Review 4 Flashcards
Telomere
- Protect ends of chromosomes from degradation
- If not telomeres:
a. Genes will be lost
b. Act as a buffer zone
c. Prevent chromosomes from sticking to each other
Single Copy DNA
- Holds most of the organism’s important genetic information
- Transcribed and translated
- Lower mutation rate
Somewhat Repetitive DNA
- Found near centromeres
- May contain genes that are transcribed and translated
- Higher rate of mutation
Highly Repetitive DNA
- No genes
- Not transcribed and translated
- E.g. telomeres
Topoisomerase
- Unwinds DNA
2. Breaks backbone temporarily for DNA
Helicase
Breaks H-Bonds
RNA Primer
Adds some nucleotides for DNA polymerase to continue catalyzed by DNA primase
Polymerase and addition to the 5’ end
It works by not adding to the 5’ end
Strands in Transcription
Template strand = Noncoding Strand
Complimentary strand = Coding Strand
Primary modifications to pre-mRNA in Eukaryotes
- Addition of 5’ Cap - Modified Guanine (Phosphate I think), converts to a 3’end?
- 3’ Poly-A tail (adenine addition), act as buffer for exonuclease.
- Intron splicing
Functions of 5’ Cap and 3’ poly A tail modifications
- Helps with translation
- Reduces ends from damage
- Helps ensure RNA robusticity
Sites on Ribosome and Functions
- A - Amino-acyl site
- P - Peptide bond site
- E - Exit Site
Binding Spot of ribosome on mRNA on Eukaryotes vs. Prokaryotes
Shine-Dalgarno sequence for Prokaryotes and 5’ cap for eukaryotes
Translation: Prokaryotes vs. Eukaryotes
Prokaryotes- 1st amino acid is Formyl-methionine (f-Met) while Methionine in eukaryotes
Function of f-Met detection in Humans
- Acts as an alarm system in the human body
- Means Bacteria is around
- Triggers immune response
DNA Repair Systems
- 3’ Exonuclease activity - Proofreading
- Mismatch repair mechanism - After Replication
- Nucleotide Excision Repair - DNA Damage
3’ Exonuclease Activity
- Occurs at 3’ end
2. Nucleotide is excised and replaced with RNA primer
Mismatch Repair Mechanism
Done by proteins that recognize a problem because it distorts the sugar molecule:
1. Mark incorrect base with a cut
- Exonuclease removes the incorrect nucleotide
- DNA pol inserts correct nucleotide
- DNA ligase connects nucleotide to the side and correct complement
How Mismatch distinguishes between parental and daughter strand
Parental strand is methylated and Daughter strand is not.
3 Damages UV can do to DNA
- Cause pyrimidine dimer
- Distorts DNA, make it stick out
- Alters band
Process that fixes DNA UV Damage
Nucleotide Excision Repair
Factors that contribute to DNA damage
Endogenous - Internal e.g. reactive oxygen species like peroxides, oxides
- Exogenous - External - X-rays, UV rays, and gamma rays
Nucleotide Excision Mechanism
- Endonuclease will remove pyrimidine dimer or particular wrong nucleotide
- DNA pol brings the right nucleotide
- DNA ligase attaches to next to complimentary to it
What if nucleotide Excision repair does not work?
- Cells can become dormant (senescence; where it just remains and does nothing)
- Apoptosis
- Unregulated cell division (cancer)
2 main Moments of Protein modifications
- Co-translational e.g. acetylation
2. Post-translational (mostly occur in ER and Golgi)
Post-translational Modification that affects structure
- Glycosylation
- Lipidation/Prenylation - addition of lipid groups to certain membrane-bound enzymes
- Carboxylation - addition of carboxylic acid groups, usually to serve as calcium-binding sites
Glycosylation
- Happens to mostly proteins embedded in the cell membrane
- Help identify types of cells
- Can be useful as receptors
Lipidation
- Addition of lipids
2. Happens to proteins that tether to the cell.
Post-translational Modification that affects function
- Ubiquitination
- Proteolysis
- Methylation
- Phosphorylation/Dephosphorylation
Phosphorylation/Dephosphorylation
Addition/removal of Pi (Inorganic phosphate group) e.g. Na/K ATP Pump:
- 3 Na+ ions attached to the protein on the intracellular side
- Binding causes ATP to hydrolyze to ADP and Pi
- Pi attaches to enzyme and this causes enzyme to close to the outside and open to the extracellular space (Phosphorylation)
- While open, 3 Na+ is released and 2 K+ ions bind, to the enzyme. When completely bound, Pi is removed (Dephosphorylation).
- Dephosphorylation causes the enzyme to open to the intracellular space while close to the extracellular space.
- 2 K+ ions are removed.
Goal of Na/K+ ATP Pump
To have lower Na+ in the cell and higher outside
Methylation
Specifically histones:
- DNA wrapped around histones
- Histones are methylated
- Turns on or off genes
Proteolysis
Sometimes proteins need to be cut (maybe twice) to make it active.
