Protein Structure and Function

Question 1

Roles played by proteins:

Answer 1

Biochemical, cellular, physiological, phenotypic

Question 2

Classes of Proteins

Answer 2

Enzymes
Structural proteins
Motility proteins
Regulatory proteins
Transport proteins
Hormonal proteins
Receptor proteins
Defensive proteins
Storage proteins

Question 3

Enzymes

Answer 3

Catalysts; increase rates of chemical reactions

Question 4

Structural proteins

Answer 4

Provide physical support and shape

Question 5

Motility proteins

Answer 5

Involved in contraction and movement

Question 6

Regulatory proteins

Answer 6

Control and coordinate cell function

Question 7

Transport proteins

Answer 7

Move substances across membranes

Question 8

Hormonal proteins

Answer 8

Communication between cells

Question 9

Receptor proteins

Answer 9

Enable cells to respond to stimuli

Question 10

Defensive proteins

Answer 10

Protect against disease

Question 11

Storage proteins

Answer 11

Reservoirs of amino acids

Question 12

Amino Acids

Answer 12

Monomers of proteins; 20 different amino acids; modified amino acids also exist; amino acid sequence unique for each particular protein; same basic structure; all amino acids (except glycine) contain a chiral/asymmetric alpha carbon; each amino acid has a unique R group which have different properties (basic, acidic, hydrophilic, hydrophobic)

Question 13

Polymerization of Amino Acids

Answer 13

Amino acids are linked together into a linear polymer by dehydration/condensation reactions which form a peptide bond

Question 14

Directionality of polypeptides

Answer 14

N-terminus (amino group) and C-terminus (carboxyl group)

Question 15

Protein Synthesis

Answer 15

The process of elongating a chain of amino acids; immediate product is a polypeptide

Question 16

Difference between polypeptides and proteins:

Answer 16

A polypeptide is the linear sequence of amino acids (primary structure); a protein is the association of secondary and tertiary structures to provide a functioning product

Question 17

Monomeric protein

Answer 17

Contains a single polypeptide subunit

Question 18

Multimeric protein

Answer 18

Contains two or more polypeptide subunits; dimers, trimers, tetramers, etc

Question 19

Bonds and interactions important in protein folding and stability:

Answer 19

Hydrogen bonds
Ionic bonds
Disulfide bonds
Van der Waals Forces
Hydrophobic interactions

Question 20

Levels of Organization in Protein Structure:

Answer 20

Primary - sequence of amino acids
Secondary - local folding of polypeptide
Tertiary - three dimensional conformation
Quaternary - interactions between monomeric proteins to form a multimeric unit

Question 21

Secondary Structure

Answer 21

Describes local regions of structure that result from hydrogen bonding between NH and NO groups along polypeptide backbone
Two major patterns: alpha helix and beta sheets

Question 22

Alpha Helix

Answer 22

Spiral in shape; 3.6 amino acids per turn; hydrogen bonds between NH and CO of every 4th amino acid; R groups outwardly facing; can have hydrophobic or hydrophilic faces

Question 23

Beta Sheets

Answer 23

Beta strands; formed by hydrogen bonds between different polypetides or different regions of a single polypeptide; parallel or antiparallel conformation

Question 24

Motifs

Answer 24

Certain units of secondary structure that consist of short stretches of alpha helices and beta sheets; found in many proteins; ie - hairpin loop, helix-turn-helix

Question 25

Tertiary Structure

Answer 25

Reflects the unique aspect of the amino acid sequence because it depends on interactions of the R group; difficult to predict; results from the sum of the hydrophobic interactions and electrostatic interactions; provides function of protein

Question 26

Native Conformation

Answer 26

The most stable three-dimensional structure of a particular polypeptide

Question 27

Broad Categories of Proteins

Answer 27

Fibrous and globular

Question 28

Fibrous Proteins

Answer 28

Extensive regions of secondary structure; highly ordered, repetitive structure; ie- fibroin (silk), keratin (hair), collagen (skin and tendons), elastin (ligaments and blood vessels)

Question 29

Globular Proteins

Answer 29

Folded into compact structures; most common; more diverse; many have domains

Question 30

Domains

Answer 30

A discrete locally folded unit of tertiary structure; usually has a specific function; typically 50-350 amino acids; proteins with similar functions will often share a common domain; proteins with multiple functions usually have a separate domain for each function

Question 31

Prediction of Tertiary Structure

Answer 31

Primary structure determines the final folded shape of a protein; however, we are not able to predict how a given protein will fold due to the infinite possibilities and specific function

Question 32

Quaternary Structure

Answer 32

The level of organization with the subunit interactions and assembly; specifically applies to multimeric proteins; some proteins consist of multiple identical subunits, or a variety of subunits

Question 33

Formation of Tertiary Structure

Answer 33

Usually spontaneous, however, chaperones are sometimes required to aid in overcoming energy requirements and avoidance of thermodynamic pits

Question 34

Beyond Quaternary Structure

Answer 34

Higher levels of assembly are possible for multiprotein complexes; often formed for multistep processes

Question 35

Misfolding of Protein

Answer 35

Cause of several diseases:

Alzheimers, Huntingtons, Cystic fibrosis, BSA (Mad Cow), certain cancers

Question 36

Modes of Protein Function Regulation

Answer 36

Proteolysis, phosphorylation/dephosphorylation; ligand binding; zymogens; GTPase switches; redox state; recruitment; localization

Question 37

Experimental Determination of Protein Structure

Answer 37

X-ray diffration- crystallized samples; highest resolution

Cryoelectron microscopy- allows structure determination of non-crystalline specimens; useful with multiprotein complexes