DAT: 9.1-9.11 Molecular Genetics

Central Dogma

Flow of genetic information: DNA → RNA → Protein

Nucleoside

Molecule made of one sugar (ribose or deoxyribose) and one nitrogenous base

Nucleotide

Nucleoside plus phosphate group(s); the building block of DNA and RNA

DNA (Deoxyribonucleic Acid)

Double-stranded molecule with deoxyribose sugars; missing a hydroxyl group on the 2′ carbon

RNA (Ribonucleic Acid)

Single-stranded molecule with ribose sugars containing hydroxyl groups on both 2′ and 3′ carbons

Purines

Nitrogenous bases with two rings (adenine, guanine)

Pyrimidines

Nitrogenous bases with one ring (cytosine, thymine, uracil)

Base Pairing (DNA)

A pairs with T, G pairs with C

Base Pairing (RNA)

A pairs with U, G pairs with C

Hydrogen Bonds in Base Pairs

A–T (2 bonds), G–C (3 bonds); regions rich in G–C are stronger and harder to break

Nucleosome

DNA wrapped around histone proteins

Chromatin

DNA packaging pattern within chromosomes formed by nucleosomes

LOOSELY packed; ALLOWS for RNA polymerase to transcribe

Euchromatin

TIGHTLY packed; PREVENTS RNA polymerase from transcribing

Heterochromatin

Acetylation

Adds negatively charged acetyl group, loosens DNA-histone interaction

Deacetylation

Removes acetyl group, tightens DNA-histone interaction

Methylation

Epigenetic modification that usually suppresses gene transcription

Semiconservative Replication

Each DNA double helix has one old and one new strand

Antiparallel

One strand runs 5′→3′ and the complementary runs 3′→5′

Origin of Replication

DNA site where replication begins (A–T rich)

Unzips DNA by breaking H-bonds

Helicase

Relieves supercoiling ahead of the replication fork

Topoisomerase

keeps DNA uncoiled

Single-Strand Binding Proteins

Synthesizes RNA primer for DNA polymerase

Primase

DNA Polymerase

Adds nucleotides to growing strand (requires free 3′–OH)

Synthesized continuously toward replication fork

Leading Strand

Synthesized discontinuously away from fork in Okazaki fragments

Lagging Strand

Okazaki Fragments

Short DNA fragments on lagging strand

DNA Ligase

Joins Okazaki fragments into a continuous strand

DNA backbone

• 5’-3’ ends

• phosphodiester bonds form sugar-phosphate backbone

removes RNA primer strips & replaces them w/ DNA

Polymerase I

seals phosphodiester backbones btwn fragments, attaches Okazaki fragments

DNA Ligase

• replicates DNA in 5’→3’ direction, essential synthesizing & lagging strands DNA

• main builder & spell checker

Polymerase III

Gene Expression

process by which DNA results in synthesis of RNA & protein, leading to expressible changes

Gene

contains specific sequence of nucleotide monomers that codes for specific protein products

• intermediate btwn DNA & protein

• LEAST abundant

• carries instructions

mRNA

• utilized in process of translation

• clover shape

• attaches amino acid

• transport anticodons

• smallest

tRNA

• part of ribosome structure

• builds proteins

rRNA

non-template/coding/sense strand

DNA strand that isn’t used in transcription, used to make mRNA

template strand/non-coding/anti-sense strand

• strand of DNA that is used for transcription

• used to look like mRNA molecule: T instead of U

• production fo RNA molecules from DNA template in nucleus (of eukaryotes) & cytoplasm (of prokaryotes)

• DNA→RNA

Transcription

RNA polymerase binds promoter & starts copying

Initiation (Transcription)

builds RNA strand by adding bases

Elongation (Transcription)

RNA polymerase stops & releases mRNA

Termination (Transcription)

mRNA processing

before mRNA leaves nucleus, it gets edited & protected here

5’capping

provides stability for mRNA & point of attachment for ribosome

Poly A tail

addition of poly-A tail added to end of mRNA transcript

snRNP’s

remove nucleotide segments from mRNA

RNA splicing

deletes introns & splices tgt exons

RNA sequences that are REMOVED from transcript before RNA gets translated

Introns

sequences that are retained in transcript before RNA gets translated

Exons

Alternative Splicing

• diff mRNA to be generated in transcript & TRANSLATED into protein

• 1 gene to code for multiple proteins

Transcription regulation

• requires use of micro-RNA & small interfering RNA

• RNA polymerase can NOT bind→gene off

degrades target mRNA

siRNA

reduce translation

miRNA

process of creating proteins by using genetic info from mRNA

Translation

ribosome

• function in binding of tRNA anticodon w/ associated mRNA codon

• builds protein

free ribosomes

free floating directly in cytosol

bound ribosome

bound to cytosolic side of rough ER surface

where tRNA detaches from ribosomes after it releases its amino acid

E site

carries tRNA molecule that is bound to elongating peptide chain

P site

where next tRNA molecule binds to deliver its amino acid

A site

ribosome grabs mRNA and starts

Initiation (Translation)

tRNA brings amino acids, ribosome links them into a protein chain

Elongation (Translation)

ribosome hits a STOP codon → protein is released

Termination (Translation)

Wobble Pairing

3rd base of codon doesn’t have to match perfectly

IN protein but gets removed

Inteins

exists in final protein

Exteins

Reverse transcriptase

RNA→DNA

RNA world hypothesis

explains why ribosomes use rRNA & RNA central to gene expression

Telomere

protect our genome from being shortened during cell replication

end-replication problem

• can NOT fully copy very END of lagging strand

• solution is that telomerase adds telomeres to ends of chromosome

Hayflick Limit

• phenomenon that states that # of possible cell divisions is dependent on length of telomeres

• is limit on cell replication imposed by shortening of telomeres w/ each cell division

• concept used to explain cellular aging

DNA mutation

errors in DNA sequence can lead to unfavorable consequence

Point Mutations

change in single nucleotide base

single base exchanged w/ another

Substitution Mutation

NO changing occurs to desired amino acid bc of redundant genetic code

Silent Mutation

• substitution causes CHANGE in amino acid that was originally coded

• ex) GAG (glutamic acid)→GUG (valine)

Missense Mutation

substitution results in STOP codon instead of amino acid codon, termination protein prematurely

Nonsense Mutation

Frameshift Mutation

ALTERS reading frame

Insertion

ADDITION of base

Deletion

REMOVAL of base

Chromatin Fiber

overall densely packaged DNA+proteins, packed nucleosome

Genome

complete set of organism’s DNA

Genomics

study of genomes

Transcriptome

complete set of organism’s mRNA transcripts

proteome

entire set of organism’s proteins

Bioinformatics

application of computer science to analyze biological

Human genome project

global attempt to sequence human genome

Sanger Sequencing

AMPLIFIES DNA, involves splitting strand of DNA into 2 & synthesizing new strands using fluorescent nucleotides

Whole genome shotgun sequencing

breaking the entire DNA into random pieces, sequencing them, then using a computer to put them back together.

Metagenomics

sequencing DNA of entire communities of species

Genome size

tot # of nucleotides organism has

eukaryotes>prokaryotes

Gene #

prokaryotes>eukaryotes

Gene density

Transposons

elements move from 1 part of genome to another

DNA is removed from 1 location & insertion into diff location

cut & paste method

DNA is copied w/out removing original sequence & copy is inserted into diff location

copy & paste method

Retrotransposons

uses copy & paste method but w/ RNA intermediate to move into another region of DNA

Ramifications of Transposition

can disrupt gene, change gene expression, cause mutation, increase genetic diversity→disease