mod 5 chap 5 Flashcards
the order of aa determiens proteins shape and function
aa structures
Consist of central alpha carbon connected by covalents bonds with amino group, carboxyl group, hydrogen atom and variable R group or side chain
in cell pH the amino group gains proton and becomes NH3+ and carboxyl looses proton to become COO-
R groups makes aa different
aa differ in their phsyical and chemical properties
r groups are chemcal divese and grouped based on if they are hydrophobic, hydrophilic, polar, non polar, charged (acidic or basic)
properties infleucne how polypetide folds and therefore the 3d shape
hydrophobic aa dont interact with water - usually have nonpolar r groups - these r groups aggregate with each otehr and this is stablized by weak van der waal forces in which assymetries in e- distrubtuon create temp charges in inetraction molecules make them attarcted to each other - also why they are in interior of folded proteins
aa with polar r groups have permament charge seperation - hydrophilic andmake H bonds with water
r groups of acidic and basic aa are typically charged and are stronly polar - at cell pH r groups either lose or gain proteon becoing charged - they are located on outside of folded molecule - charged groups can from ionic bonds - imprant way proteins can associate with each otehr
special aa
glycine, proline and cysteine
glycine has R group of hydrogen - not assymetric moelcule - non polar and small enough to tuck into palces - also allows for freer rotation around CN bond becasie r group deosnt get in way - increases flexbility of protein which helps in folding
proline - r group linked back to amino group - creates kink or bend in polypeptide chain adn restricts rotation of CN bonds causing contraints of protein folidng in this area
cycstein - SH group - when two cystein side chain in same or diff polypeptides come close they react to form disulfide bond - stronger than ionic interactions - forms cross bridges that conenct diff parts of same protein or diff proteisn
peptide bonds
aa linked to form proteins
The bond formed is peptide bond - carboxyl of one aa reacts with amino of netx aa and water is released - the r groups point in diff directions
eletrons of ppetide bonds are more attracted to the carbonyl group than the amide beavsue of o’s electronegtaivty
peptide bond is shoretr than a single bond
not free to rortate
amino end or n terminus is the free amino group end
carboxyl end of c termius is free carboxyl end
polymer of aa connected by ppetide bonds is polypeptide
protein sequence
sequence of aa is known as primary structure - determines how protein folds
interactions between streches of aa in protein form a local secondary structure
longer range interactions between secodnayr strcutures supports the 3d shape which is tertiary structure
some proteins are made up of several indivdaul polypepetides that inetact with each otehr reuslting enselble is quaternanry structure
function of protein depends on three dimensialn shape
primary structure
sequence of aa in protein is usually repped by series of trhee letetr or one letter abbreviations for aa
the aa in proteins are listed in order from left to right - starting at aa end and proecing to carboxyl end - these ends are diff so order matters
secondayr structure
hydrogen bodns can form between carbonyl group in one peptide bond and amide of another thus allowing localized regions of chain to foled - major contributr to secodnayr strucyrue of proteins
pailing and corey strudies crystals of proteisn adn discoeed 2 secondayr structure types alpha helix and beta sheet both which are stablized by H bonding along polypeptide backbone
in alpha helices the polypeptide backbone is trwisted tightly in right handed coil with 3.6 aa per complete turn - helix is stablized by h bonds between aa’s cabronyl gruup and amide groups 4 aa ahead in seqeunce - r groups prokect outward from alpha helix - chem proeprties of projetcing r groups determiens where teh alpha helix is positioned in folded protein adn hwo it might interact with other moelcules
in beta sheet the polypeotdei folds back and forth on itself forming pleated sheet that is stablized by H bonds between carbonyl groups in one chain and amide groups in other chain across way - r groups projected alternatively above and below - betera sheets consist of 4-10 polkypetide chains aligned side by side with amide groups in each chan hydorgen bonded to carnyl on each side - are denoted by broad arrows where diretcion of arrow runs from teh amino end of polyepetide to carboxyl - beta sheets can be formed by h bonding between polypetide cgains that are parallel however antiparalell configruation is mroe stable becasue carbyl adn amdie group are mroe favoruably alighend for h bonding
