BIOPHYSICS - LESSON 4

Proteins

Most abundant biomolecule in the cell

Polypeptides

single linear chain of amino acids

Proteins

one or more polypeptide chains in SPECIFIC conformations

simple

amino acids upon hydrolysis

conjugated

simple proteins + non-protein substances

enzymatic proteins

selective acceleration of chemical reactions

defensive proteins

protection against disease

storage proteins

storage of amino acids

transport proteins

transport of substances

hormonal proteins

coordination of an organism's activities

receptor proteins

response of cell to stimuli

contractile and motor proteins

movement

structural proteins

support

amino acids

building blocks of protein

essential amino acids

must be in the diet because cells can’t synthesize them

essential amino acids

vary considerable depending on whether they are adults or children

Non-essential amino acids

can be made by cells

Non-essential amino acids

some may need to be obtained from the diet in certain cases

non-protein amino acids

a-amino acids that not incorporated into proteins

Alanine

Most abundant amino acid

Glycine

With shortest side chain

Glycine

fit into both hydrophobic and hydrophilic environments

Proteins

synthesized starting with the amino terminus and ending at the carboxyl terminus

primary structure

interactions start establishing structures - secondary and tertiary.

secondary structure

Spatial arrangement of amino acid residues that are near one another

secondary structure

Common regular folding patterns of the polypeptide chains

alpha helix

a delicate coil held together by hydrogen bonding between every fourth amino acid

beta sheet

often shown as a folded or flat arrow pointing toward the carboxyl end

Turns

a type of secondary structure that, as the name suggests, causes a turn in the structure of a polypeptide chain

δ-turns

end amino acids are separated by one peptide bond (theoretical)

γ-turns

separation by two peptide bonds

β-turn

s separation by three peptide bonds (most common)

α-turns

separation by four peptide bonds

π-turns

separation by five bond

310 helices

fourth most abundant secondary structure and has 10 amino acids in 3 turns

310 helices

appears at the amine or carboxyl end of an α-helix and stabilized by the presence of aspartate

π-helices

special type of α- helix

π-helices

α-helix with an extra amino acid stuck in the middle and has 22 amino acids in 5 turns.

Random coils

no regular, discernible structure, lack secondary structure and identifiable with spectroscopic methods

Ionic bonds

form between elements donating electrons, usually in ions

Hydrophobic forces

Non-polar amino acids (commonly found in the interior of proteins) favor associating with each other and this has the effect of excluding water.

Disulfide bonds

two sulfhydryl side-chains of cysteine

Disulfide bonds

strongest of the forces stabilizing protein structure.

Van der Waals forces

weak interactions caused by attraction between a polar molecule and a transient dipole, or between two temporary dipoles

Van der Waals forces

Weakest force

Post-translational modifications

Results in formation of covalent bonds stabilizing proteins

Proteolysis

breaking down proteins into smaller peptides or individual amino acids

Phosphorylation

addition of one or more phosphate groups to the protein

Glycosylation

addition of carbohydrate molecules to the polypeptide chain and modifying it into glycoproteins

Sulfation

addition of sulphate molecules and these modifications of proteins occurs at tyrosine

Methylation

transfer of one-carbon methyl groups to nitrogen or oxygen to amino acid side chain

Hydroxylation

addition of a hydroxy group to a protein amino acid

Folding models

formation of secondary structure → advance folding intermediate

Folding process

Shows how folded protein’s native state corresponds to the minimal free energy

Levinthal's Paradox

There are an incredibly large number of ways a protein could fold, but in reality, they fold correctly in a short amount of time.

Cyrus Levinthal

protein folding problem

Levinthal

proposed that folding occurs by a sequential process that begins with a nucleation event that guides the process rapidly and is not unlike the funnel process

Spectroscopy

electromagnetic radiation and radiation allows researchers to determine atomic coordinates (Angstrom)

Spectroscopy

X-ray diffraction/ crystallography and solution nuclear magnetic resonance

Fluorescence Spectroscopy

Utilizes fluorescence of specific amino acids

Quaternary structure

Two or more polypeptide chains together

temperature, pH, heat

protein denaturation can be affected by

Protein Denaturation

Process of breaking the weal linkages within a protein leading to modification of its structure

Protein Denaturation

Occurs at all stages except primary

Keratins

outer layer of human skin and are integral to hair, nails, claws, feathers, beaks, scales, and hooves

Fibroin

silk of spiders and the larvae of moths and other insects, fibroin is comprised of anti-parallel β- strands tight packed together to form βsheets

Elastin

elastic characteristics allowing tissues to resume to its shape and made by linking tropoelastin

Elastin

Found in arteries which helps with pressure wave propagation for facilitating blood flow

Collagen

most abundant protein in mammals (1/3 of mass)

Collagen

16 types and major component of tendons

Collagen

prominent in cornea, cartilage, bone, blood vessels and the gut