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Chapter 13 notes
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2066925-19050Chapter 13: Translation
genes encode the information/production of proteins for building polypeptides which affects the phenotype
mutations lead to defects in genotype affects phenotype
Protien Synthesis
proteins give a cell (1) structure and (2) function
Structural Genes: Genes that encode polypeptides and are transcribed into messenger RNA (mRNA)
Genetic Code:
the nucleotide language of mRNA is translated into the amino acid language of proteins
right3848100Genetic information in mRNA has three nucleotides known as codons
Start codon: AUG
Start codon: first codon that ribosome reads to start translating
Stop Codons (nonsense codons): UAA, UAG, UGA
There are 20 different amino acids to build a polypeptide (each codon is responsible for a particular amino acid)
2 nucleotides = 4^2 = 16 (not enough)
3 nucleotides = 4^3 = 64 codons
Use more than one codon to specify amino acid
Genetic Code is DEGENERATE: multiple ways to encode the same information as different codons mean the same amino acid
For example: GGU, GGC, GGA and GGG all code for lysine
right6334125In most instances, the third base is the degenerate base: WOBBLE BASE
tRNA binds tightly to the first 2 base pairs – the third position is wobbly
In the codon-anticodon recognition process, the first two positions pair strictly according to the A – U /G – C rule
However, the third position can actually “wobble” or move a bit, tolerating certain types of mismatches and allowing multiple codons to be recognized by the same tRNA
Prokaryote:
5’ AUG……UAA 3’ (coding region – translated)
Eukaroyte:
5’ (Guanosine Cap) AUG….UAA (Poly A tail) 3’ (coding region – translated)
5057775-85725tRNA has the ability to recognize which amino acid goes with which codon
Ribosome builds the polypeptide chain (has directionality 5’ 3’)
5’ NON-template 3’
3’ Template strand5’
5’ mRNA strand 3’ codons
3’ Anti Codon 5’ anti codons that specifies amino acid
Amino Acids:
20 amino acids and each one contains a different side chain (R)
Side chain determines how protein gets folded
Types:
(1) Nonpolar Amino Acids (Hydrophobic)
They are often buried within the interior of a folded protein
Some nonpolar amino acids can be found on the surface; however, they must be protected for a while (chaperone proteins)
(2) Polar/Charged Amino Acids (Hydrophilic)
Usually found on the surface of the protein
Lysine & Arginine = positive/polar charged
27908251371600Polypeptide synthesis has a directionality that parallels the 5’ to 3’ orientation of mRNA (N-terminus C-terminus)
During each cycle of elongation, a peptide bond is formed between the last amino acid in the polypeptide chain and the amino acid being added
POLYPEPTIDE BOND:::
28575004210050Condensation reaction: Carboxyl group removes the charged O- and the Amino group loses 2 hydrogen’s to yield a water
H3N+ Amino terminus (N-terminus) 5’ end of mRNA
CO-2 Carboxyl Terminus (C-terminus) (new amino acids get added to the Carboxyl terminus) 3’end of mRNA
49911006438900Protiens :
There are four levels of structures in proteins
1. Primary - amino acid sequence
2. Secondary – structures within a polypeptide formed by interactions between the atoms that make the peptide bond
Alpha (?) Helices: carbonyl and amino group line up
Beta (?) Helices
Held together by HYDROGEN/PEPTIDE bonds
Side chains influence whether goes into Alpha or Beta Sheet
Ex) PROLINE will stop the formation of an alpha helix due to large side chains
3. Tertiary – 3D structure of the polypeptide (mixture of Beta and Alpha Helices)
Hydrogen bonds – help stabilize
Ionic bonds
Disulfide bond/bridge
Van Der Waals Interactions (every atom with have a neg/pos charge at any given time)
34099502209800Hydrophobic interactions – getting hydrophilic side chains in the middle of the protein (disrupts fever water molecules)
-24765024098254. Quaternary – 2+ polypeptide interactions
Homodimer 2 of the same polypeptides
Heterodimers 2 different polypeptides
Dimer 2 polypeptides
Tridimer three polypeptides
Tetradimer 4 polypeptides
37623756200775Sorting signals direct a protein to its correct location
Each sorting signal is recognized by a specific cellular component, often a protein, that facilitates the sorting of the protein to its correct compartment (Must have a signal within sequence that allows them to be sent to the right place)
Sorting is more complicated in eukaryotes than in bacteria since eukaryotes are compartmentalized into organelles
Ex) a protein destined for the nucleus will be sent there directily from the cytoplasm via a signal
4029075-419100Recognition Between tRNA and mRN
During mRNA-tRNA recognition, the anticodon in tRNA binds to a complementary codon in mRNA
tRNA shape:
3’ end – amino acid attach
All have clover-like shapes
Intermolecular hydrogen bonds
Modifications to make tRNA unique (pick up correct amino acid!) creates a different shape
Charging of tRNAs
The enzymes that attach amino acids to tRNAs are known as aminoacyl-tRNA synthetases
There are 20 types, one for each amino acid
500 genes but only 48 different tRNA – duplication is present to increase levels of a particular protein
Very low error rate
Sequences throughout tRNA – better at recognizing where aminoacyl-tRNA synthetases should bind to
Aminoacyl-tRNA synthetases catalyze a two-step reaction involving three different molecules
Amino acid, tRNA and ATP