teriary structure
teriary structure is the three dimensional conformation of single polpeide chain
tertiary structrue is deifned by inetratcions between r groups
structure is dtemrined by spoatial distibution of hydriphilic and hydrophobic r rgoups and diff types of chem bonds and interatcions that form between r rgoups
tertairy structure includes loops, or turns in backbpen that allow r groups to sit near each otehr and form bonds
tertiary structure dtermiens function becasue itsh the three dimenisonal shape of molecule - the contours and distrubion of charges on outside and presence of pockets that might bind with smaller moelcuels on inside - enable proetin to serve as strcutrual support, emmebrane channel, enzyme or signallng moelcule
princple that strure dtermins function can be seen by diff obersvations
denaturtaion is process by whichc moelcuels have unfoeld and lose their strcture - most proteins denatured by chem treatemnte or gigh temps that disurpt h and ionic bonds - proteisn lose theri functional acivtyy
mutatnt proteisn contaning an aa that prevnts proper folding are often inactiev or dont function proeprly
quaternary structure
mmany proetisn are compelte and functional as single polypeptdie with tertiary structure but some are composed of two or more polypetide chains ro subunits with tertairy strture that ome togtehr to form a higher order quaternry structure
the activty of compelx depends on quaternayr structrue formed by combo of various tertairy strcture
polyppetdie subints can be identficla or diff
the subunits infleunce each otehr in subtle ways and infleucne tehry funtion
chaperones
the primary seuence of protein dtermiens hwo it forms the rest of strucures
someporteins can fold very slow and this is dangerous - the longer polypeptides remained in denatrued state the longer their hydrophbic groups are exposed to otehr macrmoelcules
the hydrohbic efefct with van der waal interactiosn brings the exposed hydrophobic groups toetehr and their innaproaite aggretaion may prevent proper folding
coorectly folded proteisn cn unfold ebacsue of temp which risks aggregation
cells have evolved proteisn called chaperones which help protetc slow folding or denatrued proteins until they can attain roper 3d syrcture
chaperones bind with hydrophobc groups and nonplar r groups to shield them from innaproaite aggregation and in repeated cyles of binding adn release they give polyepptide tiem to get correct shape
Translation
In translation the sequences of bases in an RNA moelcule known as messenger RNA is ussed to specifiy the order in which succesive aa are added slowly to newly seynthsized polypeptide chain
transaltion uses many moelcules
trasnlation requries many components
more than 1010 genes encode components needed for trasnlation
the cell uses ribosomes whch are made up of rna and protein that bind with mRNA and are the site of translation
the ribosome consists of a small subunit and large subunit each composed of 1-3 types of ribosmal rna and 20-59 tyoes of ribsomal protein
eukaryotic ribsomes larger
large subunit included three binding sites for molecules of trasnfer RNA which are called aminoacyl site, peptydl site and exit site
role of ribosome is to ensure that when mRNA is in place on ribsoome, the seuqence in the mRNA coding for aa is read in succesive nonoverlapping groups of three nucelotides
each nonoverla;ping group of three adjacent ncuelotides consitutes a codon - each codon in mRNA codes for single aa in polypetide chain
the diff ways of parsing the string into three letter words are known as reading frames - protein coding seqeunce in mRNA consists of seeuqnce of bases and can be trasnaltion into correct protein only if translated in proper reading frame
ribsoeomes establish correct reading frame, the actual translation of each codon in mRNA is carried out by tRNA
tRNA has characetric of self pairing
three bases in anticodon looop make the anticodon - these are the three nucleotides that undegro base paring with corresponding codon
each tRNA has nucleodtide seqeunce CCA at 3’ end and 3’ hydroxyl of the A is atatchment site for the amino acid corespidng to the anticodon
enzymes called animoacyl trNA synthetases connect speciic aa to specific tRNA molecules
