vault backup: 2025-11-25 10:18:48

content/Biokemi/Cellulära processer/Translation/Anteckningar.md

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   - translation
   - anteckningar
 föreläsare: Ana Luis
+url: https://www.youtube.com/watch?v=gjjp-NUaCXE
+date: 2024-11-25
 ---

content/Biokemi/Cellulära processer/Translation/Lärandemål.md

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+- tRNA stuktur och funktion.
+- Aminoacylering av tRNA.
+- Ribosomens struktur och funktion.
+- Mekanismen för proteinsyntes (initiering, elongering, translokation och terminering).
+- Regleringsmekanismer för proteinsyntesen
+
+Beskriva överföringen av genetisk information från mRNA till protein.

content/Biokemi/Cellulära processer/Translation/Slides.md

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+
+Chapter 8 and Chapter 20
+Ana Luis
+ana.luis@medkem.gu.se
+2025/04/28
+
+---
+
+Protein Biosynthesis
+
+(Translation)
+Chapter 8 and Chapter 20
+Ana Luis
+ana.luis@medkem.gu.se
+2025/04/28
+
+----
+
+Learning goals
+
+• Explain how nucleic acid information is translated into an amino acid sequence and define the role of aminoacyl tRNA synthetases in this process
+	•	Protein biosynthesis requires the translation of nucleotide sequences into amino acid sequences
+	•	Describe features of the genetic code
+	•	tRNA structure and function
+	•	Aminoacyl-tRNA synthetases establish the genetic code
+
+• Define the role of ribosomes in protein synthesis
+	•	Structure and function of ribosomes
+	•	Mechanism of protein synthesis (initiation, elongation, translocation and termination)
+
+• Describe how certain chemicals can inhibit protein synthesis
+	•	Antibiotics and toxins inhibit protein synthesis
+
+----
+
+Why is important to understand the translation mechanisms?
+![[Pasted image 20251125093128.png]]
+### TRANSLATION
+
+#### Inhibition of translation of specific mRNAs can lead to diseasess
+- Fragile X mental retardation syndrome:
+- absence of the set of protein isoforms, derived from 
+  alternative splicing of the Fragile X mental retardation 
+  gene 1 (FMR1)
+
+#### Bacterial toxins can block of protein biosynthesis protein biosynthesis
+- Diphtheria toxin
+
+#### Several antibiotics are inhibitors
+- Streptomycin
+- Tetracycline
+- …..
+
+⸻
+
+Translation = the process of protein biosynthesis
+
+Adenine (A)
+Cytosine (C)
+Guanine (G)
+Uracil (U)
+Nucleic acid
+
+→ 
+
+Amino acids
+(A) Alanine
+(R) Arginine
+(N) Asparagine
+(D) Aspartic acid
+(C) Cysteine
+(E) Glutamic acid
+(Q) Glutamine
+(G) Glycine
+(H) Histidine
+(I) Isoleucine
+(L) Leucine
+(K) Lysine
+(M) Methionine
+(F) Phenylalanine
+(P) Proline
+(S) Serine
+(T) Threonine
+(W) Tryptophan
+(Y) Tyrosine
+(V) Valine
+
+-----
+
+Translation = the process of protein biosynthesis
+
+The basics of protein biosynthesis are the same across all kingdoms of life:
+• mRNA is decoded in the 5′-to-3′ direction one codon at a time
+• the protein is synthesized in the amino-to-carboxyl direction
+mRNA
+A U G G U G G C U A A G C G G U G A
+Methionine Valine Alanine Lisine Arginine Stop
+5’ 3’
+Amino group
+Carboxyl group
+Amino group
+Carboxyl
+
+⸻
+
+tRNA
+
+a.a.
+Translation = the process of protein biosynthesis
+• anticodon - portion of the tRNA that base pairs with the codon
+C G I
+3’ 5’
+G C C
+5’ 3’
+Codon
+• codon - three coding bases on the mRNA template
+• transfer RNA (tRNA) - function as adaptor molecules between a codon and
+an amino acid (a.a.)
+Anticodon
+mRNA
+The basics of protein biosynthesis are the same across all kingdoms of life:
+The correct protein biosynthesis requires an accurate recognition of codons by anticodons
+
+-----
+
+General characteristics of Transfer RNA (tRNA) molecules
+
+• Each tRNA is a single chain containing between 73 and 93 nucleotides.
