequence, we have to cap and tail the mRNA , pre-mRNA molecule, not using it just yet

add 5 prime cap to 5 prime end of pre-mRNA molecule a

add 5[ cap to 3 prime poly A tail

cut intervening out and stitch exons together

generate a fully mature mRNA molecule for translation

don’t have introns which is why we don’t do that , and don’t cap and tail in prokaryotes-bc in prokaryotes we transcribe and translate in the same place, no nuclear membrane everything happens at same spot

eukaryotes-some things happening in nucleus and other things in cytoplasm, translation happen sin cytoplasm

mRNA is unstable molecule, needs a cap and tail so it can survive journey to cytoplasm

5’ cap-going to be our translational start site for eukaryotes

moving through translation

initiation, elongation, termination

hydrolyze ATP and GTP

tightly regulated and controlled to not burn through ATP

translation-directionality here as well

generating peptide sequence from N terminal to C terminal, pre amino to 3 carboy terminus

happens very fast=900 amino acids per minute, differs

want translation to happen quickly bc RNA is not stable, before RNA is degraded

trnaslation=ribosome site of translation

couple transcription and translation so shift is quicker

doesn’t matter if prokaryotic or eukaryotic, everyone forms a polyribosomal complex of mRNA, more than one ribosome working at RNA sequence

ribosome

site of protein synthesis-parts of translational rang tin small and large

small subunit is 30S, large subunit is 50S

come together and holoribosomal complex is 70S in side bc S unit is not additive

mRN sequence dictates which amino acid and which order

tRNA brings those amino acids in

rRNA-for structural role of ribosome

mRN sequence dictates which amino acid and which order

tRNA brings those amino acids in

rRNA-for structural role of ribosome

16S rRNA-associated with 30 subunit or small subunit -carrie a sequence complementary of shine dalgarno sequence-conserved in molecule and use as translational start site in prokaryotes

eukaryotes use 5 prime cap, shine dalgarno sequence for priokaerotes, making sure that ribosomal blank is accurate

23 S rRNA-it’s a ribozyme that contains catalytic activity, forms the peptide bonds

mRNA sequence-

mRNA molecule-chunk it into 3 bp chunks=codons

each codon codes for a specific amino acid

tRNA’s have to have a way to recognize the codon sequence-carries anti codons, sequence is complimentary to the codon sequence

genetic code-start codon, mosty AUG-codes for methionine

6` codons are sense codons-code of ramino acids

3 other codons-called nonsense condos,-3 stop codons

UGA, UAG, UAA

2 of those stop codons for transcriptional termination

20 amino acids

code=degenerate-some condos code for the same amino acids-this is important bc so mutation occurs, we blunt how much mutations will be

orgs can use wobble

idea that you need a perfect match for first and second but the htird pari does not have to be exact

complimentary codon after 2 can have a third poision that is loose

wobble allows that cell doesn’t have to code for a tRNA for each of our 61 codons, as long as you have tRNA it can bind to wobble for other codons, saves us space

multiple codes of the same amino acid to limit mutations

wobble: 1st and 2nd base need to be an exact match, but not the rest

mRNA-tells which amino acid are needed

Ribosome-structure and fucntion

tRNA-actually bring these amino acids in

tRNA is the same across all 3 domains

RNA can have secondary structure even though t’s single stranded bc the bases that we have base pair with one another-causes secondary structure

clover leaf configuration of tRNA-70-95 base pairs in length, ont he short side

landmark features-have an anticodon arm-carries anticodons

5 prime and 3 prime end-acceptor stem

3 prime end ends in CCA and attach to the A where we put the amino acid

amino acid attach to acceptor span,

make tRNA first then add amino acids to them

prices of adding amino acids is called amino acid activation

aminoacyl-tRNA synthetases-amionoacyl tRNA add the amino acids onto there

at least 20-one for each amino acid out there

Amion acid activation

add amino acid to tRNA-needs ATP for it (amino acid, tRNA, ATP by hydrolyzing it to add them together)

