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Biochem > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

What are proteins composed of?

A

Amino acids

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2
Q

What are the 20 AAs referred to as?

A

Common or Standard AAs

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3
Q

What is physiological pH?

A

7.4

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4
Q

Which AA has a secondary amino group and what is another name for it being a secondary amine?

A

Proline

Imino

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5
Q

What is a significant AA present in collagen?

A

Proline

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6
Q

Amino acids are bound via what type of bond?

And through which type of rxn?

A

Peptide linkage/
Amide bond

Condensation/dehydration rxn

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7
Q

AAs can act as an acid or a base, commonly known as…

A

Amphoteric

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8
Q

Neutral molecules which contain both positive and negative charges are called

A

Zwitterions

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9
Q

Where are nonpolar side chains typically found?

A

Interior of proteins in aqueous solutions or on outer surface in hydrophobic environments (membrane in lipid bilayer)

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10
Q

Does proline enhance or interrupt the a-helices found in globular proteins?

A

Interrupt

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11
Q

Where and what is being replaced to cause sickle cell anemia?

A

At the 6th position of the b-subunit of hemoglobin, glutamate is being replaced by valine

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12
Q

Typical life span of healthy red blood cell?

A

90-120 days

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13
Q

Which AAs contain Sulfur?

A

Cysteine and Methionine

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14
Q

Which group often serves as an attachment site for phosphate groups?

A

Hydroxyl groups

-OH

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15
Q

Which group(s) can serve as an attachment site for oligosaccharide chains in glycoproteins?

A

Amide and hydroxyl groups

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16
Q

Which group(s) are important components of the active site of enzymes?

A

Sulfhydryl groups

-SH

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17
Q

What bond is formed when a sugar binds to Asparagine in a condensation rxn?

A

N-Glycosidic bond

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18
Q

What bond is formed when a sugar binds to Serine in a condensation rxn?

A

O-Glycosidic bond

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19
Q

Nonessential AAs

A 
Alanine
Arginine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine
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20
Q

All essential AAs

A 
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
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21
Q

Which chiral form of AAs are found in the proteins, D or L?

A

L

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22
Q

Asymmetric mirror images are called

A

Enantiomers

Optical isomers

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23
Q

Difference between stereoisomer and enantiomer

A

Stereoisomer- differ only in spatial arrangement of their atoms

Enantiomer- non-superimposable mirror images

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24
Q

What does a standard buffer contain?

A

A weak acid and its conjugate base (weak base)

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25
Q

Relationship between Ka, pKa and acid strength

A

Larger Ka -> smaller pKa -> stronger acid

Smaller Ka -> larger pKa -> weaker acid

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26
Q

Ka equation

A

Ka = [H+][A-] / [HA]

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27
Q

pKa equation

A

pKa = -log Ka

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28
Q

Henderson-Hasselbalch equation

A

pH = pKa + log [A-]/[HA]

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29
Q

How many pH units should a buffer be within of the acid’s pKa value?

A

+/- 1 pH unit

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30
Q

What form is predominantly present in a buffer solution when the pH > pKa?

A

Deprotonated

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31
Q

How many pKa values do AAs have?

A

At least 2

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32
Q

The pH at which a molecule possesses no net charge…

A

Isoelectric point

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33
Q

How to solve for isoelectric point?

A

Take average of the 2 pKa values.
If basic, take average of upper 2
If acidic, take average of lower 2

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34
Q

Type of bonding in primary structure

A

Covalent peptide bonds

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35
Q

Type of interaction in secondary structure

A

H-bonding between amino and carbonyl groups

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36
Q

Type of interaction in tertiary structure

A

Hydrogen bonds
Disulfide bons
Ionic interactions
Hydrophobic interactions

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37
Q

Interaction in quaternary structure

A

Interaction of more than one polypeptide chain

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38
Q

How to break peptide bonds?

A

Hydrolyzed nonenzymatically by prolonged exposure to strong acid or base at high temps

Enzymatically, peptidases (proteases)

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39
Q

2 categories of peptidases

A

Exopeptidases

Endopeptidases

40
Q

Types of exopeptidases and where they cut

A

Aminopeptidases- cuts amino end

Carboxypeptidases- cuts carboxyl end

41
Q

Which direction to read an AA peptide sequence?

A

From N-terminus to C-terminus

42
Q

What is a residue?

A

An individual component AA in a polypeptide

43
Q

When naming a polypeptide, what happens to the endings of AA residues?