+• The secondary structure resembles a cloverleaf
+(~50% of the nucleotides are base-paired)
+Five groups of bases are not base-paired, but participate in
+hydrogen-bonding interactions:
+	•	3′ CCA terminal region (acceptor stem)
+	•	TψC loop
+	•	“extra arm”
+	•	anticodon loop
+	•	DHU loop
+• The three-dimensional structure is L-shaped
+• tRNAs contain 7 to 15 unusual bases
+	•	methylated or demethylated derivatives
+of A, U, C, and G
+
+⸻
+
+• At the 3’ end, an activated amino acid is attached to a hydroxyl group of
+adenosine in the CCA region of the acceptor stem
+	•	the CCA region has the ability to change its conformation during protein synthesis
+• The anticodon loop is near the center of the sequence
+General characteristics of tRNA molecules
+
+⸻
+
+Genetic code
+
+C G I
+3’ 5’
+G C C
+5’ 3’
+Codon
+Anticodon
+mRNA
+• Genetic code: the relation between the sequence of bases in DNA
+and the sequence of amino acids in proteins
+mRNA
+A U G G U G G C U A A G C G G U G A
+Methionine Valine Alanine Lysine Arginine Stop
+5’ 3’
+DNA
+PROTEIN
+
+⸻
+
+Amino acids are encoded by groups of three bases starting from a fixed point
+
+• Features of the Genetic code:
+– three nucleotides (codon) encode an amino acid
+– has directionality
+– nonoverlapping
+– has no punctuation
+– is degenerate (most amino acids are encoded by more
+than one codon)
+mRNA
+A U G G U G G C U A A G C G G U G A
+Methionine Valine Alanine Lysine Arginine Stop
+5’ 3’
+• 61 codons encode specify amino acids (20 in total)
+• 3 codons are stop codons that designate termination
+of translation.
+
+⸻
+
+’Wobble’ effect in base-pairing
+
+’Wobble’ effect: Some tRNA molecules can recognize more than one codon
+tRNA a.a.
+1
+C G I
+3’ 5’
+G C C
+5’ 3’
+Codon
+Anticodon
+mRNA
+tRNA a.a.
+1
+C G I
+3’ 5’
+G C A
+5’ 3’
+Codon
+Anticodon
+mRNA
+
+⸻
+
+’Wobble’ effect in base-pairing
+
+Anticodons base-pair with codons
+’Wobble’ effect: Some tRNA molecules can recognize more than one codon
+Codons that differ in either of their first two bases (from 5’) must be recognized by different tRNAs.
+The first base of the anticodon (5’) determines the degree of wobble
+• The redundancy, or degeneracy, of the genetic code indicates that recognition of
+the third base of a codon is sometimes less discriminating than the other two
+“wobble” = steric freedom in the pairing of the first base of the anticodon with the third base of the codon
+
+⸻
+
+’Wobble’ effect in base-pairing
+
+“wobble hypothesis”: established hypothesis that predicts the binding of anticodons to codons
+TABLE 30.2 Allowed pairings at the third base of the
+codon according to the wobble hypothesis
+Anticodons base-pair with codons
+C
+C
+G
+
+⸻
+
+’Wobble’ effect in base-pairing
+
+“wobble hypothesis”: established hypothesis that predicts the binding of anticodons to codons
+TABLE 30.2 Allowed pairings at the third base of the
+codon according to the wobble hypothesis
+C
+U
+A/
+G
+
+⸻
+
+’Wobble’ effect in base-pairing
+
+“wobble hypothesis”: established hypothesis that predicts the binding of anticodons to codons
+TABLE 30.2 Allowed pairings at the third base of the codon
+Example: If first base of the anticodon is inosine, the
+anticodon can recognize three different codons
+Inosine is formed by the deamination of adenosine
+	•	has a heterocyclic nitrogen base that can form
+hydrogen bonds with adenine, cytosine and uracil
+The purine base inosine pairs with cytidine, uridine or adenosine
+
+⸻
+
+Amino acids required for protein biosynthesis must first be attached to specific tRNA molecules
+
+• The attachment of a given amino acid to a particular tRNA establishes the genetic code
+Aminoacyl-tRNA synthetases
+Aminoacyl-tRNA synthetases attach specific amino acids to tRNAs
+tRNA
+amino acid
+Aminoacyl-tRNA
+amino
+	•	acid
+
+⸻
+
+Ester linkages couple amino acids to tRNA
+
+The process of attaching an amino acid to tRNA is called aminosylation
+CCA arm of tRNA
+	•	Amino acids are bound to the 3’end of the tRNA via an ester bond
+between the carboxyl group on the amino acid and either the 2’ or 3’
+hydroxyl group of the terminal adenosine of the tRNA
+3’
+Aminoacyl-tRNA: Amino acid bound to tRNA
+3’
+
+⸻
+
+Each aminoacyl-tRNA synthetase is specific for a given amino acid
+
+How aminoacyl-tRNA synthetases evolve to differentiate between different amino acids?
