BMED5207 Exam 1 - slides

Primary protein structure

the sequence of amino acids and peptide bonds

Secondary protein structure

the folding of the polypeptide chain into different shapes

Tertiary protein strucutre

combinations of various secondary structures that form distinct domains

quaternary protein structure

a combination of more than one polypeptide

Polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

Alanine polarity

hydrophobic non-polar

Valine polarity

hydrophobic non-polar

isoleucine polarity

hydrophobic non-polar

Leucine polarity

hydrophobic non-polar

Methionine polarity

hydrophobic non-polar

Phenylalanine polarity

hydrophobic non-polar

Tyrosine polarity

hydrophobic non-polar

Tryptophan polarity

hydrophobic non-polar

Cystine polarity

hydrophobic

Glyine polarity

hydrophobic

Proline polarity

hydrophobic

Lysine polarity

hydrophilic basic

Arginine polarity

hydrophilic basic

Histidine polarity

hydrophilic basic

Aspartate polarity

hydrophilic acidic

Glutamate polarity

hydrophilic acidic

Serine polarity

hydrophilic polar, uncharged

Threonine polarity

hydrophilic polar, uncharged

Asparagine polarity

hydrophilic polar, uncharged

Glutamine polarity

hydrophilic polar, uncharged

How is a peptide bond formed?

dehydration of one amino acid C-terminus to another amino acid N-terminous

Which bonds are able to rotate in a polypeptide?

between the C(alpha)-N and C(alpha)-carbonyl carbon

alpha helix stability

hydrogen bonds between the backbone hydrogen and amide hydrogen atoms of every fourth residue

alpha helix activity

determined by the R groups that project outward from the helix

amino acids not commonly found in alpha helices

proline and glycine

beta sheet stability

hydrogen bonds between backbone oxygen and amide hydrogen on different strands

beta sheet activity

determined by the R groups that project above and below the plane of the sheet

forms of beta sheets

antiparallel, parallel, sheets formed from beta strands from different polypeptides

amino acids that are commonly found in beta turns

glycine and proline

heptad repeats

same/similar amino acids re-appear on one face of an alpha helix every 7 amino acids

amphipathic helices

have hydrophobic and polar residues on opposite sides of the helix

Unstructured regions

flexible, mixed amino acid characteristics; may be a flexible linker between two structured regions

common amino acids found in alpha helix

m, a, l, e, k, r, h, q

common amino acids found in beta sheets

w, y, f, i, v, t, c

common amino acids found in beta turns

g, p, d, s, n

Tertiary Structure

the overall conformation of a polypeptide chain

Categories of Tertiary Structure

globular proteins, fibrous proteins, integral membrane proteins, disordered/unstructured proteins

Globular proteins

water soluble, compactly folded structures, often roughly spherical

fibrous proteins

large, elongated, often stiff molecules (ex. actin and collagen)

Integral membrane proteins

embedded within the phospholipid bilayer of a membrane; hydrophobic helices of 20-25 residues are common

Disordered/Unstructured proteins

flexible proteins with no fixed conformation; function as linkers between structured domains (ex singaling, regulation, scaffolding)

What type of interactions contribute to the stability of tertiary structure in proteins?

Hydrophobic interactions between non-polar side chains

What type of bonds are involved in stabilizing the tertiary structure of proteins?

Hydrogen bonds between polar side chains and backbone amino acid carbonyls

motif

regular combinations of secondary structures with a specific function, can be encoded by a highly conserved sequence motif

coiled coil motif

two alpha helices wound around each other, have heptad repeat sequences with hydrophobic residues at positions 1 and 4

How are is the seam of a coiled coil motif stabilized?

interactions between hydrophobic side chains at regular intervals along each strand

Examples of coiled coil motif

AP1 transcription factor, c-Fos and c-Jun heterodimer, leucine zipper (basic regions bind DNA)

How to identify a coiled coil motif?

look for common AA of alpha helices, possible heptad repeats of hydrophobic residues at positions 1 and 4

EF hand motif

A type of helix-loop-helix motif in many proteins, including many calcium-binding and DNA-binding regulatory proteins

EF hand motif secondary structures

two alpha helices with a short loop between

How to identify EF Hand motif from a protein sequence?

common AAs of alpha helices (malek, rhq) with a short stretch between with charge aas (D,E) for Ca2+ binding

EF hand motif example

calmodulin

What is the zinc-finger motif?

