Lecture 12 - Proteins and Translation

What do proteins do

Form cellular structures and catalyze chemical reactions within the cell

Majority or 55% of the cell’s dryweight is

proteinaceous

What are proteins made of

amino acids

How are amino acids linked together

Peptide bonds

3 major components of translation

ribosomes, mRNA, and tRNA

What are ribosomes

They catalyze peptide bond formation

What does mRNA do

Encode genetic information

What does tRNA do

Binds an amino acid and the ribosome

What is the structure of amino acids

An amino group and a carboxyl group which are both bonded to the alpha carbon

What is an amino group

NH2 functional group that can accept a proton

to produce an amino cation NH3+.

What is a carboxyl group

COOH functional group that dissociates to

give the carboxylate anion (COO-), and a hydrogen ion.

The alpha carbon is bonded to a hydrogen and

the variable side of the chain group, R

Side Chain

Varies between different amino acids, defining its identity

How many canocical amino acids are in all living organisms? Know that they can make an infinite number of different proteins.

20

4 main groups of amino acids

Ionizable acidic, ionizable basic, non-ionizable polar, and nonpolar

Ionizable acidic

Contain a negatively charged residue at neutral pH

Ionizable basic

Contain a positively charged reside at neutral pH

Non-ionizable polar

Have a polar group but no full charge at neutral pH

Nonpolar

Have no partial or full charge

What does peptide bond formation do

Creates a link between two amino acids

How are peptide bonds formed

By dehydration synthesis reaction which joins the carboxylic acid group of the first amino acid to the amino group of a second amino acid

Individual amino acids which have been joined are referred to as

amino acid residues

Primary structure of proteins

The linear sequence of amino acids from the N-terminus to the C-terminus

Triplet code

Three, non-overlapping continuous nucleotide bases (codon) are translated into a single amino acid

There are more codons or more amino acids

Codons

Degeneracy

Some codons encode the same amino acid

How many total codons are there

64

How many of these codons encode an amino acid

61

What are the stop codons

UGA, UAA, UAG

Usage can vary - some amino acids have more codons than others

Leucine has 6 while methionine has one

Genetic code is

universal

How do you where to start reading the genetic code

At the start codon AUG/ATG

What is frameshift

The DNA/mRNA sequence gets an insertion or deletion of 1 or 2 nucleotides, which shifts how the ribosome groups the bases into codons.

Transfer RNA (tRNA)

Three-dimensional RNA molecule used in translation

Anticodon

A three nucleotide region which has a sequence that is complementary to the mRNA codon it recognizes

Codon=? Anticodon=?

mRNA, tRNA

3’ OH acceptor stem

Binds the amino acid of interest. When a tRNA is

bound to an amino acid it is referred to as being “charged”

Ribosome

Site of protein synthesis in cells. This contains ribosomal RNA (rRNA)

What does the rRNA do

Catalyzes peptide bond formation in the ribosome

Ribozyme

Enzyme which contains RNA that enables a catalytic chemical reaction

Sizes of ribosomes in prokaryotes:

50S (large) subunit and 30S (small) subunit

Shine-Dalgarno sequence

A sequence in the RNA in prokaryotes that enables binding of the ribosomes

The shine dalgarno sequence can be considered the

landing spot or (RBS - Ribosomal binding site) for the (16S rRNA) 30s small subunit before it starts making the protein

In the shine-dalgarno sewuence the ——- ——— sequence precedes the start codon

purine-rich leader sequence (5’-GGAGGU-3’)

Three steps of translation

Initiation, elongation, and termination

Initiation

Begings at the start codon (AUG) - here the first amino acid (methionine) is added

Elongation

Amino acids are added in succession to the growing peptide chain as the ribosome moves along the mRNA. Energy dependent, uses GTP as the energy source

Termination

When a stop codon is reached, no amino acid is added. Instead release factors cause the ribosome to dissociate from the mRNA and newly formed protein

Proteins

are polymers of amino acids that can be folded into complex globular shapes

Many conformations are possible for proteins

due to the flexibility of amino acids

Native conformation

The 3D structure of a protein that is biologically active

Structure= ___ in proteins

Funtion

Many proteins have large segments which have no obvious or

regular, repeating structure

Primary structure (1degree)

Order in which amino acids are covalently linked together (Read from N to C terminus)

Secondary Structure (2 degree)

Ordered 3D arrangement of the backbone of the polypeptide (no R groups)

Tertiary Structure (3 degree)

3D arrangement of all atoms in a

protein, including those in the side chains (R groups) and in

non-protein co-factor

Quarternary Structure

Arrangement of multiple

polypeptide chains with respect to one another. Subunits:

Individual parts of a large molecule