Molecular Basis of Medicine I

Stores DNA

Replication and Transcription

Nucleus Functions

Protein Synthesis

Ribosome Functions

Synthesis/Folding of secreted and membrane proteins

Rough ER

Lipid synthesis, detox, Ca2+ storage

Smooth ER

Modifies, sorts, and packages proteins and lipids

Golgi Apparatus Functions

Sort internalized cargo and membrane proteins

Endosome Functions

Acidic degradation, recycling, and autophagy

Lysosome Function

ATP production, metabolism, apoptosis signaling

Mitochondria Functions

Very-long-chain fatty acid oxidation and ROS detox

Peroxisome Functions

Cell shape, intracellular transport, movement

Cytoskeleton

Lysosomal Dysfunction Can:

Impair degradation, trafficking, autophagy, and signaling

Macromolecules Essential to Cellular Function

Carbohydrates

Lipids

Proteins

Nucleic Acids

What part of AA is important for protein folding?

R group

Central Dogma

DNA → RNA → Protein

• Transcription → Translation

→ Folding/Modification → Cellular Function and Disease

__________ interactions stabilize protein structure

Noncovalent

Unwinds the DNA double helix by separating the two strands

Helicase

Relieves tension that develops ahead of replication for as DNA is unwound

Topoisomerase

Bind the separated DNA strands and keep them from coming back together

Single-strand binding proteins (SSB)

Synthesize RNA primer

Provides starting point needed for DNA polymerase

Primase

Adds DNA nucleotides to the growing DNA strand

DNA synthesized 5’ → 3’

DNA polymerase

Leading Strand

Synthesized continuously

Lagging Strand

Synthesized discontinuously

Okazaki Fragments

Seals gaps remaining between DNA fragments after RNA primers are removed and replaced with DNA

DNA Ligase

Required to recruit/maintain DNA polymerase III during eukaryotic replication

Sliding clamp and clamp loader

Allow DNA to condense into nucleus

8 core proteins

• 147 base pairs of DNA would around each core

Histone

Opens chromatin and protomes gene expression

• HAT: add acetyl groups

• HDAC: remove acetyl groups

Histone Acetylation

Suppresses/silences gene expression

• DNMT: add methyl groups to DNA

• TET: promote DNA demethylation

DNA Methylation

A-T vs G-C H bonds

A-T: 2

G-C: 3

DNA polymerase (I and III) recognizes and removes incorrectly incorportated nucleotides during replication

Proofreading

Repairs replication errors that remain after proofreading

Defects can cause colon cancer (and others)

Strand Discrimination is Prokaryotes lacking methylation

Mismatch repair

Repairs individual damaged bases

• DNA glycosylases

• AP endonucleases

Oxidative Lesions, Deoxyuracil, Depurination, Deamination

Base excision repair

Steps of BER

1. DNA Glycosylase

   1. Recognizes damaged base and removes it

2. AP Endonuclease

   1. Acts as the resulting AP site allowing DNA polymerase to come in

3. DNA polymerase

   1. Replaces missing nucleotide(s)

4. DNA ligase

   1. Seals nick

Deamination

Removal of an amino group from a nitrogenous base

Depurination

Removal of an entire purine base

Sugar-phosphate backbone remains but there is no base present

Repairs bulky lesions that distort DNA helix

Nucleotide excision repair

UV Light Damage

UV produces pyrimidine dimers that can cause issues w/ DNA replication

→ cancer

Can cause Xeroderma pigmentosum

Double-strand break repair

Homologous Repair

• Higher fidelity

Non-homologous Repair

• Can result in fusion chromosomes

MMR Protein found in Prokaryotes vs Eukaryotes

• Mut - Pro

• MSH - Euk

Theta vs Rolling-Circle Replication

• Circular DNA

• Virus

Elongation carried out by:

DNA pol III

Removing RNA primer:

DNA pol I

Steps of DNA Replication

1. Initiation

2. Elongation

3. Termination

Initiates DNA replication by synthesizing RNA-DNA primers

Pol Alpha

Synthesizes the leading strand

Participates in DNA repair

Pol Delta

Synthesizes the leading strand

Participates in DNA repair

3’ → 5’ proofreading (exonuclease)

Pol Epsilon

Replicates and repairs mitochondrial DNA

3’ → 5’ proofreading (exonuclease)

Pol Gamma

Involved in base excision repair of nuclear DNA

Pol Beta

Causes DNA to be extended during each replication cycle

Reverse transcriptase

Has own RNA template

Telomerase

ONE origin of replication & circular chromosome

In cytoplasm

Prokaryotic DNA Replication

Multiple linear chromosomes and origins of replication

In nucleus

Replication Forks

Eukaryotic DNA Replication

RNA Polymerase

Uses DNA as template

• Reads 3’ → 5’

Produces RNA

• Synthesizes 5’ - 3’

Prokaryotic Transcription Initiation

-10 and -35 (upstream TSS)

Promotors bind to SIGMA initation factor

Prokaryotic Transcription Elongation

NO proofreading

RNA pol recruited to make RNA from DNA template

Coupling in Prokaryotes

Transcription and Translation

• No nucleus separating the transcription machinery from cytoplasmic ribosomes

Prokaryotic Transcription Termination

RHO protein recruited by RNA pol to allow transcription termination

In Nucleolus

rRNA Transcripts

Insensitive to a-amanitin toxin

RNA Pol I

In Nucleoplasm

mRNA and snRNA transcripts

Strongly inhibited by a-amanitin toxin

RNA Pol II

In Nucleoplasm

tRNA and rRNA transcripts

Inhibited by high concentrations of a-amanitin toxin

RNA Pol II

Eukaryotic Transcriptional Regulation

TATA box → TBP/transcription factors → recruit RNA Pol II

Controls how much a gene is transcribed

Transcriptional Regulation

Controls what mature mRNA is produced from precursor RNA

• Alternative Splicing

• Alternative Polyadenylation

RNA Processing

Export of mature mRNA from the nucleus is regulated

• Degraded is it doesn’t leave

mRNA Transport

Translation can be regulated by:

• Presence/absence of 5’ cap

• Length of poly-A tail

mRNA Translation

Changing mRNA stability changes how long the transcript remains available for translation

mRNA Degradation

Proteins can be selectively degraded by Proteasomes

Tagged by Ubiquitin

Protein Degradation

5’ Cap Functions

Protecting RNA from degradation

Helping with RNA export

Contributing to translation

Poly-A Tail Functions

RNA stability

Translation/regulation