Biol 141 Class 9

Protein Structure and Central Dogma

Proteins

All proteins are made up of the same building blocks: 21 amino acids

• Made up of carbon, oxygen, nitrogen, hydrogen, and sulfur atoms

• They’re monomers that form polymers (peptide chain) through polymerize

Chemical classification of amino acids

When we categorize amino acids we are just talking about there R groups (side chains)

• The side chains determine an amino acid’s properties and is the only part that varies from amino acid to amino acid

Different side chains:

• Polar

• Nonpolar

• Charged (So polar)

Hydrophobic Amino Acids

Have carbon-rich side chain, which doesn’t interact well with water

• They are non-polar

Hydrophilic amino acids

Have polar amino acids that interact well with water

Charged Amino Acids

Interact with oppositely charged amino acids or other molecules

Protein Structure

1. Primary Structure

2. Secondary Structure 

3. The Tertiary Structure 

4. Quaternary Structure 

The Primary Structure

Is the linear sequence of amino acids as encodes by DNA

• The amino acids in a protein are joined by covalent peptide bonds, which link the amino group of one amino acid to the carboxyl group of another

• A water molecule (H2O) is released each time a bond is formed 

• The linked series of carbon, nitrogen, and oxygen atoms make up the protein backbone (Amino groups → Carboxyl group)

Linear sequence of amino acids from Amino (N) to carboxyl (C) terminus

The Secondary Structure

Protein chains often fold into 2 types of secondary structures: 

1. Alpha Helix 

• It is the right-handed coil stabilized by hydrogen bonds between the amine and carboxyl groups of nearby amino acids 

2. Beta Sheets 

• They are formed when hydrogen bonds stabilize 2 or more adjacent strands 

They are formed by hydrogen bonds between backbone atoms

The Teritary Structure

It is the 3d shape of a protein

• The shape is determines by the characteristics of the amino acids making up the chain 

Formed by interaction between amino acids side chains (disulfide covalent bonds, ionic bonds, hydrogen bonds, hydrophobic interactions)

• Bonding R groups

The Quaternary Structure

2 or more polypeptide chains come together to form one functioning molecule with several subunits

• It is a larger 3d structure of multiple peptide chains together

Formed by interactions between amino acid side chains (disulfide covalent bonds, ionic bonds, hydrogen bonds, hydrophobic interactions) on different peptide chains

Interactions between subunits

Peptides Schematic

Peptides are made up of amino acids

• Directionality- Go from N- terminus (Amino group) to C- terminus (Carboxyl group)

• To find amino acids in a peptide follow the N-C-C backbone

• Like DNA they go from 5’ → 3’

Central Dogma 

Illustrates the DNA function

• DNA provides instructions to build mRNA which goes to the ribosome to make protein

DNA → RNA → Protein

Transcription

• DNA → mRNA

Translation

• mRNA → Protein

Types of RNA

1. mRNA- messenger (the coded message)

2. rRNA- ribosomal (machinery/factory)

3. tRNA- transfer (the decoder/adapter)

All used “to translate” information from DNA to proteins 

Other RNAs regulate translation 

• miRNA- microRNAs- regulate translation in eukaryotes (RNA interference)

Transcription Elongation

RNA polymerase adds RNA to 3’ end

• Growth 5’ → 3’ RNA pol moves 3’ → 5’ on template 

• Energy for base addition come from base (JUST LIKE DNA SYNTHESIS) - mRNA(n) +NTP → mRNA (n+1) + diphosphate

• Added base is complementary to template strand 

- Non-template strand also complementary to template

- mRNA has same sequence as non-template strand (also known as the coding strand)

The Genetic Code

Universal

• Used by all organism 

Redundant 

• More than 1 codon per amino acid 

Unambigous

• Each codon only codes for 1 amino acid 

Start Codon (AUG)

Codons only play a role in TRANSLATION

tRNA

Has a primary, secondary, and tertiary structure

Primary

• Linear sequence 5’ → 3’

Secondary 

• Cloverleaf

Tertiary

• L-shaped 

Ribosomes

Ribosomes= Protein Polymerase

• Very large molecular machine 

• 2 subunits, ribosomal RNA and proteins 

• Can bind 1 mRNA + 3 tRNA ( at A, P, and E sites)