these enzymes are diretcly responible for transalting codon seqeunce in nucelic acid in polypeptide
most organisms have one aminoacyl tRNA syntehase for each aa - enzyme binds to mutlpel site on tRNA that has anticodn corepoding to aa and it catalyzes the formation of covalent bond between aa and tRNA
tRNA without aa is uncharged, with is charged
the specificty of DNA RNA and codon antidocn interatcions result from base pairing
5’ base in codon mRNA pairs with last 3’ base in anticodon
Genetic code
codon aug specifies aa methonine by bas eparing with anticodn of a charged tRNA denoted tRNA met
most codons specify an aa acordingto genetic code
has 64 codons with 61 codons speicying 20 aa
dodons that do not specifiy aa are stop codons - UAA, UAG, UGA
termiantion codons or nonsense codons
stop codons signal where ransation terminates and the proetin is relased from ribosome
genetic code is redunant or degreneate
the codon at which transaltion begins is initation codon - AUG which specifies met
pokypetide is syntehzied from amino end to carboxyl end so met forms the amino end
met is often cleaved off by enzyme after synthesis
AUG codon also specifies the incorpation of met at inetrnal sites
position of AUG established reading frame that detrrmiens how downstream codons are read
once inital met create amino end of polypeptide chain, downstream codons are read one by one in nonoverlapping groups of three bases
at each step ribsome binds to tRNA with anticodn that base pairs with codon and aa is attached to rgwoing chain and ebcomes new cabroyl end of chain
happens until stop codon is encournter and polypetide is reelased
genetic code deciphered in 1960s by chem metdos for making syntehsic rna of kown sequnces by Khorana
steps of translation
3 sep prcoesses
initation the initatior AUG codon is regconzied and met is established as first aa in chain
elongation the succeisve aa are added one by one to growing chain
termination the additinn of aa stops and polypetide chain is relased from ribsoome
initation
initation requries number of protein initation factors that bind to mRNA
in eukarotes one groupo of initation factors bind to 5’ cap that is added to mRNA during processing
soem fo these factors recruit a small subunit of ribsome and otehrs bring up a transfer RNA with charged MET
initation complex then moves along mRNA until it encounters AUG tripelt
position of AUG established reeading frame
when first AUG codon is encournteed a large ribsomal subunit joins complex and initation factors are released
elongation
during elongation aa are added one by one to the growing polypeptide chain
with tRNA met boudn at peptdyl site, the next tRNA binds to aminacyle site
a rxn takes place in which the bond conencting met to trNA is trasnfered to amino group of next aa in line forming a peptide bond
RNA in large subunit is catalyst
new polypetide become attached to tRNA in A site
ribsome then shifts one codon to right
this moves uncharge tRNA met to E site and is reelased and peptdie ebaring tRNA shifst to P site
movement of ribsome empties A site making it avaible for next tRNA
biding of new tRNa to ribosome, the formation fo a peptide bond between the amino acids and relase of tRNA is repeated
ribsome movement along mRNA and fomration of the peptide bonds requrie energy which is obtained with help of proteisn called elongation factors
they are bound to GTP moelcuels and breka their enegry bonds to provide engry for elongation
elonation continues until tsop codon reached
these codons signal termination
termination
termintaion hapens when stop codon encountered
terminatin takes place ebacsue the stop codons dont have correspodning tRNA molecules
when ribosme encounters stop codnn a protein release factor binds to A site
release factor causes bond conencted polypeptide to tRNA to break creating carbyxl terminus of poleptide and completing chain
once polypetide is realsed teh small and large ribsomal subunits disassociate
difference between eukaryotes and prokaryotes
translation initation differs between the two
this difference has implciatiosn for number of proteisn that a single mRNA can produce
in eukaryotes intation compelx forms at 5’ cap and scans along mRNA until AUG encountered
in prokaryotes the mRNa have no 5’ cap and initation complex is formed at one or more internal sequences in the mRNA kown as shine dalgarno sequcne
ability to initation trasnaltion internally allows prokaryotic mRNA to code for more than one protein - polyicstronic mRNA
AUG is usually after the shine dalagrno sequence
