Chapter 4: Protein Structure and Function

polar covalent bonds

form between atoms that don’t share their electrons equally because they have different electronegativities (C-N, O-H, S-H)

electronegativity

atom’s attraction (pull) for shared electrons

nonpolar covalent bonds

form between atoms that equally share their electrons because they have the same or similar electronegativities (C-C, C-H, O=O, S-C)

uncharged polar amino acids

amino acids that have oxygen or hydroxyl (OH-) group in their side chains

nonpolar amino acids

amino acids that have -CH2 or methyl (-CH3) group in their side chains

hydrogen bonds

helps stabilize protein’s folded shape; happens in the backbone of the peptide bond

Disulfide (S-S) Bonds

covalent cross-linkage bonds that form between the sulfur atoms or adjacent cysteine side chains; takes place only in the ER; stabilizes protein in most favorable conformation; important for secreted proteins to retain function; join either 2 amino acids in the same protein or different polypeptide chains in multi-subunit protein

affinity chromatography

isolates the binding partner of the protein of interest which is covalently attached to the matrix of the chromatography column; the extract containing mixture of proteins is then loaded onto the column and those proteins that associated with the protein of interest inside the cell will bind to it on the column; most efficient form of chromatography that separates polypeptides on the basis of their ability to bind to a particular molecule

homogenization

the plasma membranes of cells can be ruptured so that the cell contents are released using this process; leaves most of the membrane-enclosed organelles intact

homogenate

the resulting slurry of breaking open a cell to release it’s contents; contain large and small molecules from the cytosol after homogenization

centrifugation

a procedure to separate a homogenate into different parts on the basis of size and density by placing the homogenate in test tubes and rotating at high speeds

larger

Do the smaller or larger molecules experience the greatest centrifugal force and move most rapidly?

ion exchange chromatography

the column contains charged beads that attract proteins of opposite charges; binding strength depends on the net charge of the protein: pH of solvent will influence net charge of proteins

size exclusion/gel filtration chromatography

separates proteins based on size and shape; small proteins are retained in the column longer than larger proteins; used as a final polishing step

protein domain

any segment of polypeptide chain that can fold independently into compact, stable structure

SDS polyacrylamide-gel electrophoresis (SDS-PAGE)

individual polypeptide chains form a complex with negatively charged molecules of SDS and therefore migrate as negatively charged SDS-protein complexes through a slab of porous polyacrylamide gel; unfolded polypeptide chains migrate at a rate that reflect their molecular weight with the smallest proteins migrating most quickly

isoelectric point

a point at which the protein has no net charge and therefore won’t move in an electric field

isoelectric focusing

proteins are electrophoresed in a narrow tube of polyacrylamide gel in which a pH gradient is established by a mixture of special buffers and then each proteins moves to a point in the pH gradient that corresponds to its isoelectric point and stays there

2D gel electrophoresis

combining two different separation methods, can be used to resolved more than 1000 proteins in a 2D protein map; first, native proteins are separated in a narrow gel on the basis of their intrinsic charge using isoelectric focusing and then the gel is placed on top of a gel slab and the proteins are subjected to SDS-PAGE in a direction perpendicular to that used in the first step and then each protein migrates to from a discrete spot

prion

a misfolded protein that can transmit its misfolded shape onto normal variants of the same protein, causing aggregates to form which can spread rapidly from cell to cell; pathogenic agent; causes mad cow disease

chaperons

proteins that help incorrectly folded and newly synthesized proteins fold correctly; many are heat shock proteins (HSP); requires ATP

heat shock protein (HSP)

proteins produced when cells are exposed to elevated temperatures and other stresses

alpha helix

resembles spiral staircase in which the N-H of every peptide bond is hydrogen-bonded to the C=O of neighboring peptide bond located 4 amino acids away in the same chain; generated when single a polypeptide chain turns around itself to form structurally rigid cylinder

