L3

Question 1

Amino Acid Structure?

Answer 1

Carboxyl, Amino, Hydrogen, Side chain/R group

Question 2

What are motifs?

Answer 2

Combination of 2 or more secondary structures forming a distinct 3D shape ranging between 40 – 50 amino acids

• Associated with a specific function

Question 3

What are domains?

Answer 3

(40-350 amino acids) contiguous
section of a polypeptide chain that folds independently of the rest of the protein

• immunogloblin
• specific function

Question 4

Topological (domains)

Answer 4

distinct location within the same protein

Question 5

What is a module?

Answer 5

a domain found in multipule proteins

Question 6

fibrous proteins

Answer 6

highly ordered, elongated/filamentous

structural role: collagen, keratin, actin

Question 7

globular proteins

Answer 7

compact folding, irregular, mix of secondary structures

functional role 0 enzymes, hormones, immunoglobulins

Question 8

integral membrane proteins

Answer 8

embedded in membranes

Question 9

forces that drive protein folding:

Answer 9

hydrogen bonds, electrostatic, van der waals, hydrophobic interactions

Question 10

what is protein folding dictated by?

Answer 10

sequence of amino acid side chains

Question 11

what is protein folding restricted by?

Answer 11

The planar sturcture of peptide bond

Question 12

What are chaperons?

Answer 12

Folding aided by chaperones reduces misfolded proteins

• atp dependant

Question 13

what are the two types of chaperons?

Answer 13

molecular: prevent aggregation and degradation to short segmented regions by stabilizing them.

Chaperonins: folding chambers, provide a microenvironment for proper folding.

Question 14

Misfolded proteins

Answer 14

form aggregates

• resistant to degradation
• associated with pathologies

Question 15

What are pirons

Answer 15

infectious proteins that cause a group of fatal neurodegenerative diseases known as prion diseases.

Question 16

what is denaturation?

Answer 16

unfolding or tertiary and secondary conformations. Disruption of non-covalent links.

• loss of structure = loss of function
• reviersible

Question 17

antibody - protein structure dictates protein function

Answer 17

An antibody is composed of four polypeptide chains (two identical heavy chains and two identical light chains) arranged in a Y-shape, possessing tertiary and quaternary structural levels.

Antibodies are secreted proteins produced by B cells and are found in the extracellular space to recognize and bind to specific antigens as part of the immune response.

Question 18

What action induces protein
conformational changes?

Answer 18

interaction/binding with another protein or molecule, environmental changes, covalent bond attachment or removal

Question 19

function of enzymes?

Answer 19

enzymes are catalysts

lower activation energy by stabilizing transition state intermediates

1. Key-and-Lock Model
2. Induced fit Mode

Question 20

enzyme active sites

Answer 20

binding sites - binds ligand

catalytic - chemical alteration of substrate

reactive side groups that initiate catalysis

Question 21

what are cofactors?

Answer 21

non-protein helpers essential for enzyme activity

Question 22

What are coenzymes?

Answer 22

organic cofactors, often derived from vitamins

ex” NAD+, FAD, Coenzyme A, biotin

Question 23

What does enzyme [protein] specificity mean

Answer 23

an enzyme’s ability to bind to and catalyze a reaction for only a particular substrate or a limited set of substrates.

determined by the unique three-dimensional structure of the enzyme’s active site, which has a complementary shape and chemical properties that allow it to interact precisely with its specific substrate, much like a “lock and key”.

Question 24

What are nucleases?

Answer 24

enzymes that carry out the hydrolysis of phosphodiester bonds of nucleic acids, DNA and Rna

Question 25

what do endonucleases do?

Answer 25

internal cut, recognizes and cleaves specific sequences

Question 26

what do exonucleases do?

Answer 26

trim/remove nucleotides from the free ends 5’ –to– 3’ exonuclease 3’ –to– 5’ exonuclease

Question 27

degradation (proteolysis)

Answer 27

determines protein lifespan

Question 28

lysosomal proteolysis

Answer 28

bulk proteolysis (old and damaged organelles)

Question 29

proteasome proteolysis

Answer 29

protein degradation molecular machines atp dependant

Question 30

what is allostery?

Answer 30

noncovalent binding of a ligand to a different site than the active site that modifies the protein conformation and changes the protein function to a different one.

Question 31

competitive and non-competitive (allostery)

Answer 31

positive - activator negative- inhibitor

Question 32

What is feed-back inhibition?

Answer 32

ensures that the activities of reaction sequences are adjusted to cellular needs

Question 33

what are small g proteins?s

Answer 33

single-subunit proteins that act as molecular switches within cells. binding and hydrolyzing GTP to GDP to control various cellular processes.

Question 34

what is timed regulation? (switch)

Answer 34

small g proteins (monomeric, GTpase, GTP-binding proteins). is a slow GTpase -- hydrolyze

Question 35

When (TRS)

Answer 35

bound to GTP - small g protein active bound to GDP - small g protein inactive

Question 36

GAP

Answer 36

promotes GTP hydrolysis

Question 37

GEF

Answer 37

a protein that acts as a "go" switch for small GTPases, such as Ras and Rho proteins, by catalyzing the exchange of GDP (inactive) for GTP (active)

Question 38

GDI

Answer 38

stabalizes inactive form

Question 39

What is post-translational modification?

Answer 39

covalent attachment: - phosphorylation - ubiquitination - acetylation - n-acetylglucoseamine - methyl = palmitlym

Question 40

what is phosphorylation

Answer 40

switch regulation. phosphase groups (covalently attached) modified structure

Question 41

Reversible phosphorylation included:

Answer 41

kinase - phosphorylation protein (uses ATP) phosphatase - dephosphorylation protein

Question 42

What is proteolytic cleavage and proteins ?

Answer 42

prohormes - inactive hormone precursor zymogens - inactive enzyme precursor precursor must be hydrolyzed (proteolysis) to fold properly

Question 43

Bound to -GTP →

Answer 43

small G protein active

Question 44

Bound to -GDP →

Answer 44

small G protein inactive