Biochemistry notes
Protein Synthesis
)(1st
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: Team Leader
: Team membersYahya Al-Aseeri Metallic 0 Mind
Biochemistry notes
Protein Synthesis
(1st)
Overview- Protein Synthesis called Translation - Translation
needs Genetic Code . - Genetic Information : - Stored In
Chromosomes . - Transmitted to daughter cells by DNA replication .
- Genetic Information is expressed through Transcription to RNA
mRNA Subsequent translation into proteins .
Note :- Any alter in the nucleic acid sequence may result in an
improper Amino Acid being inserted into protein chain ,potentially
cuasing Disease or even death- Many Proteins are covalently
modified to - Activate them - Alter their activities - Target them
to extracellular or intracellular destination
:
The Genetic Code* Each Individual word in the code is composed
of three Nucleotide bases . *These Genetic words are called
Codons
A - Codons- Present In mRNA . - They are presented by the
language of : C, G , A , U - Their nucleotides should be written
from 5-end to 3-end - there are 64 different combinations of
bases
Adenine (A) Guanine (G) Cytosine ( C ) Uracil (U)
NO T (thymine ) (MCQ) J >>>
Biochemistry notes
Protein Synthesis
(1st)
How To Translate a Codonyou can translate the codons to Amino
acid . - For Example , 5-AUG-3 codes for methionine . - 61 of 64
are coded for the 20 common amino acid
Termination ( or stop or nonsense ) codons : {UAG - UGA - UAA
}If One of these amino acid appears in mRNA : termination will
occur and they do not code for Amino acid sending signals that the
process is complete
: 1) Met & Trp is the only amino acids that form by only one
codon 2) others amino acids formed by more than one codon as u see
3) Not in every protein we find Met
Biochemistry notes
Protein Synthesis
(1st)
any mutation that altered the manner in which the code was
translated would have caused the alteration of most, if not all,
protein sequences, which would certainly have been lethal
Characteristics of the genetic code Specificity- The genetic code
is specific - a p articu lar codon always co des for the same amino
acid
Universality J - the sp ecificity o f th e genetic code has b
een con served from very early stages of evo lution [Note: An
exception occurs in mito cho ndria, in which a few cod ons have
different meanings like , UGA codes for trp .]
Degeneracy (Redunduncy )- a given amino acid may have mo re than
one triplet coding for it. For example, arginine is specified by
six d ifferen t codons.
M et
Nonoverlapping and commaless- The genetic code is nonoverlap
ping and commaless, that is, the code is read from a fixed starting
point as a continuous sequ ence of bases, taken three at a time. Fo
r example, ABCDEFGHIJKL is read as ABC/DEF /GHI/JKL with out an y p
unctuation between th e codons.
Biochemistry notes
Protein Synthesis
(1st)
C. Consequences of altering the nucleotide sequence: Alteration
in single nucleotide base (point mutation) :1. silent mutation :
the codon containing changed base may code for the same amino acid
( e.g. UCA UCU = serine ) 2. missense mutation : the codon
containing changed base may code for different amino acid ( e.g.
UCA =serine CCA = proline ) 3. Nosense mutation : the codon
containing changed base may become termination codon ( e.g. UCA =
serine UAA = termination codon)
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Biochemistry notes
Protein Synthesis
(1st)
Alteration in amount or structure of protein produced by
translation :A. Trinucleotide repeat expansion :( MCQ)O c ca si on
a l l y , a se qu en ce of t hr ee bas e s t ha t is rep ea te d i
n t a nd em w i l l b ec ome amp l if ied i n n u m be r, s o t h a
t t oo man y co pi es of t he tr i p le t occ ur . I f t h is o cc
ur s:
1) Within coding region of gene :t he pro t ei n w i l l co nt a
i n man y e x t r a c o pie s of o ne am in o a c id .