(1) aminoacyl-tRNA synthetases recognizes only one amino acid
(2) binds an ATP to amino acid and creates AMP – Amino Acid
(3) Bring in tRNA – breaks bond between AMP – amino acid to attach
39243004095750 Bacteria Translation:
Bacteria contain one type of ribosome found in their cytoplasm
Synthesis and assembly of all ribosome components occurs in the cytoplasm
During bacterial translation, the mRNA lies on the surface of the 30S subunit
As a polypeptide is being synthesized, it exits through a hole within the 50S subunit
Has a 30S and 50S subunit
Ribosomes contain three discrete sites
Peptidyl site (P site) – contains polypeptide chain
Aminoacyl site (A site) – next amino acid enters the ribosome
Exit site (E site) – exit/empty tRNA exits ribosome from E site
*base pairing allows codons to attach to ribosome by hydrogen bonding
28956007000875Initiation in Bacteria
The binding of mRNA to the 30S subunit is facilitated by a
Shine-Dalgaro Sequence
9 base pair sequence – used to place the AUG in the P site of the prokaryotic ribosome
Start codon – starts in p site to initiate translation
Fmet – modified version use to initiate synthesis (does not get added to polypeptide chain)
IF3 (initiation factor 3)
Brings in IF2
Promotes the binding of the initiator tRNA fmet
IF2 and IF3 get released and 50S subunit associates with the 30S subunit
tRNA fmet is the only charged tRNA that enters through the P site – all others enter through the A site
Elongation in Bacteria
tRNA enters from the A site and polypeptide chain moves to the P site until the empty tRNA gets released at the E site
38576252124075Decoding Function of the Ribosome: 16S rRNA (a part of the 30S ribosomal subunit) plays a key role in codon-anticodon recognition
It can detect an incorrect tRNA bound at the A site
It will prevent elongation until the mispaired tRNA is released
Translation Termination in Bacteria
The final stage occurs when a stop codon is reached in the mRNA
These codons are not recognized by tRNAs, but by proteins called release factors
Release factors mimics the structure of the tRNA so that it can fit into the A site
A stop codon causes release factor to base pair with the mRNA. This will detach the finished polypeptide from the last tRNA and allow it to dissociate from the ribosome. Translation stops.
Bacteria have three release factors
RF1, which recognizes UAA and UAG
RF2, which recognizes UAA and UGA
RF3, which does not recognize any of the three codons
It binds GTP and helps facilitate the termination process
Ex) Hit UAA codon and recognized by release factor
Release factor binds and catalyzes release of peptide. Kicks out the tRNA present at the A site. Whole thing falls apart/dissociates
mRNA & ribosomal subunits are used by diff ribosome
Bacterial Translation Can Begin Before Transcription Is Completed
Bacteria lack a nucleus
Therefore, both transcription and translation occur in the cytoplasm
As soon an mRNA strand is long enough, a ribosome will attach to its 5’ end
COUPLING: translation begins before transcription ends
A polyribosome or polysome is an mRNA transcript that has many bound ribosomes in the act of translation
Translation in Eukaryotes:
Eukaryotic cells have two types of ribosomes:
One type is found in the cytoplasm (either free or bound to the ER)
The other is found in organelles (mitochondria or chloroplasts)
Transcription occurs in the nucleus and is released into the cytoplasm for translation
Eukaryotic Ribsomes: Small (40S) and large (60S) ribosomes (assembled in nucleolus and then transported to the cytoplasm)
Polyribosome: multiple ribosomes translating at the same time. Ribosome scans until AUG. Small ribosome sticks & sticks tRNA into P site.
Initiation in Eukaryotes:
Translation in eukaryotes is similar to that in prokaryotes
38100003057525Eukaryotes have G’Cap ------ PolyA tail (without cap/tail – translation can not occur)
Major differences occur during translational initiation:
the assembly of the initiation complex is similar to that in bacteria, but additional factors are required
The initiator tRNA carries a methionine rather than a formylmethionine
The start codon for eukaryotic translation is AUG (enters into the P site)
It is usually the first AUG after the 5’ Cap
5’cap must be present or translation will not occur
The 5’ cap attracts binding proteins of tRNA (methionine)
Poly A tail – more poly A binding is increased levels of translation
Some initiation factors associate with polyA binding proteins at the polyA tail
Proteins at the polyA tail help to stimulate the binding of initiation factors
PolyA tail is protected by proteins that are attracted to initiation factors that are attracted to the cap. More initiation factors lead to happier cap proteins which results in increased protein translated
*Interaction between 5’ and 3’. Initiation factors that bind to the cap are from polyA binding protein happier cap proteins more efficient proteins.
Overall Summary of Initiation:
A number of initiation factors bind to the 5’ cap in mRNA
These are joined by a complex consisting of the 40S subunit, tRNAmet, and other initiation factors
The entire assembly moves along the mRNA scanning for the right start codon
Once it finds this AUG, the 40S subunit binds to it
The 60S subunit joins
This forms the 80S initiation complex
Termination in Eukaryotes:
Eukaryotes only have one release factor
eRF, which recognizes all three stop codons
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