PHSC1212 Biochemistry - Lecture 6 Protein Structure pt 1

Enzymes, structural, movement, defense, regulation, transport, storage, stress response

protein functions and roles

Enzymes

proteins that catalyze reactions

Antibodies

proteins for immune system defense

Hormones and growth factors

proteins for regulation

Catalase or heatshock

proteins that protect cells from stress

Superfamilies, families, shape, prosthetic groups

different ways to classify proteins

Protein superfamilies

classification of proteins with overall structural similarities

3D shapes

What is similar when proteins are part of the same superfamily?

Functions

Proteins in the same superfamily may or may not have the same what?

Protein families

classification of proteins with amino acid sequence similarities

Amino acid sequences and functions

What is similar for proteins part of the same families?

30% amino acid sequence similarity

What makes proteins classified in the same family?

Cytochrome P450s

important superfamily and enzymes highly expressed in liver cells and responsible for metabolizing drugs

Shape and prosthetic groups

How are proteins classified besides families and superfamilies?

Fibrous and globular

two shapes of proteins

Long, rod like, and insoluble

characteristics of fibrous proteins

Structure

function of fibrous proteins

Compact, glob like, water soluble

characteristics of globular proteins

Globular

90% of proteins are which shape?

Metalloproteins

an example of a metal ion prosthetic group attached to a protein

Pockets, clefts, and active sites

found in globular proteins, and enable functional diversity

Hydrophilic amino acids on exterior

What makes globular proteins water soluble?

Primary

level of protein structure involving just an amino acid sequence

Secondary

level of protein structure with repeating structural patterns

Hydrogen bonding of peptide backbone

causes the amino acids to fold into a repeating pattern in secondary structures

Tertiary

level of protein structure involving 3D folding due to side chain interactions

Quaternary

level of protein structure with multi-protein complexes with multiple polypeptides

Primary structure

the specific amino acid sequence of a protein (what order)

Homologous

two proteins with similar sequences are referred to as homologous

How R chains line up

What is determined by the amino acid sequence that impacts how pieces of a protein interact and ultimately fold?

Secondary structure

refers to the repeating patterns that certain regions of a protein fold into

Alpha helix and beta pleated sheet

most common protein folding patterns; secondary structure

Angles of rotation at alpha carbon

What do alpha helix and beta sheets differ based on?

N-H hydrogen bonding with carbonyl

What stabilizes both secondary structures?

Alpha-helix

a rigid, rod-like structure formed when the polypeptide chain twists into a coil

Glycine and proline

two amino acids that do not promote alpha helix formation

Too small, too much flexibility

Why doesn't glycine promote alpha helix formation?

Too rigid, prevents rotation, N-H not available for H bonding

Why doesn't proline promote alpha helix formation?

Too many charged and/or bulky R groups

Besides Glycine and Proline, amino acids with what do not promote alpha helix formation?

Tryptophan

amino acid that doesn't promote alpha helix formation due to bulky R group example

3

How many amino acids make up one twist of an alpha helix?

Beta pleated sheets

form when two or more polypeptide chain segments line up, side by side

Parallel or antiparallel

two orientations of beta pleated sheets

Parallel

less stable beta sheets orientation due to greater distance between hydrogen bonding partners

Greater distance between hydrogen bonds

Why are parallel beta pleated sheets less stable?

Antiparallel

more stable beta sheet orientation

Structural motifs

supersecondary structures containing combinations of alpha helices and beta pleated sheets

Tertiary structure

refers to the unique 3D conformation of a protein

Prosthetic group

a non-protein component (like a metal ion or small organic molecule) that binds tightly to the protein and is essential for the function of the protein

Non protein component bound to a protein

What is a prosthetic group?

Protein function

What can prosthetic groups be essential for?

Heme

a prosthetic group found in hemoglobin

Hemoglobin

Where is heme found?

Oxygen

What binds to hemoglobin via the heme group?

Hydrophobic and electrostatic interactions, hydrogen and covalent bonds, hydration

stabilizing interactions for tertiary structures

Salt bridges

stabilizing interaction of tertiary structures formed between ionic R groups

Covalent bonds

stabilizing interaction for tertiary structures with disulfide bridges between cysteine R-groups

Form hydration shell and bridge distant polar groups

How can water be a stabilizing interaction for tertiary structures?

Glutathione breaks bonds

Why do proteins inside the cell not contain disulfide bonds?

Proteins protected inside lysosomes or peroxisomes

Which intracellular proteins might have disulfide bonds?

Domains

distinct regions within a protein's tertiary structure that usually have specific functions

Within a protein's tertiary structure

Where are domains located?

Binding prosthetic group, enzymatic activity, interaction with another protein

three possible functions of a domain

Quaternary structure

refers to the interactions of multiple separate polypeptide chains within a single protein

Subunit

another name for each polypeptide

Disulfide bridge

What holds together the heavy chains of IgG?

Through nonpolar interactions

How do light chains interact with heavy chains of IgG?

Hydrophobic interactions, electrostatic interactions, hydrogen bonds, hydration, covalent cross links

interactions that stabilize quaternary structures

Amino acid modification

Some covalent bonding in quaternary structures may require what?

Oligomers

name for proteins with quaternary structure because of their multiple subunits

Dimers

proteins with two subunits

Trimers

proteins with three subunits

Tetramers

proteins with four subunits

Homodimer

a protein composed of two identical subunits

Heterodimer

a protein composed of two different subunits