I. Huntington protein (11-34 CAG = 11-34 glutamine) huntingon
disease (MCQ) (neurogenrative ). * N.B : Huntington protein is
unstable 2) In untranslated portion of gene decrease in produced
protein : I. Fragile X syndrome (7-50 CGG) II. Myotonic dystrophy
(5-35 CTG)
B. Splice site mutations: Mutation at splice site no removal of
introns from pre-mRNA apparent protein production
C. Frame shift mutations : frame shift mutations : Addition or
deletion of 1 or 2 nucleotides to interior of message sequence (not
3) (MCQ) Reading frame of mRNA is altered Resulting amino acid
sequence may become different from this point on
-
Addition or deletion of amino acid: Addition or deletion of 3
nucleotides (amino acid) Not frame shift mutations Reading frame of
mRNA is not altered
Biochemistry notes
Protein Synthesis
(1st)
Loss of three nucleotides maintains the reading frame, but can
result in serious pathology.For example , cystic fibrosis ( CF ): -
a hereditary disease - primarily affects the p ulmo nary and dig
estive systems - is most common ly caused b y deletion of three n
ucleotides from the coding region o f a gene , resulting in the lo
ss of phenylalanine at th e 508th p osition (F508) in the protein
en cod ed by that gene. This F508 mutatio n prevents normal folding
of the CF transmembrane conductance regul ator ( CFTR ) protein ,
leading to its destruction by the proteasome .
Note :
-----------------------------------------CFTR normally functions
as a chloride ch annel in ep ithel ial cells, and its lo ss results
in the prod uctio n of thick, sticky secretions in the lu ngs and p
ancreas, leading to lung d amage and digestive deficiencies . In o
ver seventy percent o f p atients with CF, the F508 mu tation is
the cau se of th e disease.
Biochemistry notes
Protein Synthesis
(1st)
III. Components Required for Translation:1-
all the amino acids that are found in the finished product2-
the mRNA ( to be translated)34-
transfer RNA (tRNA) . fun ctional ribosomes .5-
energy sources .6-
enzymes
7- protein factors
Amino acidsAll the amino aci ds m ust be present at the time of
protein synthesis
( If one amin o acid is missing (for example, if the diet do es
not con tain an essential amino acid), translation stops at the
codon sp ecifying th at amino acid. )
Biochemistry notes Transfer RNA
Protein Synthesis
(1st)
-At least one specific typ e of tRNA is req uired per amin o
acid -In h umans, th ere are at least fifty species of tRNA -so me
amino acids h ave more than on e specific tRNA mo lecule. -But
every single tRNA is directed for one amino acid
Amino acid attachment site - Each tRNA molecule has an
attachment site for a specific (cognate) amino acid at its 3 -end.
- charged : tRNA has a covalently attached amino acid - Uncharged
:tRNA is not bound to an amino acidWh en an ami no ac id be come ac
t iv at e d ? - w he n i t at t ac he d t o t - RN A
Anticodon:E ac h tRN A mo le cu le a l so co nt ain s a t h r
eeba se nu c leo t id e s e qu en cet h e an t ic od on t ha t r e
cogn i z es a sp ec if i c c od on o n t h e mR N A
tR N A a r e a bl e to carr y a sp ec if i c am in o a ci d a nd
t o r ec og ni ze t h e c odon f or t h at am in o a ci d. tR N A,
t h er ef o re, f u n ct i on as a da pto r mol ec u l es . ( MCQ
)
Biochemistry notes Aminoacyl-tRNA synthetases:
Protein Synthesis
(1st)
- This famil y of enzymes is required fo r attachment of amino
acids to their corresponding tRNA . - Each member of this family
recognizes a specific amino acid and the tRNA that correspond to
that amino acid (isoaccepting tRNA).
Aminoacyl-tRNA synthetases:- catalyzes a two-step reaction - The
overall reaction requires adenosine tripho sph ate (ATP), which is
cleaved to ad enosine mon ophosph ate (AMP) and inorg anic pyroph
osphate (PP i ) - The extreme specificity contribu tes to the hig h
fidelity of translation of the genetic message . - have a p
roofreading or editing activity th at can remove mischarged amino
acids fro m the enzyme or th e tRNA molecu le.
Biochemistry notes
Protein Synthesis
(1st)
Messenger RNAT h e s pe ci f ic mRN A r eq uir e d a s a t empl
at e f o r t h e s yn t h es is of t he de si r ed po l y pe pt i
de ch ai n m u st be pr e se nt
Functionally competent ribosome-Rib oso mes are large complexes
of protein and rib oso mal RNA (rRNA) -They consist of two subunits
o ne large and one small . -Their relative sizes are g enerally
given in terms of their sedimentation coefficients, or S (Svedberg)
valu es. - Because the S values are determined both by sh ape as
well as mol ecular mass, their n umeric values are not strictly
additive. Fo r example, the prokaryotic 50S and 30 S rib osomal sub
units together form a 70S ribosome. The eukaryotic 6 0S and 40S
subu nits form an 80S ribo some.] (MCQ)(IMP) - Prokaryotic and eu
karyotic ribo somes are similar in stru cture, and serve the same
function, namely, as the factories in wh ich the synthesis of
proteins occurs.
