Proteins

Question 1

Primary Structure

Answer 1

Determined by AA sequence. If it is abnormal, it causes disease. Amino group on the left & carbozyl groupson the right. When naming it is left to right.

Question 2

Peptide Bond

Answer 2

Between a-carboxyl group and a-amino group of two amino acids. Shorter than a single bond and is rigid and polar. There is no ration at C & N terminals.
Typically in trans formation.

Question 3

Breaking a Peptide Bond

Answer 3

Heat alone will not work. Needs a combination of a strong acid or base and heat.

Question 4

Polypeptide

Answer 4

Each component of the polypeptide chain is a residue. Which is multiple peptide bonds connecting multiple Amino Acids. A portion of the AA is left after hydrolysis.

Question 5

Polarity of Polypeptides

Answer 5

C and N terminals are the only charged groups.

Side chains may have a charge.

Question 6

Secondary Structure

Answer 6

Polypeptide chain forms linear sequence which becomes the backbone. This is made from a regular arrangement of Amino Acids. These linear sequences help form the secondary structures. EX: a-helices, B-sheets and bends.

Question 7

a-Helices

Answer 7

most common helix. Spiral structure that is tightly packed and has a polypeptide backbone. Side chains extend outward and help to avoid steric interference. They are stabilized by hydrogen bonds that extend II and up the spiral and 4 residues ahead. (except the 1st and last residue). There are 3.6 amino acids turn.
EX: Myoglobin (globular) & Keratin (fibrous)

Question 8

Disruptions of A-helices

Answer 8

Proline: creates a kink in the chain because it does not conform to the right handed helix structure.
Charged Amino Acids: create ionic bonds & electrostatically repel each other.
Tryptophan: too bulky of a molecule
BCAA: too bulky

Question 9

B-sheets

Answer 9

All residues have hydrogen bonds. Pleated surface with two or more polypeptide chains or segments of polypeptide chains. may be formed by a single poplypeptide that folds back on itself. Right handed curl in globular protein

Question 10

Parallel B-sheets

Answer 10

N-terminal of the hseets are on the same end

Question 11

AntiParallel B-Sheets

Answer 11

N-terminal of the hseets are on opposite ends

Question 12

B-bends

Answer 12

Reverse direction of the popypeptide chain. This makes it form a compact globular shape. Found on surface of proteins. Often composed of successive antiparallel B-sheets. Stabilized by ionic and H bonds. Contain 4 amino acids. Of those proline and glycine are common.

Question 13

Non-repetitive Secondary Structures

Answer 13

1/2 of the average globular protein is organized into a-helices or b-sheets. The rest of the polypeptide chains have a loop or coil conformation are are not random just lack regular structure.

Question 14

Super-secondary Structures

Answer 14

Globular proteins are constructed by combining secondary structure elements. usually produced by packing side chains from adjacent secondary structural elements close to each other. This forms primarily in the core. They are connected by loop regions.

Question 15

Tertiary Structure

Answer 15

Refers to the folding and final arangement of all the domains. Structure is determined by the primary structure. Hydrophilic groups are on the surface and hydrophobic groups on the interior. Interactions between the AA side chains help folding to form compact structures.

Question 16

Domain

Answer 16

3D structure and functional units of polypeptide chain. More than 200 AA’s in length consisting of 2 or more domains. Core of the domain is built from combinations of supersecondary structures. Folding of the peptide chain occurs inside.

Question 17

Disulfide bonds

Answer 17

Covalent link between SH of 2 cysteine residues. Folding brings the the two into proximity allowing the bond to form. Prevents denaturing in the environment. Found in immunoglobulins secreted by cells.

Question 18

Hydrophobic Interactions

Answer 18

Occurs between AAs with nonpolar side chains (contain O or N). Located in the interior of the polypeptide molecule. Charged molecules are on the surface of the molecule

Question 19

Hydrogen Bonds

Answer 19

Amino Acid side chains contain oxygen of nitrogen bound to hydrogen. Formbed between polar groups on the surface to enhance solubility.

Question 20

Ionic Bonds

Answer 20

Negatively groups interacting with positively charged groups.
EX: Aspartate or glutamate with lyside, arginine or histadine.

Question 21

Protein Folding

Answer 21

Determined by the interactions of side chains chemical properties. Determined by the bonds formed. Correctly formed proteins have low energy states.

