Chapter 8 – DNA, Genetics & Gene Regulation

DNA

Deoxyribonucleic acid; the hereditary molecule that stores genetic information.

Nucleotide

The monomer of nucleic acids made of a phosphate group, a 5-carbon sugar, and a nitrogenous base.

Components of a nucleotide

Phosphate + Pentose sugar + Nitrogenous base.

Phosphodiester bond

Covalent bond that joins nucleotides together in DNA and RNA.

Nitrogenous base

Nitrogen-containing molecule that carries genetic information.

Purines

Adenine (A) and Guanine (G); double-ring bases.

Pyrimidines

Cytosine (C), Thymine (T), and Uracil (U); single-ring bases.

DNA sugar

Deoxyribose.

RNA sugar

Ribose.

DNA bases

Adenine, Thymine, Cytosine, Guanine.

RNA bases

Adenine, Uracil, Cytosine, Guanine.

Difference between DNA and RNA

DNA contains deoxyribose and thymine; RNA contains ribose and uracil and is usually single-stranded.

Chargaff's Rule

A = T and C = G.

Erwin Chargaff

Discovered that A=T and C=G in DNA.

Rosalind Franklin

Used X-ray crystallography to discover DNA's helical structure and phosphate backbone on the outside.

James Watson

Helped determine DNA's double-helix structure.

Francis Crick

Worked with Watson to determine the double-helix structure of DNA.

Double helix

Twisted ladder structure of DNA.

Complementary base pairing

A pairs with T; G pairs with C.

Antiparallel DNA strands

DNA strands run in opposite directions (5' --> 3' and 3'--> 5').

5' end

End of DNA containing the phosphate group.

3' end

End of DNA containing the hydroxyl (OH) group.

DNA directionality

DNA is always synthesized 5'

Template strand

Original DNA strand used to synthesize a complementary strand.

DNA replication

Process of making an identical copy of DNA before cell division.

Purpose of DNA replication

To produce two identical DNA molecules before cell division.

Semiconservative replication

Each new DNA molecule contains one original strand and one newly synthesized strand.

Replication is anabolic

It builds DNA from nucleotide monomers.

Replication is endergonic

Requires energy input.

Energy source for DNA replication

Deoxyribonucleotide triphosphates (dNTPs).

dNTPs

DNA building blocks (dATP, dTTP, dCTP, dGTP).

Ingredients for DNA replication

Template DNA, RNA primer, dNTPs, enzymes.

Helicase

Unzips DNA by breaking hydrogen bonds.

Gyrase

Relieves tension ahead of the replication fork.

Primase

Synthesizes RNA primers.

Primer

Short RNA strand that provides a free 3' OH for DNA polymerase.

DNA Polymerase III

Main enzyme that builds new DNA.

DNA Polymerase I

Removes RNA primers and replaces them with DNA.

Ligase

Seals gaps between DNA fragments.

Leading strand

Synthesized continuously toward the replication fork.

Lagging strand

Synthesized discontinuously away from the replication fork.

Okazaki fragments

Short DNA fragments made on the lagging strand.

Replication fork

Y-shaped region where DNA replication occurs.

Why DNA polymerase needs a primer

It can only add nucleotides to an existing 3' OH.

Replication always occurs

5'- 3'.

Why the lagging strand forms fragments

DNA polymerase only synthesizes 5'- 3', but DNA strands are antiparallel.

DNA storage in eukaryotes

DNA wraps around histones to form nucleosomes, chromatin, and chromosomes.

Histones

Proteins that DNA wraps around.

Nucleosome

DNA wrapped around histone proteins.

Chromatin

DNA-histone complex.

Chromosome

Condensed chromatin visible during cell division.

DNA storage in bacteria

Circular chromosome located in the nucleoid; no histones or nucleosomes.

Nucleoid

Region containing bacterial DNA.

Central Dogma

DNA - RNA - Protein.

Transcription

Process of making RNA from DNA.

Translation

Process of making proteins from mRNA.

Gene

DNA sequence that encodes a functional product.

RNA Polymerase

Enzyme that synthesizes RNA.

Promoter

DNA sequence where RNA polymerase binds to begin transcription.

Initiation of transcription

RNA polymerase binds the promoter and separates DNA strands.

Elongation of transcription

RNA polymerase builds RNA from the template strand.

Termination of transcription

RNA polymerase reaches the terminator and releases RNA.

Template strand

DNA strand read by RNA polymerase.

Coding strand

DNA strand with the same sequence as mRNA except T is replaced by U.

Direction of transcription

DNA is read 3'- 5'; RNA is synthesized 5'

RNA building blocks

rATP, rUTP, rCTP, rGTP.

Does transcription require a primer?

No.

Does transcription require helicase?

No; RNA polymerase opens the DNA.

mRNA

Messenger RNA that carries genetic information to ribosomes.

tRNA

Transfer RNA that carries amino acids.

rRNA

Ribosomal RNA that makes up ribosomes.

Introns

Noncoding regions removed from RNA.

Exons

Coding regions that remain after splicing.

RNA splicing

Removal of introns and joining of exons.

Poly-A tail

Added to the 3' end of eukaryotic mRNA to increase stability.

5' cap

Modified guanine added to the 5' end of eukaryotic mRNA.

Purpose of Poly-A tail and 5' cap

Protect mRNA and increase its lifespan.

Why bacteria cannot splice RNA

They lack a nucleus, so transcription and translation occur simultaneously.

Translation

Converts mRNA information into a protein.

Codon

Three-base sequence on mRNA coding for one amino acid.

Genetic code

Relationship between codons and amino acids.

Start codon

AUG (codes for Methionine).

Stop codons

UAA, UAG, UGA.

Anticodon

Three-base sequence on tRNA complementary to an mRNA codon.

Ribosome

Site of protein synthesis.

Ribosome Binding Site (RBS)

Sequence on bacterial mRNA where the ribosome binds.

16S rRNA

Ribosomal RNA that binds the RBS.

Translation initiation

Ribosome binds mRNA and finds the AUG start codon.

Translation elongation

tRNAs bring amino acids while the ribosome forms peptide bonds.

Translation termination

Occurs when a stop codon is reached and a release factor releases the protein.

Peptide bond

Bond connecting amino acids.

Energy used in translation

GTP.

Genome

Complete set of genetic information.

Why different cell types exist

All cells have the same DNA but express different genes.

Gene expression

Process of producing RNA or protein from a gene.

Gene regulation

Controls which genes are turned on or off.

Activator

Protein that increases transcription.

Repressor

Protein that blocks transcription.

How repressors work

Bind DNA near the promoter to prevent RNA polymerase from binding.

Environmental signals

Molecules that activate or deactivate repressors.