hydrogen bond forms between amino acid and adenine molecule-hydrolyzes ATP here too-hydroxyl is the molecule previously there and it is one after

protein synthesis

initiation

careful here where we start

tightly regulated to make sure we’re starting in the right place

involves;

small and large subunit are separate from each other bc it requires energy to put them together

we put small and large subunits together to make proteins though

use AUG to start -codes for methionine except when AUG is used as a start codon in bacteria-forms formal methionine-slightly diff has a formal group that’s added tot he molecule, so we have to add the carboy terminus so we’re not adding to the wrong side

only use formal methionine at the start

archaea and eukaryotes don’t use formal methionine though

shine dalgarno sequence-conserved-small subunit carries a sequence that’s complimentary to the shine dalgarno sequence

lining them up appropriately makes it the first AUG downstream

line up the 30S to shine dalagarno RNA, then we can bring in the 50S, we form the imitator complex as a result of blank can't't be activated until we have the small and large subunit

helpers

IFS-initation factors

IF3 blocked 50 s from binding to the 30S bc IF binds with the 30S, synthesis occurs

2 things happening at the same time: 1. we have invitation factor 1 that binds to 30S subunit, causes a conformational change in the subunit so IF3 disassociates, small subunit is open to being bound to 50S as a result

30S is localized to the shine delgarno sequence

tRNA molecule carries the imitator amino acid, binds other the GTP(complex with IF2)

this molecule localizes to the P site

once it localizes to the P site, 50S subunit comes into bind, as the 50S is binding to the 30S subunit, GTP becomes hydrolyzes to ATP

GDP molecule is disassociated from thet-RNA

50 and 30 are together with the initatiro Trna

aminoacyl-tRNA binding

transpeptidation reaction

translation-scoot down the RNA

peptide donor P site-

P site-peptidyl site-bind initiatory first tRNA molecule, where we find tRNA with growing peptide chain

A site-acceptor site or aminoacyl site-where the next tRNA with the next amino acid comes into the bind

E site-

tRNA with growing peptide chain on it

sitting in the P site

toward the 3 prime end we have the A site

5 prime end we have the E site

then e add next amino acid by brining the next tRNA that has the next amino acid

to do this tRNA molecule has to bind with the complex with GTP EF2

then moves to the A site, with appropriate binding hydrolysis of GTP to GPD allowing molecule to dissasociat from the tRNA molecules

peptide bond between amino acid and polypeptide chain-carboxyterminus and amino terminus of amino acid

forming that peptide bond is job of the 23 S rRNA

after this bond we have a peptide chain in A site, use translocation to move-EFG come bind to EF GTP make a complex, once hydrolyze hot GTP we get moevement down our rRNA-scoot over a codon, tRNA’s get shifted empty site in E site and other molecule is in A site

tRNA in P site wait s until e bring in our next blank to the A site, keep repeating as we move down the rRNA molecule until hitting the stop codon

23 rRNA-portion that allows us to make our peptide bonds and blank forming in in the polypeptide

formed in the carboxyl group of the C-terminal amino acid

carboxyl group and amino acid chain, carboxyl terminus to amino terminus so heading in the carboxyl direction

as

as we hydrolyze GTP it gives us energy to read our ribosome

as we have ribosome moving down a codon, a couple of other things happen

peptide-tRNA moves form A site to P site

empty tRNA sitting in the P site gets scooted over to the P site until we hit termination

end condos are stop coodns-no coding for amino acids

UAA, uAG, and UGA

proteins that we have called release factors

3 proteins that work

release factor 1 is associated with UAA and UAAG

release facto2 is associated with UAA and UGA

release factor 3-does recognize stop codons, diff job \

tightly regulated process so that we’r not using evnergy randomly

generating a polypeptide chain by scooting and adding move amino acids

once you hit the stop codon(which sits in the A site)

