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Biochemistry I/II > Lecture 1 and 2 > Flashcards

Lecture 1 and 2 Flashcards

1
Q

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

A

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

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2
Q

What does zwitterionic mean?

A

At ~pH 7.4, COO- and NH3+

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3
Q

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.

A

interior; exterior

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4
Q

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

A

Glycine

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5
Q

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

A

Proline

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6
Q

Which two amino acids have non-polar side chains?

A

Glycine and Proline

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7
Q

What are the 6 polar amino acids?

A

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

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8
Q

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

A

Ser, Thr, and Tyr

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9
Q

Asn, Gln undergo what type of glyocsylation?

A

N linked

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10
Q

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

A

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

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11
Q

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

A

cysteines; disulfide

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12
Q

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

A

True

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13
Q

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

A

Glutamic Acid
Aspartic Acid

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14
Q

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-)?

A

Glutamic (Glu) and Aspartic Acid (Asp)

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15
Q

Which amino acids have a net positive charge; cationic?

A

Histidine
Lysine
Arginine

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16
Q

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+).

A

Lysine and Arginine

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17
Q

___ 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).

A

Histidine

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18
Q

True or False: Charged amino acids cannot undergo hydrogen bonding

A

False - they can !

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19
Q

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)

A

C. Serine (Ser)

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20
Q

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)

A

C. Threonine (Thr)

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21
Q

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

A

Isoforms or Isoenzymes

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22
Q

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

A

carboxyl ; α-amino

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23
Q

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

A

rigid ; planar

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24
Q

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

A

polar

25
Q

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

A

secondary

26
Q

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

A

α-helix

27
Q

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

A

intrachain ; parallel

28
Q

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

A

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

29
Q

____ induce kinks into secondary structures (alpha helix)

A

Prolines

30
Q

What amino acids can disrupt
secondary structures?

A

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

31
Q

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

A

True

32
Q

____: 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).

A

B-sheets

33
Q

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

A

False - right

34
Q

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

A

β-bends or turns

35
Q

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

A

4; proline; glycine

36
Q

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

A

surface

37
Q

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

A

Supersecondary structures or motifs

38
Q

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

A

Tertiary structure

39
Q

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

A

Domains

40
Q

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

A

supersecondary structures or motifs

41
Q

Tertiary structure is stabilized by what four types of interactions?

A
  • Disulfide bonds
  • Hydrophobic interactions
  • Hydrogen bonds
  • Ionic interactions
42
Q

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

A

cystine

43
Q

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

A

Hydrogen bonding

44
Q

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

A

True

45
Q

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

A

ionic interactions

46
Q

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

A

True

47
Q

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

A

True

48
Q

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

A

Recombinant Insulin (negative charge)

49
Q

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

A

Recombinant Insulin Glargine

50
Q

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

A

True

51
Q

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

A

True

52
Q

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)

A

C. Proline (Pro)

53
Q

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

A

A. Carboxyl group and Amino group

54
Q

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

A

B. False

55
Q

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

A

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).

56
Q

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

A

Uncompensated

57
Q

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

A

Partially compensated state

58
Q

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

A

low

59
Q

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

A

high

Biochemistry I/II (23 decks)

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