beta sheet

individual polypeptide chains (strands) are held together by hydrogen-bonding between peptide bonds in different strands; the amino acid side chains in each strand project alternately, above and below the plane of this

antiparallel beta sheet

each section of polypeptide chain runs in the direction opposite to that of its immediate neighbors in a beta sheet

parallel beta sheet

the neighboring sections of the polypeptide chain run in the same orientation in a beta sheet

myoglobin

if protein is made of one polypeptide chain, it becomes functional by reaching its tertiary structure; when this becomes denatured, it loses its secondary and tertiary structures; transport protein

hemoglobin

if a protein is made of 2 or more polypeptides, it becomes functional by reaching its quaternary structure; when this becomes denatured, it loses its secondary, tertiary and quaternary structures; an abundant red blood cell that contain 2 identical alpha-globin subunits and 2 identical beta-globin subunits symmetrically arranged and each contain heme groups with iron atoms for O2 binding; transport protein

protein family

each has an amino acid sequence and 3D conformation that closely resembles that of the other

serine proteases

family of protein-cleaving (proteolytic) enzymes that include the digestive enzymes (chymotrypsin, trypsin and elastase) and proteases involved in blood clotting

binding site

any region on protein’s surface that interacts with another molecule through sets of noncovalent bonds

dimer

formed by interaction between a single, identical binding site on each monomer; 2 identical folded polypeptide chains form a symmetrical complex of 2 protein subunits

tetramer

formed by interactions between 2 nonidentical binding sites on each monomer

protein subunit

a separate polypeptide chain of a protein that assembles with other polypeptide chains to from a protein complex

protein motif

simple combination of secondary structures of proteins; not stable by itself

helical filament

formed with identical proteins with 2 different binding sites

ring

formed if 2 binding sites of identical proteins are disposed appropriately to each other

actin filament

helical structure formed from many identical protein subunits; motor protein

fibrous proteins

proteins that have relatively simple, elongated 3D shape; have roles in the cell that require proteins to span a large distance

collagen

a triple helix formed by 3 polypeptide chains, each containing the nonpolar amino acid glycine and at every 3rd position; structural protein

collagen fibrils

many rodlike collagen molecules that are cross-lined in the extracellular matrix form this; extremely strong and help hold tissues together

elastin

formed from relatively loose and unstructured polypeptide chains that are covalently cross-linked into a rubberlike elastic meshwork; individual protein molecules can uncoil reversibly whenever they’re stretched

biochemical pathway

consists of multiple chemical reactions that occur at the same area and the product of one enzyme becomes the substrate of the next

antibody

composed of 2 identical heavy chains and 2 identical light chains held together by S-S bonds, creating a Y shape; immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those on the surface of an invading microorganism; binds to a target molecule very tightly, either inactivating the target directly or marking it for destruction

immunoglobulin

defense protein that recognizes foreign organisms and cancer cells

enzymes

proteins that catalyze chemical reactions

ferritin

storage protein that stores iron in the liver

insulin

signal proteins tat control blood glucose levels

receptors

proteins that detect signals and transmit them to the cell’s response machinery

transcription factors

regulatory proteins that regulate gene expression

hydrolase

general term for enzymes that catalyze a hydrolytic cleavage reaction

nuclease

breaks down nucleic acids by hydrolyzing bonds between nucleotides

protease

breaks down proteins by hydrolyzing peptide bonds between amino acids

ligase

joins 2 molecules together

isomerase

catalyzes the rearrangement of bonds within a single molecule

polymerase

catalyzes polymerization reactions such as the synthesis of DNA and RNA

kinase

catalyzes the addition of phosphate groups to molecules; can attach phosphate groups to proteins

phosphatase

catalyzes the hydrolytic removal of a phosphate group from a molecule

oxido-reductase

general name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced; includes oxidases, reductases and dehydrogenases

ATPase

hydrolyzes ATP

lysozyme

an enzyme that cleaves the polysaccharide chains that form the cell walls of bacteria

allosteric enzymes

enzymes that have 2 or more binding sites that influence one another

feedback inhibition

an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway; triggers conformational change

allosteric regulation

binding an effector molecules at a site other than the enzymes active site

positive feedback

the process in which the enzyme’s activity is stimulated by a regulatory molecule

high

When ATP levels are low, are ADP levels low or high?