stop codon doens’t relase anyhthing so relate factor 1 comes in

release factor binding to the A site-has hydrolytic acitivyt and can cleave the bond between the polypeptide chain to the tNRA

polpypetide and tRNA is release to the enviro

must get release factor out of the A site, by using release factor 3

, binds just out of the A site, by doing this we haec conformational change, allowing molecule to disassociated from blank

release factor combines with A site

release factor 3 is blank

hydrolyes GTp allowing release factor 3 to get out of

release factor stuck in A site

binds a little outside of A site, allowing enzyme to dissasociate from the ribosome

hydrolyzes GETp to give us the energy that we need to do this

IF3 comes back nd binds to 20S subunit causing the 50 and the thirty to separate from each other

process of termination again

translation

prokaryotic-shine delgarnao tells ribosome where to set down on sequence, multiple shine delgarno on a ribosome

eukaryotics-we use the 5 prime cap to help ribosome localize

prokaryotic is polycistronic-can code for more than one protein due to multiple shine delgrano sequence

3 diff portions out of one RNA molecule

eukaryotic-we onaly have one cap so this can’t happen

prokaryoties-transcription and translation is coupled due to no nucleus

eukaryotic-we have to cap and tail bc mRNA is not stable and must be stable when it gets tor ribosome

once ribosome gets out of the way of shine delgrano sequence, next RNA can bind hoping with translational efficiency with multiple ribosomes at the same time

one thing that needs to happen is the protein folding

influences of folding-the sequence of amino cids themselves

diff non covalent charge interactions

all orgs across 3 domains use helpors-chaperons or chaperoning

chaperons-bind to polypeptide sequence and help drive folding, preventing aggregation and misfiled proteins,

might need to have some post translational modification

most common types of PTM-addition of functional groups-phosphorylate or adenylate or methylate-phosphorylation is the most common type of

eukaryotes-due glcosylation-adding sugar residues to diff areas of our thing

might need to be transported, we don’t always use proteins where we make them

protein transport is more important for eukaryotic orgs due to higher level of compartmentalization

protein transport works the same way-idea that if you need to go somewhere other then where you were made you are going to have a short hydrophobic sequence, will tell the cell where you need to go they are all slightly diff due to where sequence need to go, they are like zip codes, tell the cell where it needs to go

then short sequence is cleaved off where it needs t o be, will be fully functional

mutations

stable, heritable changes

get some change to base sequence of DNA that can be passed down from ten to ten

mutations can be good or bad

great thing for genetic diversity

point mutations-smalll mutations that involve less of DNA sequene

the most common,

effect 1-3 base pairs

can get small deletions, additions of base pairs, alterations in base pairs

larger mutations that effect more sequence so a bit less common

duplications of areas

genomes

inversions-breaks and rearrangeents

translocations-one part of the sequence move somewhere else

mutations can be spontaneous or induced(we are putting pressure on the system bc we want mutations to arise)

spontaneous mutations

low rate than in induce mutations bc they are occurring randomly

tend to occur in process of DNA replication

we have 1 in 1 million bases

DNA does not make much mistakes due to proofreading and being a careful enzyme

when they occur during NDas replication, they occur at characteristic areas???

stretches of the same base in a DNA sequence

can result in an insertion or a deletion-due to stretch of the same base-long

insertion-sitting down inappropriately, not in the right position, back t sits bak which creates an insertion so we remake the T-when it renal it did not reanneal int he margins correctly-insertion process

new strand-reason why

how we generate deletion:

template strain reanneals inappropriately /sits back a little bit

induced mutations-trying to make them happen

end up with a higher mutation rate

broad category-chemical agents and physical agents

3 classes of chemical agents

base analogs chemicals that look similar to our traditional bases, if you have cells replicating with these base analogs bc the analogs are so similar to traditional bases, they get incorporated into DNA strand

