Term
| Describe the basic structure of an amino acid |
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Definition
1. N provides the amino group = basic
2. Carboxyl provides the acid group
-donates the proton to become COO-
3. They are differentiated by the side R group |
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Term
Describe the following types of amino acids
1. Hydrophilic or polar
2. Acidic
3. Basic
4. Hydrophobic or nonpolar |
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Definition
1. O or S
2. COOH (Aspartic Acid[D], Glutamic Acid[E])
3. NH2 (Lysine[K], Arginine[R], Histidine[H])
*L and R make up histone tails
4. only Carbons and hydrogens |
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Term
| How are amino acids linked together? |
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Definition
Peptide bonds
C-OH + H-N = C-N + H20 |
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Term
Describe the structure of proteins
1. Primary
2. Secondary
3. Tertiary
4. Quaternary |
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Definition
1. amino acid sequence
2. spatial interrelationships
-alpha helix and beta sheets
3. overall folding in 3D space
-disulfide bonds (covalent)
-also hydrogen, ionic, van der waals, hydrophobic
4. association of two or more polypeptides |
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Term
| Describe the components of a ribosome |
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Definition
1. 50% protein/50% RNA
2. two subunits
3. 3 types of RNA
-mRNA, tRNA, rRNA
*several ribosomes per mRNA |
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Term
Describe the Prokaryotic Ribosome
1. Large subunit
2. Small subunit |
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Definition
1. 31 ribosomal proteins + 5s rRNA + 23s rRNA = 50s subunit
2. 21 ribosomal proteins + 16s rRNA = 30s subunit
Total = 70s ribosome (20nm)
*all coded for on one gene |
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Term
Describe the Eukaryotic Ribosome
1. Large subunit
2. Small subunit |
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Definition
1. 49 ribosomal proteins + 5s rRNA + 5.8s rRNA + 28s rRNA = 60s subunit
2. 33 ribosomal proteins + 18s rRNA = 40s subunit
Total= 80s ribosome (24nm)
*5.8s, 28s, 18s all on one gene (RNA poly 1)
-5s is on different gene (RNA poly 3) |
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Term
Describe tRNA
1. Discovery
2. Function
3. Enzyme |
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Definition
1. proposed by Francis Crick to be a transfer molecule
2. contains the anticodon sequence that binds to the codon needed and carries the amino acid to the ribosome
-amino acids are bound to 3'OH by the carboxyl group
3. Aminoacyl-tRNA synthetase |
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Term
| Describe how tRNA is the adapter molecule |
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Definition
-Chapeville and von Ehrenstein
-Cysteine was reduced to Alanine by Raney nickel
-all the cysteine were translated as alanine
*proved tRNA was the adapter molecule |
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Term
Describe the following:
1. Start codon
2. Stop codons |
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Definition
1. AUG - methianine
2. UGA, UAG, UAA |
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Term
| What are the 3 terms describing the genetic code? |
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Definition
1. Degenerate - multiple codons per AA
-some mutations don't affect AA sequence
2. Ordered
-some mutations code for similar AA
3. Universal (mostly)
-code is the same across species |
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Term
| Describe the 3 binding sites on the ribosome |
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Definition
1. A (aminoacyl)
-binds the incoming aminoacyl tRNA with the next amino acid
2. P (peptidyl)
-binds the tRNA to which the growing polypeptide is attached
3. E (exit)
-binds the departing uncharged tRNA
-improves accuracy of binding and keeps overall shape |
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Term
Describe the Translation in Prokaryotes
Initiation
1. First complex |
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Definition
1. f-methionyl-tRNAf met serves as initiator tRNA
-same codon as methianine (AUG)
-interacts with IF-2
*f-meth-tRNA f met is a special methionine that starts translation in prokaryotes
*IF-2 is a helper protein |
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Term
Describe Translation in Eukaryotes
Initiation
1. Initiator tRNA
2. Start sequence
3. Kozak's rule
4. CBP |
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Definition
1. special methionine, but not formylated
- tRNA i met
2. no specific sequence on mRNA
-start codon discovered by scanning (40s moves along mRNA)
3. A or G -3 from AUG and G following start helps improve efficiency
4. Cap Binding Protein
-binds to 7-methyl guanosine cap at 5' end
-moves 5-->3 to find first AUG
-once found, initiation factors release and 60s binds |
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Term
Describe the Translation in Prokaryotes
Elongation
1. Binding of tRNA to A site |
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Definition
1. correct tRNA is determined by mRNA sequence in A site
-ribosome also senses correct match
a. strongest bond
b. favors the chemistry of the proper bases
-EF-TU carries GTP is required
-EF Ts regenerate GDPs to GTP |
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Term
Describe the Translation in Prokaryotes
Initiation
3. Shine-Dalgarno |
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Definition
3. AGGAGG near the 5' end UTR of mRNA
-located approximately 7 bases upstream of the AUG
-bases interact with the 3' 16s rRNA in the 30s ribosomal subunit
*enables the mRNA and 16s tRNA to bind properly |
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Term
Describe the Translation in Prokaryotes
Initiation
2. Second complex |
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Definition
2. IF-3 binds with 30s ribosome and mRNA
-IF-1 with GTP binds to IF-3 and IF-2 with tRNA
-50s ribosome comes in and and IF-1,2,3 are released
*IF-3 keeps large subunit away from small unit
*IF-1 carries GTP |
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Term
Describe the Translation in Prokaryotes
Initiation
4. Conclusion |
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Definition
a. IF-3 must leave before 50s enters
b. bind of 50s requires GTP hydrolysis and release of IFs
c. tRNA must be positioned in the P site
*only tRNA that has direct entry to P site |
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Term
Describe the Translation in Prokaryotes
Elongation
2. Transfer of chain from P to A |
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Definition
2. peptide bond is formed between C on AmAc on tRNA in P site and N on tRNA in A site
-facilitated by peptidyl transferase of 23s rRNA in 50s and GTP hydrolysis
*N (head) attacks C (feet) on 3' end of tRNA |
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Term
Describe the Translation in Prokaryotes
Elongation
3. Ribosome Translocation |
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Definition
3. ribosome must move 3 bases toward the 3' end of the mRNA
-requires EF-G and GTP
a. uncharged tRNA in P site occupies E site
b. charged tRNA with growing polypeptide chain occupies P site
c. A site is open for next EF-Tu/GTP/tRNA to bind
*2 GTPs per amino acid
1 for initiation, 1 for elongation |
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Term
Describe the Translation in Prokaryotes
Termination |
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Definition
1. Stop codons: UGA, UAA, UAG
2. Release factors bind to stop codon
-not tRNAs
3. Peptidyl transferase adds H2O to C terminus of P site polypeptide
-dissociates from ribosome
-translation is finished |
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Term
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Definition
(#AA x 2) - 1
300 bases=100 codons=99AA=197 GTPs |
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Term
| Describe the Wobble Hypothesis |
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Definition
-there are less tRNAs than there are codons
-first two bases follow a strict base pairing rule, but the third is less stringent (3' mRNA or 5' tRNA)
1. G can bind to U
2. Inosine is just like a G so it can bind to A, U, C |
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