+A closer look at the amino acid threonine, valine and serine
+
+⸻
+
+Threonyl-tRNA Synthetase contains an activation site
+
+Each aminoacyl-tRNA synthetase is specific for a given amino acid
+How aminoacyl-tRNA synthetases evolve to differentiate Threonine, Valine and Serine?
+Activation site
+responsible for activating threonine by binding it
+to adenosine triphospate (ATP) and further
+transfer of these amino acid to the tRNA molecule
+• Aminoacyl-tRNA synthetases have highly
+discriminating amino acid activation sites
+
+⸻
+
+Each aminoacyl-tRNA synthetase is specific for a given amino acid
+
+• To avoid coupling to the incorrect amino acid, threonyl-tRNA synthetase (tRNAThr)
+contains a zinc ion at the active site that binds to the amino and hydroxyl groups
+of threonine
+• Valine is similar in overall structure to threonine but
+lacks the hydroxyl group, so it does not bind to tRNAThr
+• Serine is occasionally linked to tRNAThr because
+of the presence of the hydroxyl group
+(Thr)
+(Val)
+(Ser)
+How aminoacyl-tRNA synthetases evolve to differentiate Threonine, Valine and Serine?
+
+⸻
+
+Threonyl-tRNA Synthetase contains an activation site and an editing site
+
+Activation site
+responsible for activating threonine by binding it
+to adenosine triphospate (ATP) and further
+transfer of these amino acid to the tRNA molecule
+Editing site:
+acts as a profreader and removes any incorrect
+bound amino acid from the tRNA molecule
+
+⸻
+
+Proofreading by Aminoacyl-tRNA Synthetases Increases the Fidelity of Protein Biosynthesis
+
+• Threonyl-tRNA synthetase has an editing site that hydrolyzes Serine if this
+is linked to threonine-tRNA
+	•	Because Thr contains an extra methyl group, it is sterically excluded
+from the editing site
+	•	The aminoacylated CCA arm of the tRNA is flexible and can swing out
+of the activation site and into the editing site to remove Ser
+• Most aminoacyl-tRNA synthetases contain editing sites and
+activation sites to ensure very high fidelity.
+Threonyl-tRNA synthetase Thr-tRNA
+
+⸻
+
+Aminoacyl-tRNA synthetases interaction with tRNA
+
+Threonine-tRNA synthetase
+tRNA
+• Threonine-tRNA synthetases bind to both the acceptor stem
+and the anticodon loop of the tRNA
+Aminoacyl-tRNA synthetases assign a particular amino acid to a specific tRNA - the true translators of the genetic
+code
+• Some synthetases recognize their tRNA partners primarily on
+the basis of their anticodons
+• Synthetases may also recognize other
+aspects of tRNA structure that vary among
+different tRNAs
+	•	many of the recognition sites are loops rich in
+unusual bases
+Number of interactions between tRNA
+and aminoacyl-tRNA synsthetases
+
+⸻
+
+The ribosome is the site of protein synthesis
+
+Ribosomes coordinate the interplay of aminoacyl-tRNAs, mRNA, and proteins
+aminoacyl-tRNAs
+
+⸻
+
+The E. coli ribosome has a sedimentation coefficient of 70S
+
+composed of:
+	•	large (50S) subunit
+	•	small (30S) subunit
+34 proteins (L1–L34)
+23S rRNA
+5S rRNA
+21 proteins (S1–S21)
+16S rRNA
+• Two-thirds of the mass of ribosomes is RNA
+• Ribosomal RNA (rRNA) is the catalyst for protein synthesis
+
+⸻
+
+The ribosome has three binding sites for transfer RNAs
+
+• Three tRNA-binding sites:
+	•	A site (aminoacyl)
+	•	P site (peptidyl)
+	•	E site (exit)
+• mRNA fragment is bound within the 30S subunit
+• Each tRNA contacts both 30S and 50S subunits