5 bromouracil-like thymine =example

DNA modifiying agents-structurally change our bases-add methyl or remove a methyl group, alter the traditional structure of your bases changing the base pairing properties

LAST ONE

intercalating agents-they get up in the center of the DNA ladder structure

or middle of rung and distortt the DNA structure into forming bubbles ont he DNA strand, results in a deletion or an insertion

nitrou oxide-won’t base pair correctly

acridine organge-intercalating agent

nitrou oxide-won’t base pair correctly

acridine organge-intercalating agent

physical agent-UV light causes pyrimidine-specific thymine damage

x rayes-do a ton of damage

if we alter hate structure of the bases, we can end up changing our base pairing properties

pop off adenine, convert it to hypoxanthine-then connects to cytosine

pop off amino group of cytosine, becomes a uracil and base pairs with an adenine instead of a guanine

pop off guanine, becomes xanthine(base pair is the same as guanine) so you’ll still base pair with a cytosine

changing dna that you are changing effecting the RNA and protein

UV light-focused on generating pyrimidine-thymine dimers

in presence of UV light we hydrolyze hydrogen bond between A’s and T’s reforming a bond between the thins creating a thymine diaper and distorting the structure of the molecule

wild type-move common form of a gene , mutation-wild type genes sequence to slightly altered type

forward mutation-wild type to mutant form

reversion mutation: wild type changing our phenotype, can have a secondary at the first type that gets it back to the original type

suppressor mutation-you have a mutation that hcnges your phenotype, another mutation happens away somewhere else that has a mutation that suppresses seeing the phenotype being caused by the first mutation , you don’t see effects of it it’s suppressed

silent mutation

protein coding genes

genetic code is degenerate in nature-have more than one codon that can code for the same amino acid, blunting the impact of mutation

if you code for CCU and code for CCC, it’s the same amino cid anyway

=a silent mutation

missnese mutatio

protein coding genes

missnese mutation-single base substitution that changes codon for one amino acid into codon for another amino aicd

pop out one base pair and have another base pair adding in

if amino acid that we change to have sim properties to amino acid that was there before you might not change the structure or the function, if they have diff properties than the amino acid that was there before then we can change the protein and the function

non polar amino acid barrier in the center and have a missense mutation into a polar amino acid it won’t wanna be buried inside it will want to be in hydrophilic area which will unfold the protein and it’s function

where mutation occurs is important-mutation in the active site of the protein causes.a big impact on structure and the function

nonsense mutation

nonsense codons do not code for amino acids, they’re stop codons

converts a sense codon to a stop codon

causes: does with where int he sequence we ended up inserting that stop codon

if 95 percent of sequence is translated, might not do much, if it’s in the beginning of the sequence, problems with structure and function

impacted by where in the sequence it happened

frame shift mutation

we read codon in groups of 3

have an insertion or deletion of a base pair, shifted out of 3,3,3

everything after the frameshift will be read inappropriately

some ways, impact is isimilar to the nonsense mutation, if you have a frameshift occurring, all of what it should be will be diff, problem if it should be the end, could shift yourself outside of the stop codon, adding sequence to the end of the protein, step more impactful form nonsense mutation

conditional-have a mutation nd only see the effects under specific environments conditions

not expressed at all, only under 1 certain mutation

most commonly used type is a top sensitive mutance: lower temp is not suppressed, higher temp is

auxotrophic mutance

orgs that have a mutation in some sort of biosynthetic pathway that prevent them form making a needed macromolecule like an amino acid or a nucleotide

issues with making proteins nd generating DNA or RNA

they always have that mutation in their genome, it’s expressed all the time

we can only allow that org to grow under specific conditions

ex: you can’t make alanine so you add alanine back to your media

make them out of prototrohic strain-can make all of their nutrients on their own

mutations inr regulatory sequences

promotor regions

done by RNA polymerase, tells the RNA polymerase where to bind, RNA won’t be able to find the promoter, won’t be able to transcribe that area of DNA