Lecture 1 and 2

Question 1

Each amino acid has an α-Carbon atom bound to:
___, ___, ___, and R group

Answer 1

-Carboxyl (-COOH) group
-Primary amino (-NH2) group
-Hydrogen
-Distinctive side chain (-R)

Question 2

What does zwitterionic mean?

Answer 2

At ~pH 7.4, COO- and NH3+

Question 3

In aqueous environments (i.e., cytoplasm), nonpolar R-groups cluster in a protein’s ___

In hydrophobic environments (i.e., cell membranes) nonpolar R-groups arrange at a protein’s ___ in the lipid environment.

Answer 3

interior; exterior

Question 4

Which amino acid lacks a hydrocarbon side chain, so it is often found on the exterior of proteins in β-bends to provide flexibility?

Answer 4

Glycine

Question 5

R-group and α-amino N (2° amino group) form a rigid ring structure that adds rigidity to proteins and
disrupts 2° structure

Answer 5

Proline

Question 6

Which two amino acids have non-polar side chains?

Answer 6

Glycine and Proline

Question 7

What are the 6 polar amino acids?

Answer 7

1) Tyrosine
2) Threonine
3) Serine
4) Glutamine
5) Asparagine
6) Cysteine

Question 8

What three amino acids are phosphorylated by kinase enzymes; dephosphorylated by phosphatases?

Answer 8

Ser, Thr, and Tyr

Question 9

Asn, Gln undergo what type of glyocsylation?

Answer 9

N linked

Question 10

True or False: hydrophilic properties of non-polar amino acids is due to the electronegativity of oxygen in H2O

Answer 10

FALSE - hydrophilic properties of polar amino acids is due to the electronegativity of oxygen in H2O

Question 11

Oxidation of -SH groups of two ____ allows them to participate in covalent cross-links called ___ bonds to form a cystine dimer

Answer 11

cysteines; disulfide

Question 12

True or False: Disulfide bonds
stabilizes 3-dimensional structure and prevent denaturation of
proteins outside of the cell

Answer 12

True

Question 13

Which two AA have net negative charge; anionic; exhibit electrostatic repulsion?

Answer 13

Glutamic Acid
Aspartic Acid

Question 14

In which AA’s do acids donate protons (H+s) from their R-groups at physiologic pH (pH 7.4) to form fully ionized, negatively charged carboxylate groups (-COO-)?

Answer 14

Glutamic (Glu) and Aspartic Acid (Asp)

Question 15

Which amino acids have a net positive charge; cationic?

Answer 15

Histidine
Lysine
Arginine

Question 16

What two + amino acids
accept protons (H+s) to their R-groups at physiologic pH to form fully ionized, positively-charged amino groups (-NH3+, =NH2+).

Answer 16

Lysine and Arginine

Question 17

___ is a weak base; however, when incorporated in a protein, its side chain can be positively-charged or neutral depending upon its ionic environment (i.e., Hb binding to O2).

Answer 17

Histidine

Question 18

True or False: Charged amino acids cannot undergo hydrogen bonding

Answer 18

False - they can !

Question 19

Which of the following amino acids is often
phosphorylated by kinase enzymes?

A. Proline (Pro)
B. Cysteine (Cys)
C. Serine (Ser)
D. Aspartic acid (Asp)

Answer 19

C. Serine (Ser)

Question 20

In an aqueous environment (i.e., cytoplasm), which
amino acid residue is most likely to be on the exterior
of a protein?

A. Alanine (Ala)
B. Leucine (Leu)
C. Threonine (Thr)
D. Tryptophan (Trp)

Answer 20

C. Threonine (Thr)

Question 21

_______: different primary structure but perform the same or similar functions.

Answer 21

Isoforms or Isoenzymes

Question 22

Peptide bonds are a covalent linkage between the ___ group of one amino acid and the ____ group of another

Answer 22

carboxyl ; α-amino

Question 23

Partial double bond nature makes peptide bonds ___and ___ (usually in transconfiguration).

Answer 23

rigid ; planar

Question 24

The –C=O and –NH groups of peptide bonds are uncharged but ___ since they can participate in hydrogen bonding

Answer 24

polar

Question 25

Protein ____ structure is a non-random, regular repeating local periodicity in the arrangement of amino acids in a polypeptide

Answer 25

secondary

Question 26

____: spiral structure with tightly-packed, coiled polypeptide core with R-group side chains extending outward.

Answer 26

α-helix

Question 27

Alpha helices are stabilized by ____hydrogen bonding between peptide bonds four amino acids apart that run ___ to the helical axis to stabilize the helix.

Answer 27

intrachain ; parallel

Question 28

True or False: In an alpha helix, all bonds undergo hydrogen bonding

Answer 28

False - All but first and last peptide bonds undergo hydrogen bonding

Question 29

____ induce kinks into secondary structures (alpha helix)

Answer 29

Prolines

Question 30

What amino acids can disrupt secondary structures?

