Final Extra Flashcards

U1

U1

Binds to the 5’ splice site (initial)

U2

Binds to the branch point site and adenosine bulges out

Adenosine in splicing

Attacks 5’ splice site, which catalyzes the 3’OH on 5’ to attack the 3’ splice site.

Nuclear pore complex

Saves unimpaired mRNA from their default fate of degradation. Moves mRNA into cytoplasm away from exonuclease.

Pre-mRNA

Has RNA pol, guanyl transferase, poly(A) polymerase, and U1 snRNP.

Larger rRNAs

Made up by RNA pol 1

Catalyzes bond between amino acids

Smaller rRNAs

Made by RNA pol 3

Interacts with anticodon

Pre-rRNA

methylated, cleaved. Modified (isomerization) (uridine → pseudouridine)

Wobble base pairing

U → A or G

G → A or C

I → U, A, or C

tRNA

Binded to tryptophan, has a proofreading function.

Amino acid is added to polypeptide c-terminal

Functional domains

Independent, different proteins make same domain, domains can be used in different cells, multiple domains can be made by one protein.

IF1

attaches to mRNA in prokaryotic initiation

IF2

GTP-binding protein and attaches to first amino acid in prokaryotic initiation

IF3

Prevents premature attachment of large subunit

eIF1 / 1A

Binds to mRNA and changes confirmation in eukaryotic initiation

eIF3

Interacts with eIF4G

eIF4E

Binds to 5’ cap in eukaryotic initiation

eIF4A

Helicase properties, uses ATP hydrolysis to unwind ds mRNA in eukaryotic initiation

EF-Tu

Accuracy check of the transcription elongation factors

Binds to codon-anticodon, correct pairing will trigger conformational change.

Transcription factors

A single gene can be regulated by multiple, it can be involved in regulating multiple genes, it’s role differs in different contexts

Enhancer sequences

Studied by GFP, deletion mapping, and reporter gene fusion

Eukaryotes regulate

With positive and negative feedback

Prokaryotes regulate

With tryptophan repressor (binds to operon when tryptophan is present) and Lac operon.

Post-transcriptional regulation

Alternative splicing, editing issues, alternate cleavage and polyadenylation, mRNA regulation

Exonic splice enhancer/suppressor

Controls how often an exon is included or excluded

UTR

mRNA stability, translation and localization, and degradation

RNAi

Small manipulated RNA pieces regulate eukaryotic genes. ssRNA, RISC complex, miRNA, siRNA.

Yamanaka factors

Cell → pluripotent cells (induced pluripotent seme cells)

Morphogens

Guides phenotype and development of cell fate (concentration dependent of cell signaling) (signaling factors)

Src mutations

Tyr 527 → loses inhibitory interaction

SH3 → loses inhibitory interaction

Overabundance of Tyr

Nonsense after C-terminal (pY)

Angiogenesis

Making tumour blood supply

Growth factors

Promotes tumours, up and downstream

Signaling factors that stimulate cellular processes like survival, growth, repair and differentiation. Paracrine.

RTK

Promotes tumours, upstream and downstream.

Part of enzyme coupled reactions (Epidermal growth factor receptor). Helps stuff grow. Helps receptor function and tyrosine kinase activity.

Ras GTPase

Promotes tumours, upstream

Drives growth, proliferation and migration of cells when active (GTP form). Activated by GEFs.

PI3K

Promotes tumours downstream.

Converts PIP2 → PIP3, which recruits Akt.

Akt

Promotes tumours downstream.

Serine/threonine kinase that binds to PIP3, influences proliferation and cell metabolism.

Src

Promotes upstream

Viral oncogene, helped discover lots to do with cancer.

PTEN

Inhibits tumours downstream

Loss of this phosphatase increases Akt signaling in cancer cells.

MAPK

Promotes and inhibits tumours downstream

Scaffold protein mediated, promotes proliferation, active downstream of Ras.

Cancer promotion

Genomic instability, cell division, heterogeneity, driver mutation

snoRNA

Processes rRNA for rDNA

2D gel electrophoresis

Separates proteins by mass and charge to create an array of dots that reflect proteome of the cell type analyzed

Exon shuffling

What creates new combos of protein domains, as opposed to alternative splicing.

miRNA

Likely evolved from siRNA viral defense mechanism

CRISPR

Discovered by short repetitive sequences in prokaryotic genomes, HR pair creates specific changes in genome, involves crRNA direction a nuclease to cleave.

Master regulator

A transcription factor with a key role in directing cell fate

GCPR

Function as GEFs when activated. All contain a serine/threonine kinase domain domain.

Secondary Messengers

Direct connection between signalling molecules (neurotransmitter, growth)

HDAC

Recruited by Rb, promotes more closed chromatin confirmation. Rb is a tumour suppressor

R point

Until this, Rb is bound to E2F. It occurs in G1 and regulates progression into S-phase. Many growth promoting and growth inhibiting pathways converge on regulating this.

MDM2

Is more likely to be polyubiquitinated p53 in untreated non-stressed cells.

Increase protein

Gene amplification, loss of the 3’ UTR miRNA, kinase domain missense mutation, frame fusion of kinase

snRNA

In splicing, this base pairs with 5’ splice site, 3’ splice site and a branch point in the intron.

Situ hybridization

mRNA detected through base pairing with probe. Confirm specific sequence is in one area (elongation helper)

RNA sequencing

All mRNA is analyzed. Find genes that differ. What is highly transcribed.

Fragment RNA → Reverse transcription → PCR → Sequence

Operon

A secondary messenger informs of status. Each contains regulatory DNA sequences, promote or inhibit transcription.

mRNA localization

Sequences in the 5’/3’ UTR come into contact with things and they either anchor, protect or transport in local area. One stays stem cell, one differentiates.

lncRNA

Can bind complementary sequences and recruit proteins to act on those genes. Complementary base pair to target particular RNA or DNA. Regulation using non-coding RNA.

RISC complex

1 strand is degraded, leaving miRNA. Argonaute proteins in it are the key.

crRNA

CRISPR used this as a small non-coding RNA molecule to seek & destroy invading viral genomes (complementary base pair and target nuclease digestion)

Tyrosine kinase

Is autoinhibited. Whole complex turned off until growth is activated. Maximally ready to go when Tyr416 is phosphorylated.

Truncanation

Tumour virus helped to identify one of the oncogenic mechanisms of activation. Cytoplasmic domains join and are mimicked. Removes extracellular domain, leading to cancer.

Tumour microenvironment

The surrounding network of ECM, signaling molecules, immune cells, fibroblasts, blood vessels, and resident normal tissue. Tumour stroma.