Chapter 15: Genes and Proteins

gene expression

Using a gene to produce functional RNA or protein.

Archibald Garrod

Connected inherited disorders to missing metabolic enzymes.

inborn error of metabolism

An inherited defect in a metabolic pathway.

alkaptonuria

Garrod's example of an inherited metabolic disorder.

alkaptonuria problem

Homogentisic acid accumulates in the body.

George Beadle and Edward Tatum

Connected individual genes to individual enzymes.

Neurospora crassa

The bread mold used by Beadle and Tatum.

Why Neurospora was useful

It can grow on a simple minimal medium.

minimal medium

Contains only nutrients needed by wild-type organisms.

complete medium

Contains extra nutrients that support metabolic mutants.

auxotroph

A mutant that needs an added nutrient to grow.

Beadle and Tatum mutation method

They exposed Neurospora spores to X-rays.

one gene-one enzyme hypothesis

Each gene controls one enzyme.

one gene-one polypeptide hypothesis

Each gene controls one polypeptide chain.

modern definition of a gene

DNA expressed as a functional RNA or polypeptide.

RNA

Usually single-stranded nucleic acid containing ribose and uracil.

DNA sugar

Deoxyribose.

RNA sugar

Ribose.

DNA unique base

Thymine.

RNA unique base

Uracil.

DNA strands

DNA is usually double-stranded.

RNA strands

RNA is usually single-stranded.

nucleic acid monomer

A nucleotide.

protein monomer

An amino acid.

central dogma

DNA to RNA to protein.

transcription

Making RNA from a DNA template.

translation

Making a polypeptide from an mRNA template.

transcription template

DNA.

transcription product

RNA.

eukaryotic transcription location

The nucleus.

translation template

mRNA.

translation product

A polypeptide.

eukaryotic translation location

Ribosomes in the cytoplasm or rough ER.

primary transcript

The first RNA copy made from a gene.

pre-mRNA

An unprocessed eukaryotic mRNA transcript.

mature mRNA

Processed mRNA ready for translation.

number of nucleotide bases

Four.

number of common amino acids

Twenty.

triplet code

Genetic information is read three nucleotides at a time.

codon

A three-nucleotide sequence on mRNA.

number of possible codons

64.

amino-acid codons

61 codons specify amino acids.

stop codons

Three codons end translation.

start codon

AUG.

AUG meaning

Start translation and add methionine.

stop-codon sequences

UAA, UAG, and UGA.

nonsense codon

Another name for a stop codon.

redundant genetic code

Several codons can specify the same amino acid.

degenerate genetic code

Another name for a redundant genetic code.

unambiguous genetic code

Each codon has only one meaning.

nearly universal genetic code

Most organisms interpret codons the same way.

reading frame

The grouping of mRNA nucleotides into codons.

template DNA strand

The DNA strand copied by RNA polymerase.

template-strand direction

RNA polymerase reads it from 3' to 5'.

coding DNA strand

The DNA strand not copied during transcription.

nontemplate DNA strand

Another name for the coding strand.

coding strand and mRNA

Their sequences match except T replaces U in DNA.

mRNA synthesis direction

RNA is built from 5' to 3'.

colinear

Gene order corresponds to amino-acid order.

RNA polymerase

The enzyme that builds RNA.

RNA polymerase primer requirement

RNA polymerase does not need a primer.

promoter

DNA region where transcription machinery binds.

transcription unit

The DNA region copied into one RNA molecule.

terminator

A sequence that signals transcription to end.

transcription initiation

RNA polymerase binds and begins RNA synthesis.

transcription elongation

RNA polymerase extends the RNA strand.

transcription termination

RNA synthesis stops and the transcript is released.

transcription bubble

The locally unwound DNA inside RNA polymerase.

initiation site or +1 site

The first nucleotide transcribed into RNA.

upstream

Before the transcription start site.

downstream

After the transcription start site.

consensus sequence

A common DNA pattern recognized by proteins.

bacterial promoter -10 region

A consensus sequence about 10 bases upstream.

bacterial promoter -35 region

A consensus sequence about 35 bases upstream.

sigma factor

Helps bacterial RNA polymerase recognize a promoter.

RNA polymerase core enzyme

Bacterial polymerase without sigma factor.

RNA polymerase holoenzyme

Bacterial core enzyme plus sigma factor.

core-enzyme function

Performs transcription elongation.

holoenzyme function

Recognizes promoters and begins transcription.

bacterial transcription termination

RNA polymerase releases RNA at a terminator.

rho-dependent termination

Rho protein ends bacterial transcription.

rho-independent termination

An RNA hairpin ends bacterial transcription.

hairpin structure

RNA folds back and base-pairs with itself.

RNA polymerase I

Makes most eukaryotic rRNA.

RNA polymerase II

Makes eukaryotic pre-mRNA.

RNA polymerase III

Makes tRNA, 5S rRNA, and some small RNAs.

transcription factor

A protein that helps regulate transcription.

general transcription factors

Help RNA polymerase II bind a promoter.

transcription initiation complex

RNA polymerase II plus transcription factors at a promoter.

preinitiation complex

Proteins that recruit RNA polymerase II.

TATA box

A T- and A-rich promoter sequence.

TATA-box location

About 25 bases upstream of the start site.

CAAT box

A promoter sequence that binds transcription factors.

GC-rich box

A G- and C-rich promoter regulatory sequence.

Octamer box

A promoter element that can increase transcription.

enhancer

A DNA region that increases transcription efficiency.

FACT complex

Moves nucleosomes during transcription.

eukaryotic termination signal

AAUAAA.

AAUAAA function

Signals cleavage of eukaryotic pre-mRNA.

RNA processing

Changes that convert primary RNA into mature RNA.