ADP

activates the enzyme that catalyzes the conversion of sugar to produce more ATP

negative

Do phosphate groups carry a positive or negative charge?

active

When GTP is bound to GTP-binding proteins are they active or inactive?

inactive

When GTP is hydrolyzed into GDP, is the GTP-binding protein active or inactive?

motor proteins

responsible for muscle contraction, separation of chromosomes during mitosis and movement of materials and organelles within the cell

p53

a tumor suppressor protein that regulates a cell’s response to DNA damage, stops cell division when DNA is damaged and triggers the production of the DNA repair enzymes

ubiquitylation

post-translational modification tags a protein for degradation

structural proteins

proteins that provide mechanical support to cells and tissues

transport proteins

proteins that carry small molecules or ions

storage proteins

proteins that store amino acids and ions

transcription regulators

proteins that bind to DNA to switch genes on or off

amino acid sequence

a unique order of amino acids in each type of protein which is exactly the same from one molecule of that protein to the next

polypeptide backbone

formed from a repeating sequence of the core atoms (-N-C-C-) found in every amino acid

N-terminus

the end of the amino acid that carries the amino group (NH3+ or NH2)

C-terminus

the end of the amino acid that carries the free carboxyl group

side chains

the part of the amino acid that’s not involved in forming peptide bonds and project from the polypeptide backbone

flexible

Are long polypeptide chains flexible or rigid?

noncovalent bonds

H bonds, electrostatic attractions and van der Waals attractions

weaker

Is a noncovalent bonds stronger or weaker than a covalent bond?

hydrophobic force

a weak interaction where hydrophobic molecules tend to be forced together to minimize their disruptive effect on the hydrogen-bonded network of the surrounding water molecules

denaturation

the unfolding of a protein; can occur due to treatment with solvents that disrupt the noncovalent interactions holding the folded chain together

renaturation

a protein refolds spontaneously into its original conformation after denaturation when a solvent is removed

helix

generated simply by placing many similar subunits next to one another, each in the same strictly repeated relationship to the one before; can be right or left handed, depending on the way it twists

right

Are alpha helices right or left handed?

coiled-coil

this structure form when the alpha helices have most of their nonpolar side chains along one side, so they can twist around each other with their hydrophobic side chains facing inward, minimizing contact with their aqueous cytosol; forms when 2-3 alpha helices wrap around one another to form a particularly stable structure

amyloid structure

beta sheets are stacked together in long rows with their amino acid side chains interdigitated like the teeth of a zipper

primary structure

level of organization that includes the amino acid sequence of a protein; begins protein structure

secondary structure

structure/level of organization that includes alpha helices and beta sheets

tertiary structure

the full 3D conformation of a protein formed by an entire polypeptide chain, including the alpha helices and beta sheets, and all other loops and folds that form between the N and C termini

quaternary structure

the structure/level of organization if the protein molecule exists as a complex of more than one polypeptide chain

intrinsically disordered sequences

continually bend and flex due to thermal buffeting; large proteins than contain as many as several dozen domains, which are often connected by relatively short, unstructured lengths of polypeptide chains

globular protein

a protein where the polypeptide chain folds up into a compact shape like a ball with an irregular surface; enzymes tend to be this type of protein

intermediate filaments

a component of the cytoskeleton that gives cells mechanic strength

covalent cross-linkage

can either tie together 2 amino acids in the same polypeptide chain or join together many polypeptide chains in a large protein complex; helps maintain protein structures in the harsh conditions outside the cell