Question 22

Denaturation of Proteins

Answer 22

Unfolding and disorganization of the secondary and tertiary structurs. Sometimes this is reversible, typically permanent. Insoluble and precipitate in solution.
Agents: Heat, Detergent, Heavy Metals, Mechanical Mixing, Organic Solvents, Strong Acids and Bases.

Question 23

Chaperones

Answer 23

AKA: Heat Shock Proteins. Assist with proper folding. Interact with the polypeptide in various stages. Protects proteins as they fold by preventing exposed regions from being tangled. Keep proteins from being folded until synthesis is done. Act as a catalyst to increase the rate of folding.

Question 24

Quaternary Structure

Answer 24

2 or more polypeptide chains which may not be related structurally. Held together by noncovalent interactions. They may function together or independently of each other.

Question 25

Misfolding of Protein

Answer 25

Tagged and degraded within the cell. May result in disease. Occurs spontaneously or by genetic mutation. Spontaneous is amyloids. Accumulation of spontanesouly produced proteins can be found in degenerative diseases such as alzheimers and prions.

Question 26

Alzheimers

Answer 26

misfolding gene mutation or abnormal clevage of proteins. Leads to long fibrillar protein assemblies of B-sheets. Proteins accumulate in brain and blood vessels. Second factor neurofibrallary tangles in the brain.

Question 27

Prion

Answer 27

Infective protein. Forms insoluble fibrils, is resistant to proteolytic degradation. causative agent of transmissible spongiform encephalopathies. Creutzfeldt-Jakob disease. Scaple in Sheep and bovine spongiform enephalopathy.

Question 28

Hemeproteins

Answer 28

Heme contained in tightly bound group. Role is determined by the environment of 3D structure of the protein. EX: Heme of the cytochrome is an electron carrier. Heme group of enzymes catalyze the breakdown of hydrogen perioxide, and in hemoglobin and myoglobin bind and carry oxygen.

Question 29

Heme

Answer 29

complex protoporphyrin IX. Heme iron can bind to histadine and the other oxygen. Iron isheld in the center of heme by 4 nitrogen bonds. Heme iron can allow for 2 additional bonds. 1 is held by histadine, the other can bind to oxygen or constituents.

Question 30

Myoglobin

Answer 30

Single polypeptide chain. Hemeprotein present in heart and skeletal muscle. Reservoir and carrier or O2. Increases the rate of transport within the muscle cells. Protein portion creates a microenvironment for the reversible binding of oxygen to the heme.

Question 31

Structure of Myoglobin

Answer 31

80% a-helices. Terminates in proline or by a B-sheet. Heme group is lined with nonpolar amino acids. Interior or myoglobin composed of nonpolar amino acids. Stabilized interiorly by hydrophobic bonds. Charged AA are located on the surface of the molecule and are stabilized by H bonds.

Question 32

Hemoglobin

Answer 32

Found only in red blood cells. Transports CO2 O2 and H. Hemoglobin a is the major form. Tetramer is a 4 polypeptide chain of 2 alpha and 2 beta. Held together by noncovalent interactions. Stabilized by hydrophobic ionic and hydrogen bonds. It transports H and CO2 from tissue to lungs and can carry 4 moleculees of O2 from the lungs to the cells of the body. Oxygen binding of hemoglovin are regulated by allosteric effectors.

Question 33

Deoxygenated Hemoglobin

Answer 33

T form. Taut or tense formation therefore it has restricted movement. LOW oxygen affinity form. two AB dimers interact through a network of ionic and hydrogen bonds that constrain movement of the polypeptide chains.

Question 34

Oxygenated Hemoglobin

Answer 34

R form. Relaxed formation. HIGH oxygen affinity form. The binding of oxygen to hemoglobin causes the rupture of ionic and hydrogen bonds between AB dimers.

Question 35

Oxygen Dissociation Curve

Answer 35

Saturation of O2 Plot of Y measured at different partial pressures of oxygen. Myoglobin has higher affinity at all pO2 values in tissues than hemoglobin does in the lungs. Half saturation is P50 the higher the affinity the lower the P50 number. Higher affinity the more tightly packed the O2 molecules are.

Question 36

Myoglobin CURVE

Answer 36

Hyperbolic shape