Amino Acids, Proteins, Enzymes - Molecular and Cell Bio Exam 1

Protein functions

• structure component

• transport

• enzymes

• transmitting information

• defense

• etc.

Basic amino acid structure

• Carboxyl (COO-)

• Amino (NH3)

• R group

• alpha carbon

Hydrophobic/lipophilic amino acids

• non-polar R groups (only H-C molecules)

• Found inside of proteins, away from aqueous environment

Hydrophilic (Polar + non-charged) amino acid

• polar, non-charged R groups (contain O or N)

• Found outside of proteins, in contact w/ aqueous environment

Hydrophilic (Polar + charged) amino acid

• polar, charged R groups (+ or - charges on the R group)

• Found outside of proteins, in contact w/ aqueous environment

Peptide bond

• Amino acids held together by this bond

• Amino group of one and carboxyl group of another forming the bond

• built from amino → carboxyl

• Doesn’t change R group

Primary structure

• Amino acid sequence/polypeptide chain

• Assembled from mRNA from N terminus —> C terminus

• plays big role in shape of the protein

Secondary structure (alpha-helix)

• hydrogen bond between amino acids is formed about every 4 residues downstream to get the helical structure (bonds NH and CO)

• R groups projecting out determine if hydrophobic, hydrophilic, or amphipathic

Secondary structure (beta sheet)

• hydrogen bonds between amino acid chains laying side by side (bond NH and CO)

• chains are parallel or antiparallel

Tertiary structure

• overall 3D shape of the protein

• determined by non-covalent interactions between R groups

• hydrophobic R → middle of structure

• hydrophilic R → surface of structure

Chaperones

Special proteins that assist the protein folding process. Helps prevent improper folding and increases the speed

Protein folding

• occurs spontaneously

• driven by interactions between water, amino acids, and each other

Prion protein (PrP)

1. Normally forms a-helixes, but can adopt a ß-sheet configuration by mis-folding

2. non-covalently interacts w/ other proteins, causing their mis-folding

3. ß-sheets line to form insoluble structures

4. can kill cells and form plaques

Quaternary structure

multiple tertiary structures together

Dimer

two tertiary structures coming together to form a receptor

Tetramer

four tertiary structures coming together to form a receptor

Intrinsically disordered proteins (IDPs)

have entirely disordered structures, allows proteins to adapt their structure (more flexible)

Intrinsically disordered regions (IDRs)

have portions that are disordered, allows proteins to adapt their structure (more flexible)

Enzymes

• proteins that can increase the rate of chemical reactions, since most chemical reactions necessary for life happen too slowly

• catalysts

Two properties of catalysts

• Catalyst doesn’t get consumed or permanently altered

• Catalyst doesn’t alter the equilibrium between reactants and products

How do enzymes speed up reactions?

• enzymes lower the energy of the transition state, making it easier for the reaction to take place

• specific to certain chemical reactions

• substrates bind on the active site

Lock and key theory

substrate binds to enzyme and it reacts (no changes to shape)

Induced fit theory

substrate and enzyme are distorted to transition state conformation when substrate binds

Cofactors

Help enzymes by participating in catalysis

Coenzymes

type of cofactor that binds loosely to enzymes, recycled during catalysis and are low-weight organic molecules

Prosthetic groups

type of cofactor that binds tightly or covalently to enzymes

Allosteric regulation

small molecules bind to allosteric site to regulate enzyme activity by changing its shape when binding

• inhibition: substrate can’t bind to enzyme (non-competitive inhibition)

• activation: substrate can bind to enzyme

Competitive inhibition

inhibitor binds to the active site, preventing substrate from binding

Feedback inhibition

the product from a reaction inhibits an enzyme needed for its synthesis. b/c more molecules are more likely to bind to the enzyme, preventing the reaction

Kinases

enzyme that phosphorylates, adds phosphate to other proteins

Phosphatases

enzyme that dephosphorylates, removes phosphate from other proteins

What can phosphorylation do to an enzyme

can activate or inhibit an enzyme