each shine dalagrno seuqence sevres as initation site for translation so all peptides can be translated
polycisttonic mRNA reuslts from transcript of a group fo functionally related genes located in tandem along DNA and transcribes as singe unit from one promoter
this type of gene organization is known as operon
prokatotes have many geens into operons becasue production of polycistronc. mRNA allows all proetin products to be expressed toegtehr when needed
typically genes organzied into operons are those whos products are needed either for suscdive steps in sysntehsis of essnetail small moelcule or for sucessive steps in breakdown of source of energy
Regulation of protein syntehsis
gene regulation refers to the ways in which cells control gene expression
it detrmines when a gene is expressed in which cell types and what qunatity
gene regualtion can occur at almost any step in central fogma
genes can be regualted at level of chromsome itself through modulatino of trasncription or translation ro even after protein is amde
first level is at gene itself - in order for gene to be trasncribed DNa must first be rendered accesible to trasnciptional machinery meaing specilzied proteisn that reorganize proteisn associated with DNA of geneof the gene that would orgnarly make it inaccesible
but displacemet of tehs eproteins isnt enoygh for trasncription to occur
inittaition of trasncript requires at least one tarsnciption factor that binds at gene
after trasncription the primary trasncipt is spliced, modified at 3’ and 5’ end to become messneger RNA
mRNa then tarsnproetd to cytoplasm
many proteins arent immedtly functioally active after translation and must be mdofieid in cytyplasm by cleavage or addition of fucntional groups
a posttrranstlatioanl mod is a mod that happen after translation
it rgeulated the tsructrue and ufnction of proteins
ex. adding phosphate groups
gene expresison and protein synthesis are typically regulated at multple levels simulatensouly
this allows for finer modulation of amont of transcirpt or portein produced as needs of cell changes
protein sorting
eukaryotic cells have many compartment and dif fprotein functions
protein sorting or targeting is process by which proteins end up where they need to be to perform their function
proteins are produced at free ribsomes or membrane bound ribsomes
proteisn rpdocued on free ribsomes are sorted after trnslation
these proteins often contain aa seqeunces called signal seqeunces which allow them to be recgonzied and sorted
porteins with no signal sequence remain in cytosol
proteins for mitochodnria or chlroplast have signal seqeunce at amino ends
proteins targeted for nucelus have signal seqeunce located internally
these signal sequnces called nuclear localization signals enbale proetisn to move through pores of nuclear enevelope
proteins synthesized on Er end up as transmembrane proetisn or in lumen of ER
from there they may be retaiend in lumen, packaged into evsicles and trasnported to golgi for postrarnslation mod or be secrted out of cell
these proteisn are sorted as they are trasnalteed
proteins destined for ER lumen, golgi lumen, lysosome lumen or secretion have amino terminal signal seeunce that directs the ribsome to rough ER
as free ribsome translated the protein in cytsol this seqeunce is reocgnized by RNA portein complex knwon as signal recogintion partucle
the SRP binds to signal seqeunce and free ribsome and brings pause in translation
SRP then binds withr ecpetor on rough Er so that ribsome becomes ascoaietd with rough ER
SRP recpetor brings the ribsome to channel in membrane of rough Er
the SRP then disascoated and transaltion continues and polyeptide chain grows by threading through chanel
a specic protease cleaves signal seqeunce as it emmerges in lmen of ER
some proteins retaiend in interiro of ER while some are trasnproted into vesicles
proteins destined for cell memrbane contain signal anchor seeuqnce in additionn to amino termianl signal sequnce
after growing polypeptide chaina dn ribsome are brought to ER, this compelx is threaded trhoygh channel in ER until signal anchor sequcne is encountered
the sequnce is hydropbic so it doesnt difuse in bilayer
ribsome disaacotes form channel while translation continues
translation is done and amino end of polyeptide is in ER lumen, carboxyl remains on cytsolic side and region between is in membrane
transmembrane proteisn like tehse may stay in memrbane of ER or end up in internal memrbanes or cell membrane
