Who is Archibald Garrod?
- British physician who was the first to suggest a relationship between genes and the production of proteins.
- Studied patients with Alkaptonuria.
What did George Beadle and Edward Tatum discover?
They concluded a single gene controlled the synthesis of a single gene, by studying mutated fungi.
Polypeptides denote _____.
Proteins denote _____.
What is a Codon?
Groups of three nucleotides on mRNA that code for a particular amino acid.
What is an anticodon?
Found on tRNA and recognizes/corresponds to codon on mRNA.
What are the three stop codons?
The translation chart corresponds with the _____ sequence to find the corresponding amino acid.
How does the term degenerate apply to the genetic code?
The number of possible codon combinations (64) exceeds the number of possible amino acids (20).
What is a Synonymous codons?
One codon can specify for the same amino acid.
What is a codon family?
Synonymous codons comprise a family.
What is a degenerate (wobble) base?
- Third base in the codon.
- First base in the anticodon.
Why is mtDNA have a slightly different genetic code than that of the universal code?
Due to the endosymbiotic theory.
What defines the reading frame?
The start codon (AUG) of mRNA.
What is an indel?
- It is a shift in the reading frame that alters the amino acid sequence, which creates a different polypeptide.
- Can be a deletion of insertion.
What are the two ends of a polypeptide?
- Amino terminus ( N-terminus) end
- Carboxyl terminal (C-terminus) end
Describe the primary structure of proteins.
Sequence of a chain of amino acids.
Describe the secondary structure of a protein.
- Occurs when the sequence of amino acids are linked by hydrogen bonds.
- Alpha helix
- Pleated sheet
Describe the tertiary structure of proteins.
Occurs when certain attractions are present between alpha helices and pleated sheets.
Describe Quaternary structure of proteins.
Is a protein consisting of more than one amino acid chain.
What are the purposes of proteins in the cell?
- Cell shape and organization. (cytoskeleton)
- Transport (Hemoglobin)
- Movement (Myosin in muscle)
- Cell Signaling (receptors on cell surface)
How are tRNA molecules named?
- By the amino acid that they carry.
What are the common features of tRNA?
- Three stem loops due to the complementary hydrogen bonding.
- Few variable sites that are not consistent with all tRNA.
- Has an acceptor stem with a 3' single stranded region that has a CCA.
- Anticodon is located in the second stem loop.
- 75 nucleotides long.
What enzyme catalyzes the attachment of amino acids to tRNA?
Describe the process of charging of tRNA.
- First step : Synthetase recognizes a specific amino acid and also ATP. ATP becomes hydolyzed and AMP attaches to the amino acid; pyrophosopate is released.
- Second step : The correct tRNA binds to the synthetase. The amino acid attahces covalently to the 3' endo of tRNA molecule at the acceptor stem, and AMP is released.
- Third Step: Charged amino acid is released from the enzyme.
What is the error frequenct of charging tRNA?
1 in 100k
How many different types of aminoacyl-tRNA synthetases are there?
Describe the wobble hypothesis.
- THe first two positions of codon adhere strictly to the AU/GC rule.
- The third position can tolerate certain mismatches. The first position of the anti-codon can move slightly so that H bonding can occur between mismatched codon and anticodon.
What are Isoacceptors?
- Two or more tRNAs that are able to recognize the same codon.
- One tRNA that recognizes two or more codon.
What is an Inosine?
- A base attached to a sugar.
- This gives additional flexibility to tRNA bases.
How much of a bacterial cell's mass is made up by ribosomes?
Where are ribosomes found in in eukaryotic cells?
Describe the structure of a ribosome.
- Composed of a large and small subunit. Each of which are an assembly of many different proteins and rRNA.
- Overall shape result of rRNA since it constitutes most of the mass.
- The interface between the small and large units are primarily composed of rRNA.
- Proteins cluster on the outer surface of the ribosome and on the periphery of the interface.
Describe the bacterial ribosome 70S.
- Small subunit : 30S. 21 different proteins & 16S rRNA.
- Large subunit : 50S. 43 different proteins, 23S rRNA, 5S rRNA.
Describe the Eukaryotic ribosome 80S.
- Large subunit : 60S. 28S rRNA, 5.8S rRNA, 5S rRNA, & 49 ribosomal proteins.
- Small subunit : 40S. 18S rRNA & 33 ribosomal proteins.
What are the tRNA binding sites?
- Peptidyl site (P site)
- Aminoacyl site (A site)
- Exit site (E site)
Give an overview of translation.
- Initiation : mRNA, initiator tRNA (bound to a start codon) and ribosomal subunits assemble.
- Elongation : Ribosomes slides alone mRNA in the 5' to 3' direction moving over the codons sequentially linking amino acids brought in by the tRNA.
- Termination : Stop codon signals the termination of translation at which time the polypeptides is released and ribosomal complex dissasembles.
What is tRNAfmet?
- Initiator tRNA.
- A formyl group (-CHO) is attached to the nitrogen atom in methionine after it has been attached to the tRNA.
What is the shine-dalgarno sequence?
- A sequence within the bacterial mRNA that promotes hydrogen bonding of mRNA to the 30S subunit (small subunit).
- It is complementary to a short sequence within the 16S rRNA.
For mRNA, tRNAfmet, and ribosomal subunits to associate into an initiation complex, what three initiation factors are required?
What is the function of IF1?
It seperates and prevents premature binding of 30S and 50S subunits.
What is the function of IF2?
Binds fmet-tRNA to 30S & binds to GTP.
What is the function of IF3?
Binds 30S to mRNA
In eukaryotic initiation the initiator carries what?
What binds directly to tRNAmet prior to recruitment of the 40S subunit?
How are eukaryotic mRNAs recognized by the ribosome?
- Cap-binding protein 1 (CBP1) binds to the 7-methylguanosine cap on mRNA and recruits other initiation factrs.
- Collectively these initiation factors unwind any secondary structures in mRNA and promote binding to a ribosome.
What does Kozak's rule state?
- -3 from start codon needs to be A/G
- +4 needs to be a G
Does translation in eukaryotes always start when the ribsome meets the first AUG?
- The sequence of nucleotides around the AUG codon plays an important role as to wether it will function as a start codon.
When the start codon is recognized in eukaryotes, the _____ assembles with the aid of _____ and the elongation process begins.
What is the rate of Amino acid addition in translation in both bacteria and eukayotes?
- 15-18 AA per second in bacteria
- 6 AA per second in eukaryotes
What is hydrolyzed for energy during the elongation portion of translation in eukaryotes?
What are nonsense codons?
Nonsense codons anre not recognized by tRNA with complementary sequences, istead the are recognized by what?
Proteins known as release factors which mimic the structure of tRNA.
How many release factors are needed in bacteria?
How many release factors are needed in eukaryotes?
Describe the final step in translation.
- Disassembly of mRNA, ribosomal subunits, and the release factors.
- Release factor binds to the A site.
- The bond between the polypeptide and tRNA is hydrolyzed releasing it from the ribosome.