flashcards

This guide serves to outline the topics covered in class and provide basic information.
It is not intended to be a comprehensive set of notes for every concept that may appear on the exam.

The ribosome consists of two subunits:
- Large Subunit: Composed of multiple different proteins and RNA.
- Small Subunit: Also composed of multiple different proteins and RNA.
tRNA Binding Sites:
- A - Acceptor Site: The site where the first interaction with the codon occurs.
- P - Peptidyl Site: Catalyzes the formation of peptide bonds between amino acids.
- E - Exit Site: The site where tRNA exits the ribosome after delivering its amino acid.

Eukaryotes:
- The small ribosomal subunit binds to the 5’ cap of the mRNA.
- Creates an initiation complex that includes tRNA, mRNA, and the small subunit.
- The large ribosomal subunit then binds to this complex.
Prokaryotes:
- The small ribosomal subunit binds to the Shine-Dalgarno sequence located approximately 10 bases upstream of the start codon.
- Translation begins at the start codon 5’ AUG 3’.

tRNAs occupy the P and A sites of the ribosome:
- The tRNA in the P site bonds an amino acid to the tRNA in the A site.
- The ribosomal reading frame shifts by 3 nucleotides downstream.
- Movement of tRNA:
- The tRNA that was in the P site exits through the E site.
- The tRNA that was at the A site moves to the P site, carrying a growing polypeptide chain.
Directionality: The synthesis of the polypeptide chain happens from the N-terminal to the C-terminal end, and the process occurs in a 5’ to 3’ direction.

A release factor protein binds to the stop codon, which does not have an amino acid corresponding to it.
This signals the release of the entire polypeptide chain, as well as the disassembly of the translation machinery.

Multiple ribosomes can translate the same mRNA simultaneously, which speeds up the translation process.

Folding is driven by interactions among amino acids and their properties:
- Primary Structure: The sequence of amino acids in a polypeptide chain.
- Secondary Structure: Localized folding due to interactions between neighboring amino acids, resulting in structures like alpha helices and beta-pleated sheets.
- Tertiary Structure: Complete 3D folding resulting from interactions between functional groups within the same polypeptide chain.
- Quaternary Structure: Multiple polypeptide chains or subunits interacting, e.g., hemoglobin.

Signal Sequences: These are essential for directing growing polypeptides during translation.
- Signal sequences may be inherent to the original amino acid sequence or added later.
- For example, histone proteins may contain tags that signal their transport to nuclear receptors for cellular entry.

Various post-translational modifications each serve specific functional roles, including:
- Proteolysis: The cleaving of polypeptides.
- Glycosylation: The addition of sugar residues to the polypeptide.
- Phosphorylation: The addition of phosphate groups, which can activate or deactivate proteins.

Mutations: Can occur spontaneously due to:
- Errors during DNA replication.
- Mistakes made during meiosis.
- Accidental chemical reactions.
Mutations can also be induced by environmental factors such as chemicals and radiation.

Mutation in Promoter Sequence: Affects gene expression levels, influencing whether proteins are produced or not.
Mutation in Coding Sequence: Affects the final protein composition.
Silent mutations may not alter phenotype if the changed codon still specifies the same amino acid due to redundancy (e.g., AAC → AAU both code for Asn).
Functional Changes in Proteins:
- Loss of Function: Reduces or abolishes the normal activity of the protein.
- Gain of Function: Results in new or abnormal activity of the protein.
Only mutations occurring in germ cells can be inherited.

Intrachromosomal Rearrangements: Include deletions and inversions within the same chromosome.
Interchromosomal Rearrangements: Include duplications and translocations between different chromosomes.

Question: Which post-translational modification would be used for a protein that is no longer needed but might be required later?
- A) Proteolysis
- B) Transport out of the cell
- C) Glycosylation
- D) Phosphorylation

Question: Horses with a premature stop codon developed proteins that allowed them to bypass the stop codon. What cellular processes were modified and what advantages did it confer?

Question: LARP1 binds directly to the 5′TOP motif and the cap of TOP mRNAs, blocking eIF4E from binding, which represses translation initiation.
- Options regarding LARP1's role and specifics in translation initiation.

Question: How does wobble base pairing function?
Consequence of Transcription Mutations: If the TATAAA box is mutated, transcription cannot initiate due to lack of RNA polymerase binding.
Function and Impact of Proteins: If a mutation affects protein structure or function, the protein may cease to function correctly, which is crucially aligned with its conformation.

Question: If a drug blocks the A site of a ribosome, what would be the immediate effect?
- A) Peptide bond formation would not occur
- B) tRNA would not exit the ribosome
- C) Codon recognition fails
- D) mRNA would degrade

Question: What level of protein structure (primary, secondary, tertiary, quaternary) is affected if a mutation leads AAA to become ACA?