Answer 30

Amino acids with bulky side chains (Trp, Ile, Val)

Question 31

True or False: A Large numbers of charged amino acids(i.e., Glu, Asp) may form ionic bonds or electrostatically repel each other, thereby disrupting 2 structures

Answer 31

True

Question 32

____: two or more complete polypeptide chains (β-strands) OR segments of a polypeptide joined in sheets through hydrogen bonding between all peptide bond groups PERPENDICULAR to the β-strand axis (intrachain or interchain).

Answer 32

B-sheets

Question 33

True or False: Beta sheets have a left-handed twist

Answer 33

False - right

Question 34

____: reverse the direction of a polypeptide chain (often in β-sheets) to form compact, globular shapes stabilized by hydrogen and ionic bonds.

Answer 34

β-bends or turns

Question 35

Beta bends are usually _ amino acids in length and often contain __ to provide the “kink” in the chain and __ for flexibility

Answer 35

4; proline; glycine

Question 36

Charged amino acids of Beta bends are usually on the ___ of proteins

Answer 36

surface

Question 37

______: combination of multiple secondary structures to produce recognizable structures within a tightly-packed globular protein.

Answer 37

Supersecondary structures or motifs

Question 38

____: folding of proteins into domains as determined by primary structure

Answer 38

Tertiary structure

Question 39

____: fundamental 3D structural and functional elements within a protein having unique, independent characteristics

Answer 39

Domains

Question 40

Core of domains is comprised of a combination of ___ or ___

Answer 40

supersecondary structures or motifs

Question 41

Tertiary structure is stabilized by what four types of interactions?

Answer 41

* Disulfide bonds * Hydrophobic interactions * Hydrogen bonds * Ionic interactions

Question 42

Covalent linkage between two sulfhydryl groups (-SH) of two cysteine residues to produce ___, an amino acid

Answer 42

cystine

Question 43

What type of bonding occurs between O- or N-bound hydrogen side chains (-OH, -NH3+) and electronegative groups (-COO-, -C=O)?

Answer 43

Hydrogen bonding

Question 44

True or False: There is enhanced solubility in aqueous environment due to hydrogen bonding with water.

Answer 44

True

Question 45

Negatively-charged groups can interact with positively-charged groups, leading to ___ interations

Answer 45

ionic interactions

Question 46

True or False: Disulfide bonds maintain stability of 3D shape and prevent denaturation of proteins outside of the cell

Answer 46

True

Question 47

True or False: 4 structures are held together by a mix of noncovalent interactions (hydrophobic and hydrogen and ionic bonding)

Answer 47

True

Question 48

Which type of insulin has high electrostatic repulsion and high solubility – fast-acting!

Answer 48

Recombinant Insulin (negative charge)

Question 49

Which insulin has low electrostatic repulsion and increased hydrophobicity – precipitates, slow-dissolving - slow-acting!

Answer 49

Recombinant Insulin Glargine

Question 50

True or False: A single base pair mutation in the β-globin gene changes the tertiary and quaternary structure of hemoglobin to cause polymerization into fibers that result in sickle cell anemia

Answer 50

True

Question 51

True or False: Abnormal amyloid β(Aβ) peptide aggregates accumulate with age and high levels are associated with Alzheimer’s disease.

Answer 51

True

Question 52

Which of the following amino acids creates the kink in a β-bend region of a β-sheet? A. Glycine (Gly) B. Cysteine (Cys) C. Proline (Pro) D. Histidine (His)

Answer 52

C. Proline (Pro)

Question 53

Adjacent amino acids are joined through peptide bonds formed between their _________________________. A. Carboxyl group and Amino group B. Carboxyl group and R-group C. Carboxyl group and hydrogen D. Amino group and R-group

Answer 53

A. Carboxyl group and Amino group

Question 54

α-helix formation involves hydrogen bonding between amide linkages that are perpendicular to the helical axis? A. TRUE B. FALSE

Answer 54

B. False

Question 55

Which of the following changes to the primary structure of recombinant insulin would make it faster acting? A. Add more leucine residues to B-chain B. Add more aspartic acid residues to B-chain C. Replace A-chain C- terminal asparagine with serine D. Replace A-chain C- terminal asparagine with valine

Answer 55

B. Add more aspartic acid residues to B-chain Addition of Asp to B-chain will make insulin more negative with more electrostatic repulsion and being more hydrophilic and soluble in an aqueous environment (if the change does not impair the function of insulin).

Question 56

In the ____ state, pH is abnormal and either HCO3- (metabolic) or pCO2 (respiratory) is abnormal, but no compensatory changes are evident (normal range)

Answer 56

Uncompensated

Question 57

If pH is abnormal and compensatory response is evident, what type of compensatory state is this?

Answer 57

Partially compensated state

Question 58

If there is primary acidosis that is compensated, pH will be at ___ end of normal ref. range

Answer 58

low

Question 59

If there is primary alkalosis that is compensated, pH will be at __ end of normal ref. range

Answer 59

high