Ubiquitination
- Addition of ubiquitin to a protein
2. Marks protein for degradation
LEARN LAC OPERON
Arrangement
Repressor Promoter -> Repressor Protein (Constitutively expressed) -> Promoter -> Operator -> Lac Z (Beta-galactosidase) -> Lac Y (Lactose permease) -> Lac A
Inducer Exclusion
Protein in the presence of glucose breakdown binds to Lac Y and prevents lactose entry in the cell but glucose over lactose
Chromatin Regulation
- Histone acetylation
2. Histone Deacetylation
Histone Acetylation
Lysine residues are bound to acetyl groups. This allows DNA to be open because positive lysine is now removed and electrostatic attraction is reduced. This leads to EUCHROMATIN and promotes transcription
Histone Deacetylation
Lysine is deacetylated. It is attracted to DNA (-ve) and leads to HETEROCHROMATIN. This works with CpG methylation. It silences genes
How does methylation affect genes
- Physically impedes it (transcriptional proteins to genes0
- Methyl-binding Proteins (MBP) - recruit certain proteins like histone proteins (deacetylase and acetylase) and helps in gene silencing.
Basic Transcription Apparatus
- General transcription factors
- RNA polymerase
- Mediator multiple protein complex
Activators
DNA-binding protein:
- Enhance binding of RNA polymerase:
a. Interaction with subunits of RNA pol
b. Changing DNA structure
e.g: CAP - Catabolic Activating Protein in E.coli
Enhancers
- Part of DNA that binds to activators to loop DNA that brings a specific promoter to transcription factors
- Does not need to be close to genes but can even be on another chromosome
Repressors
- Bind to operator
2. Prevents promoter RNA pol to transcribe gene
Silencers
- Bind by repressor protein
- Similar to enhancers
- Can be upstream or downstream
- When they bind, it prevent RNA pol from interacting with promoters
Prokaryotes Transcriptional Regulation
Purpose - Quickly adapt to changing environment
- Activators, repressors
- Enhancers (rarely)
Eukaryotes Transcriptional Regulation
Sophisticated (combination of factors)
1. Nuclear envelope - prevents simultaneous transcription and translation.
- Spatial and temporal control of gene expression
Introns Regulation Process
- Gets spliced
- Non-coding RNA
- Performed by spliceosome
a. Binds to two ends of introns
b. Loops in a circle and cuts
c. Ligase DNA
RNA editing
- Process that leads to sequence variation in RNA molecule
- Catalyzed by enzymes
- Rare
- Insertion, deletion, and substitution
ADAR and CDAR RNA Editing Enzymes
ADAR - Adenosine Deaminating Acting RNA (A to Inosine)
CDAR - Cytosine Deaminating Acting RNA (C to Uridine)
Non-coding RNA
TRANSCRIPTION:
1. micro RNA (miRNA) - gene silencing, prevent translation, degradation
Translation:
- ribosomal RNA
- Transfer RNA tRNA
- Small NUCLEOLAR RNA (snoRNA)
- Guide covalent modifications of rRNA,tRNA< etc.
a. Methylation
b. Pseudoridylation - addition of isomer (nucleotide uridine)
Pre-mRNA:
- snRNA (small NUCLEAR RNA)
a. Process pre-mRNA in the nucleus
b. Regulation of TF
c. Maintain telomeres
Spliceosome
snRNA + proteins (example of snRNP):
a. Two sequential transesterification reactions
i. Splice out introns
ii. Ligate the two exons
Mitogen
Something that encourages a cell to start cell division
- Triggers mitosis
Three things to trigger an oncogene
- Point mutation/Deletion
- Gene Amplification/Instability
- Chromosomal Rearrangement
Deletion/Point Mutation
Removal/Change in nucleotides
- Hyperactive protein
- Overexpressed protein
Gene Amplification
a. increased mRNA instability
b. Increased expression in cell and activity
c. Overexpressed protein
Chromosomal Rearrangement
a. Translocation to a regulatory sequence
b. Fusion to actively transcribed region
c. Overexpressed or hyperactive protein
Oncogene Examples
- Src - Sarcoma
- Ras - GTPase
- Myc - TF
- RTK - Receptor Tyrosine Kinase
- CTK - Cytoplasmic Tyrosine Kinase
Src
- Sarcoma
- Tumor of mesenchyma or connective tissue
- Codes for non-receptor kinase
Ras
- GTPase
- GTP -> GDP + Pi
- MAPK and other downstream cascade activation
Myc
- Transcription factor
- Chromsome 8 and 14
- Burkitt’s Lymphoma
RTK
- Receptor Tyrosine Kinase
- E.g:
a. VEGF
b. EGFR
c. PDGF
CTK
- Cytoplasmic Tyrosine Kinase
a. Survival
b. Migration
c. Differentiation
d. Proliferation
E.g:
Bcr -> Abl gene -> CML aka Philadelphia Chromsome
Characterize Oncogene and Tumor Suppressor Genes
Mutated Oncogene - Dominant
Mutated Tumor Suppressor Genes - Recessive
Tumor Suppressor Genes
- p53
2. pRb - Retinoblastoma Protein
pRb
- Prevents retinal cells from replicating when DNA damage
- Halts G1 -> S when DNA damage detected
- Histone Deacetylation (lowers transcription)
- Mutation = Retinoblastoma
p53
- Halts G1 -> S when DNA damage detected
- Bind DNA and activates p21 which binds to cyclin CDK and holds cell hostage at G1->S phase
- Apotosis
Mutation of p53
Can also lead to deviation from 2 hit hypothesis
1. Prevents product of normal p53 from working
- Dominant negative region and deviation from 2 hit hypothesis
