Last Two Classes

Question 1

Alternative Splicing

Answer 1

Making different polypeptide chains based on the same gene, through the use of different spliceasomes

Question 2

Template Strand

Answer 2

Strand which is transcribed during transcription from DNA into mRNA. Its complimentary strand is the coding strand

Question 3

Coding Strand

Answer 3

Strand which is not directly used during transcription, but is an analog of the transcribed mRNA, with the exception of the Urasils on the RNA being Thymines on the coding strand.

Question 4

Translation Process

Answer 4

• Transcription Factor binds to TATA box (promoter region)
• RNA Polymerase II binds to it to for the initiation complex
• RNA Polymerase II polymerizes an RNA strand by going from the 3’ to 5’ of the DNA template strand, and elongating the RNA from 5’ to 3’ (no primer needed)
• The whole DNA strand which is getting transcribed is the transcription unit
• Eukaryote Only: 5’ Guanine Cap and 3’ Adenine Tail get added to the RNA to protect it from degradation, and allow it to bind more easily to the ribosome
• RNA gets spliced by spliceasomes formed from multiple snRNPs binding together to form a complex. Introns get pinched off the strand, and Exons stay on the strand.

Question 5

mRNA code

Answer 5

• Triplet codes
• Codons are read from 5’ to 3’
• AUG, coding for Methionine, acts as the start of the protein on the strand
• Code keeps going until a Stop Codon

Question 6

Translation Process

Answer 6

• Ribosome (rRNA and proteins) binds to tRNA for methionine at A site
• Ribosome scans mRNA from 5’ to 3’ until AUG
• Large subunit attaches
• Met is moved from A to P site, and tRNA for next triplet complimentary pairs to RNA on A site
• Peptide bond is formed
• tRNAs are shifted, and the one previously on the P position leaves when reaching the E position
• Keep going until Stop codon
• Post-translational modifications
• Chain binds to RER

Question 7

Post-translational modifications

Answer 7

• Chaperonins to help folding
• Remove certain amino acids (Methionine)
• Cleave into different chains
• Synthesize into a bigger chain

Question 8

Types of Mutations

Answer 8

Silent mutations
Missense mutations - single base pair change
Nonsense mutations - premature stop codon
Frameshift mutations - insertion or deletion

Question 9

Metabolic Control Methods

Answer 9

• Allosteric regulation of enzymes

- Regulate expression of the genes encoding the enzymes

Question 10

Operon Model

Answer 10

Operator - sequence of nucleotides in promoter region or right after, controls acess of RNA poymerase
Promoter=Operator=========Genes=======
Operator, promoter, and the genes which follow are an operon
Regulatory proteins sometimes bind to operator to block RNA polymerase II

Question 11

Repressor Gene

Answer 11

Switch of the operon is operated by a repressor protein. Protein blocks transcription. Activated by a corepressor. Ex. Tryptophan

Question 12

Inducer Gene

Answer 12

By default, is bound to the operon, blocking gene expression. Ex. Lactose

Question 13

Eukaryotic Gene Expression

Answer 13

Chromatin modification:

• Histone acetylation - loosens chromatin and enhances transcription
• DNA methylation - reduces transcription

Question 14

Cell-Cell Recognition

Answer 14

• Membrane-bound surface molecules that interact directly with eachother
  or
• Cell junctions that connect cytoplasms directly

Question 15

Indirect Cell Signaling

Answer 15

Endocrine - long distance, blood stream, horomones
Paracrine - short distance, diffusion
Synaptic - long distance, nerves, neurotransmitters

Question 16

Cell Signaling Overview

Answer 16

Reception - often a ligand, binds to receptor
Transduction - pathway, often a phosphorylation cascade
Response - target cellular response, often turning on/off a gene or activate/inactivate protein

Question 17

GPCR

Answer 17

G-Protein Coupled Receptor

• Transmembrane protein working together with G-Protein in cytoplasm
• When inactive, G-Protein is bound to GDP
• When activated by ligand, G-Protein swaps for a GTP
• then, G-Protein disassociates from receptor and binds to enzyme X, activating it
• G-Protein (eventually) hydrolyses GTP and returns to original state
• enzyme X sometimes produces cAMP, a secondary messenger
• Ca2+ ions can also act as secondary messenger

Question 18

RTKs

Answer 18

• An RTK (Receptor Tyrosine Kinase) exists as a monomer. Is inactive.
• When bound to a ligand, two RTKs join to become a dimer, the active form
• Each tyrosine is phosphorylated, causing other proteins to become activated and trigger signal transduction pathways

Question 19

Receptor Types

Answer 19

Extracellular - for water soluble ligands

Intracellular - for lipid soluble ligands, often leads to gene regulation, as a transcription factor

Question 20

Phosphorylation

Answer 20

Usually done by protein kinases

Often activates proteins

Question 21

Scaffolding Proteins

Answer 21

Helps bind together relay proteins, enhancing speed and accuracy of signal transfer