Proteins

Parts of an amino acid

alpha carbon, amino group, carboxyl group, r group

What happens when pH is in the range 7.35–7.45

amino group gains an proton and carboxyl group loses one

Tetrahedron

The four covalent bonds from the alpha carbon

Characteristics of hydrophobic amino acids

Turn away from water, non polar r groups

Why do hydrophobic amino acids aggregate

Molecules form hydrogen bonds with each other rather than the hydrophobic r group

Characteristics of hydrophilic amino acids

One end of the r group is slightly more charged than the other, polar r group

Glycine

Has a hydrogen R group and can increase the flexibility of the proteins

Proline

R group is liked back to the amino acid causing the exact opposite effect of glycine

Cysteine

Forms strong disulfide bonds and aids in stability

Primary structure

First level of protein consists of a sequence of amino acids

Secondary structure

3d structure caused by hydrogen bonds

Tertiary structure

Interactions between secondary structures and determines the structure of the polypeptide

Quaternary structure

Interactions between various polypeptides

What does the function of a protein rely on

Its shape

Linus Pauling and Robert Corey

Used X ray crystallography to figure out secondary structures

Alpha helix

Polypeptide backbone is twisted into a right handed coil

Beta sheet

Polypeptide backbone folds back and forth on itself creating pleats

Reading frames

A sequence of codons for amino acids

tRNA

Matches its anticodon to an mRNA and carries the corresponding amino acid to the ribosome

Aminoacyl-tRNA synthetases

Connect specific amino acids to specific tRNA molocules

Start codon

AUG

Stop codons

UAA, UAG, UUU

How does translation work

AUG codon is recognized by initiator tRNA, ribosomes bind to tRNA and add consecutive amino acids to build a polypeptide chain, stop codon is recognized and the protein is released

Small ribosomal subunit

Binds the messenger RNA (mRNA) template and matches each codon with the correct transfer RNA (tRNA) anticodon

Large ribosomal subunit

Joins amino acids together

Elongation factors

A protein that breaks GTP and releases energy for ribosome movement

Shine–Dalgarno sequence

Found in bacterial and archaeal mRNA and aligns the ribosomes to start protein synthesis

Operon

A cluster of genes controlled by a promoter

Gene regulation

Ways that the gene controls gene expression

What must happen for DNA to be transcribed

Specialized proteins help reorganize the proteins normally bound to DNA to make the gene available

Posttranslational Modification

Regulating the structure and function of proteins

Where are proteins produced

Free ribosomes in cytosol and membrane bound ribosomes on the rough ER

Signal sequence

The sequence that allows proteins to be recognized and sorted

Nuclear localization signals

Signal sequences for nucleus proteins

How many protein families are there

25000

Folding domain

A structure that can fold independently from the rest of the protein