+
+⸻
+
+Overview of mechanism of protein biosynthesis
+
+Initiation, Elongation, Translocation and Termination
+Initiation
+
+⸻
+
+Initiation of translation
+
+• Each initiator region usually displays:
+	•	start codon: AUG (Met) or sometimes GUG, rarely UUG
+	•	purine-rich sequence ~10 nt upstream
+• Bacterial mRNAs often encode several polypeptides
+• Shine–Dalgarno sequence = purine-rich region binding rRNA to position initiator codon in P site
+
+⸻
+
+Bacterial protein synthesis is initiated by N-formylmethionyl-transfer RNA
+
+Steps:
+	1.	Met linked to tRNAfMet by aminoacyl-tRNA synthetase
+	2.	Met amino group is formylated
+	3.	fMet-tRNAfMet placed in P site
+(note: tRNAMet inserts internal Met)
+
+⸻
+
+Initiation factors (IF1, IF2, IF3)
+	1.	IF1 + IF3 bind 30S to prevent premature binding to 50S
+	2.	IF2(GTP) + fMet-tRNAfMet + mRNA bind to 30S → 30S initiation complex
+	3.	Structural changes release IF1 + IF3
+	4.	IF2 stimulates 50S binding + GTP hydrolysis → 70S initiation complex
+Streptomycin binds 30S and blocks fMet-tRNAfMet binding (bacteria)
+
+⸻
+
+Elongation
+
+Elongation factors deliver aminoacyl-tRNAs to the ribosome
+
+⸻
+
+Elongation factors deliver aminoacyl-tRNAs
+
+Steps:
+	1.	EF-Tu-GTP binds aminoacyl-tRNA → delivers to A site
+	2.	Correct codon recognition → GTP hydrolysis → EF-Tu-GDP leaves
+	3.	EF-Ts binds EF-Tu-GDP
+	4.	EF-Ts releases GDP → GTP binds → EF-Tu-GTP regenerated
+Tetracycline binds 30S → blocks aminoacyl-tRNA binding
+
+⸻
+
+Elongation – peptidyl transferase
+
+• Amino group of A-site tRNA attacks carbonyl of P-site peptidyl-tRNA
+• Peptidyl transferase center on 50S catalyzes peptide bond formation
+• Reaction is thermodynamically spontaneous but accelerated by ribosome positioning/orientation
+
+⸻
+
+Translocation
+
+Translocation repositions tRNAs and mRNA
+EF-G (translocase) catalyzes 1-codon movement (requires GTP)
+	1.	EF-G-GTP binds near A site
+	2.	GTP hydrolysis → conformational change → peptidyl-tRNA shifts A→P
+After peptide bond formation: chain is in P site (50S), anticodon still in A site (30S)
+
+⸻
+
+Termination
+
+Release factors (RFs):
+• RF1 + RF2 recognize stop codons (UAA, UGA, UAG)
+• RF3 (GTPase) removes RF1/RF2
+RF1/RF2 bind stop codon in A site
+RFs contain conserved GGQ motif with methylated Gln → promotes hydrolysis of ester linkage → releases polypeptide
+
+⸻
+
+Bacteria: transcription and translation are coupled
+
+Minimal time gap between transcription and translation
+Polysome: multiple ribosomes translating one mRNA simultaneously
+
+⸻
+
+Difference between bacterial and eukaryotic protein biosynthesis
+
+Bacteria 70S: 50S+30S
+Eukaryotes 80S: 60S+40S
+Initiation differences:
+• Initiating amino acid = Met (not fMet)
+• No Shine–Dalgarno
+• Start site usually first AUG from 5’ end
+• Many more eIFs
+Eukaryotic mRNA circularization: 5’-cap proteins + PABP at 3’-poly(A) interact → circular mRNA
+
+⸻
+
+TABLE 30.4 Antibiotic inhibitors of protein biosynthesis
+
+Streptomycin/aminoglycosides — inhibit initiation + misreading (bacteria)
+Tetracycline — blocks aminoacyl-tRNA binding (30S)
+Chloramphenicol — inhibits peptidyl transferase (50S)
+Cycloheximide — inhibits translocation (eukaryotes)
+Erythromycin — blocks translocation (50S)
+Puromycin — premature termination (aa-tRNA analog)
+
+⸻
+
+Diphtheria toxin
+
+Blocks protein biosynthesis in eukaryotes by inhibiting translocation