A 25-residue motif with two invariant cysteine residues and two invariant histidine residues

What does the Zn2+ ion bind to in the zinc-finger motif?

Conserved cysteine and histidine residues.

What structural elements are present in the zinc-finger motif?

Beta strands and an alpha helix.

In what type of proteins is the zinc-finger motif commonly found?

Many DNA binding proteins that regulate transcription.

Zinc finger motif secondary structures

one alpha helix and two beta strands

How could you identify a zinc finger motif from a protein sequence?

common AAs of alpha helix (malek, rhq) and common AAs of beta strands (wyfivt) with c and h periodically for Zn2+ ion binding in the strand region

example of zinc finger motif

BRCA1 and EGR1 (Early growth response protein 1)

What is a domain in protein structure?

A distinct region of protein structure that are often evolutionarily conserved

Functional domain in protein structure

a region that exerts a particular activity, activity is often retained when separated from the separated from rest of protein

Structural domain in protein structure

a region that forms a stable and distinct tertiary structure, will often assemble independent of the rest of the protein

Quaternary Structure

the stoichiometry (number) and orientation of subunits in a multi-protein complex

Disulfide bonds

Cystine residues covalently link under oxidizing conditions

Allostery

a change in a proteins tertiary or quaternary structure caused by non-covalent binding of a ligand, which induces structural changes that can lead to changes in activity

Cooperative binding

a form of allostery, where binding a ligand at one site has an effect on binding the same ligand at a different site

Cooperative binding example

Calmodulin and Ca2+ binding (Ca2+ binding changes conformation of calmodulin in the EF hand motifs)

What is post-translational modification?

It is the process of changing the chemical nature of amino acids in a protein.

What effects does post-translational modification have on proteins?

It alters the tertiary or quaternary structure of the protein, affecting its function.

Which AA(s) are modified with phosphorylation?

Serine, Threonine, tyrosine

What is the modifying enzyme for phosphorlation?

kinase

What is the removing enzyme for phosporylation?

phosphatase

What amino acid(s) are modified with acetylation?

lysine

What is the modifying enzyme for acetylation?

acetyltransferase

What is the removing enzyme for acetylation?

deacetylase

What AA(s) are modified with methylation?

lysine, arginine

What is the modifying enzyme for methylation?

methyltransferase

What is the removing enzyme for methylation?

demethylase

What AA(s) are modified with Glycosylation?

asparagine (N), serine (S), threonine (T)

What is the modifying enzyme for glycosylation?

glycosyltransferase

What is the removing enzyme for glycosylation?

glycosidase

What AA(s) are modified with ubiquitation?

lysine

What is the modifying enzyme for ubiquitination?

ubiquitin ligase

What is the removing enzyme for ubiquitination?

deubiquitinating enzyme (DUB)

Common reversible post translational modification

phosphorylation, acetylation, methylation, glycosylation, ubiquitination

What AA(s) could phenylalanine act as a null mutant for?

tyrosine

What AA(s) could alanine act as a null mutant for?

threonine and serine

What modified AA(s) could glutamate act as a mimic for?

phosphorylated threonine and serine

What AA(s) could arginine could act as a null mutant for?

lysine

What modified AA(s) could glutamine act as a modified mimic for?

acetylated lysine

ubitiquination

addition of an ubiquitin molecule to a protein (at lysine residues)

mono-ubiquitination

addition of one ubiquitin

multi-ubiquitylation

addition of multiple single ubiquitins

Poly-ubiquitination

addition of a polymeric chain of ubiquitins

ubiquitin molecule

contains 7 lysines; each lysine can be a site for another ubiquitin to be added (creating chains)