Topic 8: Nucleic Acids II

Mutation

a permanent change in DNA sequence

When and where do mutations happen?

during replication, with environmental damage, anywhere in genome

Why are mutations important?

some mutations are needed to allow adaptation to environment, evolution = mutation and selection

What can mutations that occur in cell division over a lifetime cause eventually?

cancers

Cancer

loss of control of the cell cycle, cells reproduce in an unregulated manner

Why are cancer cells not found as frequently as one could expect given that mutations often occur?

cells have mechanisms to keep mutation rate low so the correct DNA sequences are passed on, but some mutations passed on to allow natural selection to act

Mutation that occurs in replication

incorrect DNA sequence incorporated

What do cells do to repair mutations during replication?

proofreading, mismatch repair

What does DNA polymerase do?

proofreads nucleotide sequences and removes most replication mismatches, adds the correct nucleotide

Describe polymerase exonuclease activity

polymerase pauses and cleaves off the incorrect nucleotide from the 3’ end of the growing chain then adds the correct one

What is the rate of mistakes made when sequencing after polymerase proofreading? after repair proteins?

1/10⁷ nucleotides, final rate 1/10⁹ mucleiotides after repair proteins

How do repair proteins likely recognize the mistake sequence?

nicks in the DNA from replication

Give an example of a mutation that occurs post replication

UV light damage

Mutations/errors that occur post replication

deamination, depurination, pyrimidine dimers

Deamination

loss of amino groups from DNA bases, often converting cytosine to uracil

Depurination

spontaneous process where a purine base is cleaved from backbone making an apurinic (AP) site

Pyrimidine Dimers

DNA lesions formed when UV light causes adjacent pyrimidine (C and T) bases covalently bind, distorting DNA structure and causing high mutation rates

What can happen with DNA polymerase if pyrimidine dimers form?

DNA polymerase could recognize dimer as a single nucleotide, leading to nucleotide loss in replication called frameshifts

If a base is lost what is done to remedy that?

random nucleotide added in the next round of replication

If uracil accidentally pairs with adenine, what can happen?

there is a cytosine to thymine transition in the next round of replication

Types of post replication repair

excision, resynthesis, ligation

If replication and repair has high fidelity (accurate), then…

changes slowly accumulate

Describe DNA similarity between organisms of the same species

similar sequences, very few differences between individuals

Transposons

mobile genetic elements, short DNA segments (~100-1000 base pairs) that can insert into new locations in genome

Where are transposons found?

in nearly all cells, prokaryotes and eukaryotes

What encodes transposase?

transposons

Transposase

enzyme needed for the movement of transposons around the genome, cannot leave the cell so it is confined to cell descendents

How much of the human genome is made of transposons? What are they mainly composed of?

~1/2 the human genome, mostly Alu and L1

Describe DNA-only transposons

no RNA intermediates, move by 2 mechanisms, and most common type of transposon found in bacteria

Describe retrotransposons

move by RNA intermediate, unique to eukaryotes, ~42% of the human genome, movement resembles retroviral infection

Viruses

mobile genetic elements coated with protein that can move from cell to cell

Describe the typical virus lifecycle

use host machinery to replicate, often killing the host cell afterwards to release new viruses

Describe viruses genetic information

can be DNA or RNA, single or double stranded, genomes encode 3 to a few hundred genes

Examples of viruses and the genome types

herpes simplex virus and Epstein-Barr virus (DNA double stranded), Influenza type A and SARS-CoV-2 (RNA single-stranded)

Describe some features of DNA viruses

DNA + coat protein, takes lipids from the host cell, DNA enters the cell and viral DNA is replicated using host proteins, new viruses then assemble and spread to other cells

Describe some features of RNA viruses

some are retroviruses, RNA + envelope + coat protein, unique to eukaryotes

What are the locations that transcription can occur?

chloroplast, mitochondrion, eukaryote nucleus, cytoplasm of prokaryote, occurs at genes

Genes encode RNA =

each gene contains the info required to make a protein

Coding Region

DNA sequence that encodes RNA sequence

Control Region

DNA sequences that regulate transcription

What are some examples of a control region?

promotor, terminator

Describe the features of a typical bacterial genome

genome composed of ~500 genes, take up most of the genome

Describe the features of a typical eukaryote genome

genome compoased of ~25,000 genes, takes up much less space in the genome

How much of the human genome is made of genes?

only a few percent, most are transposons

Describe the structure of DNA

double stranded, double helix, deoxyribonucleotides, aTcg, organized as chromatin

Describe the structure of RNA

single stranded (usually), variety of 3D structures, ribonucleotides, aUcg (U two hydrogen bonds with A), organized as RNA-protein complexes

What is the role of RNA polymerase?

catelyze the same chemical reaction as DNA polymerase, but using a different substrate (ribonucleotides), ~30 nucleotides per second

Describe the unwinding process using RNA polymerase

RNA pol unwinds DNA, synthesizing complement strand and progressively releases RNA (RNA is not hydrogen bonded to DNA throughout the whole length)

What is the error rate associated with RNA polymerase?

1/10⁴ nucleotides

Why is it okay for RNA polymerase to have a higher error rate than DNA polymerase?

RNA is temporary and not passed onto offspring or daughter cells, so its sequence has less impact on the organism

Messenger RNA (mRNA)

codes for proteins

Ribosomal RNA (rRNA)

form the core of ribosome structure, catalyze protein synthesis

microRNAs (miRNA)

regulate gene expression

Transfer RNA (tRNA)

serve as adaptors between mRNA and amino acids during protein synthesis

other noncoding RNA (small RNAs)

responsible for RNA splicing, gene regulation, telomere maintenance, etc.

RNA Polymerase I

synthesizes rRNA

RNA Polymerase II

synthesizes mRNA, miRNA, some small RNAs

RNA Polymerase III

synthesizes a small variety of small RNAs, tRNAs