+
+⸻
+
+Concepts
+
+DNA
+RNA
+Protein
+Translation
+Transcription
+Messenger RNA (mRNA)
+Initiation factors
+Elongation factors
+Release factors
+Aminoacyl tRNA synthetases
+Transfer RNA (tRNA)
+Ribosome (ribosomal RNA + proteins)
+EF1 EF2 EF3
+EF-Tu EF-Ts EF-G
+RF1 RF2 RF3
+• Genetic code
+• Degeneracy
+• Codon
+• Anticodon
+• Transfer RNA
+• ’Wobble’ effect
+• Aminoacyl-tRNA synthetases
+• Aminoacyl-tRNA
+• Aminosylation
+• Aminoacyl-tRNA synthetases activation site
+• Aminoacyl-tRNA synthetases editing site
+• Ribosome
+• Ribosomal RNA
+• Ribosome E site, P site and A site
+• Shine-Dalgarno sequence
+• Initiation, elongation, translocation, termination
+• Initiation factors
+• Elongation factors
+• Termination factors
+• Polysome
+• Inhibition of trancription

content/Biokemi/Cellulära processer/Translation/Stoff.md

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+```
+mRNA kodas i 5'-till-3'-riktning ett kodon i taget
+Proteinet är syntetiserat från amino- till karboxyl-riktning
+tRNA är en adaptormolekyl mellan kodonet och aminosyran
+antikodonet parar med kodonet och är komplementar, innehåller samma information bakvänt
+För att kunna syntetisera protein måste kodonet läsas av korrekt av antikodonen
+tRNA är en kedja som innehåller mellan 73 och 93 nukleotider
+tRNA innehåller 7 till 15 ovanliga baser, metylerade eller demetylerade derivat
+Sekundärstruktuern av tRNA ser ut som ett klöverlöv
+Fem grupper av bases i tRNA är inte basparade men deltar i vätebindingar
+tRNAs sätter fast aminosyror i 3 CCA-terminalaregionen som också heter acceptor stem
+tRNAs 3' ände har först en adenosine med en hydroxylgrupp som sitter fast med aminosyran
+tRNAs 3D-struktur ser ut som ett L
+tRNAs antikodonloop sitter i mitten av sekvensen
+Genetiska koden är relationen mellan basparen i DNA och sekvensen av aminosyror i proteiner
+Genetiska koden karakteriseras av: 3 nukleotider (kodon), går i en riktning, överlappar inte, ingen punktuation
+Den genetiska koden är degenererad: flera kodon kodar för samma aminosyra, vilket minskar effekten av vanliga mutationer
+Det finns 3 kodon sekvenser som terminerar translationen (UAA, UAG, UGA)
+61 kodon kodar för 20 aminosyror
+Vissa tRNA-molekyler kan känna igen fler än ett kodon, det heter Wobble-effekten 
+Den tredje nukleotiden i ett kodon kan ’svaja’ lite, den har större sterisk frihet och behöver inte alltid baspara strikt
+Svajhypotesen förutser vilket antikodon som kan binda till ett visst kodon
+Inosin bildas genom deaminering av adenosin och kan bilda vätebindningar med adenin, cytosin och uracil
+Aminoacyl-tRNA-syntetaser kopplar specifika aminosyror till tRNA
+När man kopplar en aminosyra till tRNA heter det aminoacylisering
+Aminosyror kopplar till 2' eller 3'-hydroxylgruppen på det terminala adenosin i tRNA
+Varje aminosyra har ett specifikt enzym (aminoacyl-tRNA-syntetas), som katalyserar kopplingen av just den aminosyran till rätt tRNA-molekyl.
+Aminoacyl-tRNA-syntetas har en redigeringsplats som korrekturläser och tar bort felaktigt bundna aminosyror
+Aminoacyl-tRNA-syntetas har en aktiveringsplats som aktiverar rätt aminosyra genom att binda den till ATP innan den förs över till tRNA.
+Aktiveringsplatsen försöker välja rätt aminosyra, och redigeringsplatsen fångar upp och tar bort de små fel som ändå passerar vilket ger mycket hög noggrannhet.
+
+```