T he la r ge r ib os oma l s ub u n it c at a ly z es f or mat
io n of t h e pe pt i de bo nd s t h at li n k am in o a ci d r es
idu es in a pr ot ei n. T he smal l su b u n i t bi nd s mR N A a
nd is r es p on si b le f or t he a cc ur a c y of t ra ns la t io
n b y en su r i n g c orr e ct b as e-p ai r i n g b et w e en t h
e c o do n i n t h e mR N A a nd t he an t ic o do n o f t h e tR N
A
Biochemistry notesR i bo soma l RN A : pr okar yo t ic r ib os
ome s co nt a i n t hr e e mo le cu le s o f rR N A, w h er e as e
uk ar y ot ic r ibo som es con t ai n f o u r mo le cu le s o f rRN
A
Protein Synthesis
(1st)
C el l u l a r l ocat i o n of ri bos ome s :
- I n e uk ar y ot i c c e lls t h er ibo s om es ar e:
Free (cytosolic)LMCQ)C y t o so l ic r ib os ome s s y nt h es i
z e p r ot ein s r e qu ir e d i n t h e c y t os ol i t se lf , o
r d est in ed f o r t he n uc le us , m it o c ho nd r ia, a nd pe
r ox is ome s
R i bo soma l prot ei n s : R ib os oma l p r ote in s a r e pr
e se nt in co ns id er a bl y gr e at e r nu mbe rs in eu ka r yo t
ic r ibo s om es t h an i n p r ok ar y ot i c r ibo s om es A, P,
an d E s i t e s o n t h e r i bo so me : Th e riboso me has thr ee
bi nd i ng si t es for t RNA m ol ecu l est he A , P, a nd E si tes
ea ch of whi ch ext e nds ov er both su bu ni t s. To g et he r, t
hey c o ve r th re e nei ghbori n g c od ons. Du ri n g t rans la
ti on : t he A s it e bi n ds a n i n comi ng a mi noa c yl -tRNA
as dir e ct e d b y t he c od on curr e nt l y oc cu pyi n g t his
si te. T hi s c od on spe cifi es t he n ex t a mi no a ci d t o be
a dd ed t o t he gr owi n g pept id e c hai n . (M CQ )
Associated with RER :T he RER - as soci at e d r i bo som es a r
ere sp on s ib l e f or s y nt h es i z i n g p r ot e in s t ha t
ar e : 1- to be exported from the
cell .2- d est in ed t o become i nt eg r at ed i nt o pl asm a,
en do pla s mi c r et ic u l um , or G olg i m embr a ne s, or i nc
o r po r at e d i nt o l y so som es.
N ot e : M it oc ho ndr i a con t ai n t he i r own s et of ri
bos ome s a nd t he i r ow n u ni q ue , c i r cul ar DN A .
T h e P - sit e cod on is oc c up ied b y p ep t id y l - t RN
A. T h is tRN A ca rr ie s t h e ch ai n of am in o a c ids t h at
h a s al r ea dy be en sy n t he s i ze d.(MCQ)
Th e E si t e i s oc cu pi ed by t he emp t y tRN A as it is ab
ou t t o ex it t he r ib os ome .
(MCQ)
Biochemistry notes Protein factors
Protein Synthesis
(1st)
Initiati on, elongation, and termin ation (or release ) factors
are required for peptide synthe sis
ATP and GTP are required as sources of energyCleavage of four
high-energy bonds (MCQ) i s re quired for the addi ti on of one
amino a cid to the growing polypep ti de chain: 1- two from AT P in
the aminoa cy l-tRNA sy nthetase reaction:-
one in the removal of PPi one in the subsequent hyd rolysis of
the PPi to inorganic phosphate by py ro phosphatas .
2- two fro m GTP : - one for binding the a minoacyl-tRNA to the
A site . - one for the transloca ti on step .
[Note: Additional ATP and GTP molecules are required for
initiation in eukaryotes, whereas an additional GTP molecule is
required for termination in both eukaryotes and prokaryotes.]
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