A

All changed to -yl except last AA residue stays same

44
Q

What type of bond usually present in peptide bonds (cis/trans) and why?

A

Usually trans because of steric hindrance between the -R groups

45
Q

What does DEGENERATIVE mean?

A

Multiple codes code for same AA

46
Q

Where are bond formations in secondary structure?

A

H-bonds between C=O and N-H groups

47
Q

In a-helices, how often are H-bond interactions unto itself?

A

Approximately every 4 AAs

48
Q

Which is tighter, a-helix or b-pleated sheet?

A

a-helix

49
Q

Which direction do R-groups face in a-helix

A

Outward

So they can interact in the tertiary structure and avoid steric interference

50
Q

What AA disrupts the a-helix?

A

Proline

51
Q

Individual segments of b-pleated sheets are called…

A

b-strands

52
Q

T/F

b-sheets can be parallel and antiparallel

A

True

53
Q

What are the specific interactions that occur between R-groups in tertiary structures?

A

Hydrogen bonds
Disulfide bonds
Ionic interactions
Hydrophobic interactions

54
Q

What are Chaperones?

A

Specialized group of proteins that help in proper folding of many proteins

55
Q

Denaturation…

A

The unfolding and disorganization of the proteins tertiary and secondary structures (no hydrolysis of peptide bonds)

56
Q

Examples of denaturing agents

A 
Heat
Organic solvents
Mechanical mixing
Strong acids/bases
Detergents
Ions of heavy metals (Pb, Hg)
57
Q

How are subunits held together in quaternary structure?

A 
Noncovalent interactions
(Hydrophobic interactions, H-bonds, ionic bonds)
58
Q

Isoforms…

A

Proteins that perform the same function but have different primary structures

59
Q

Isozymes…

A

Protein isoforms that function as enzymes

60
Q

What typically happens to misfolded proteins?

A

Tagged and degraded by the cell

61
Q

What large factor contributes to the accumulation of misfolded proteins?

A

Age

62
Q

Examples of diseases that can result from accumulation of misfolded proteins and where implicated…

A

Amyloid disease- implicated in Alzheimer’s

Prion disease- induces normal protein to become abnormal. Implicated in

  • bovine spongiform encephalopathy (mad cow)
  • scrapie (in sheep)
  • Creutzfeldt-Jakob (humans)
63
Q

Are hemoglobin and myoglobin tertiary or quaternary?

A

Myoglobin- tertiary

Hemoglobin- quaternary

64
Q

What is at the center of the heme structure?

A

Fe

65
Q

What are the 5th and 6th things to bind to the Fe group in heme?

A

O2 and Histidine

66
Q

Where is myoglobin found?

A

In heart and skeletal muscle.

If found in blood, means something is wrong

67
Q

Where is hemoglobin found?

A

Red blood cells

68
Q

Function of hemoglobin?

A

Main: transport O2 from the lungs to the capillaries of tissues

Also: can transport H+ and CO2 from the tissues to the lungs

69
Q

Structure of hemoglobin?

A

2 a and 2 b subunits, each of which has a heme bi ding pocket

70
Q

What are the two states of hemoglobin and when are they in those states?

A

R (relaxed) state- oxygenated form (less ionic and H-bonding between dimers)

T (taut) state- deoxygenated form

71
Q

Type of O2 dissociation curve for hemoglobin?

A

Sigmoidal

72
Q

Myoglobin has what type of O2 dissociation curve?

A

Hyperbolic

73
Q

Hemoglobin and myoglobin both demonstrate what type of binding? Define

A

Cooperative binding- as first O2 binds, binding of additional O2 is enhanced

74
Q

Bohr effect

A

Effect of a change in the O2 binding affinity of Hb, due to the binding of other ligands

75
Q

Other ligands that bind to Hb?

A

H+
2, 3-bisphosphoglycerate
CO2

76
Q

A decrease in pH leads to a decrease/increase in oxygen affinity of Hb?
And the dissociation curve to shift left/right?

A

Decrease

Right

77
Q

Increased 2,3-BPG leads to an increase/decrease of O2 affinity in Hb?

And causes shift in dissociation curve left/right?

A

Decrease

Right

78
Q

A decrease in CO2 causes an increase/decrease in O2 affinity of Hb?

Shift in dissociation curve left/right?

A

Increase

Left

79
Q

What happens to O2 affinity in Hb when CO is bound?

A

Extreme increase in affinity of O2, so much so that it cannot release O2 to the tissue

80
Q

Hemoglobinopathies examples

A

Sickle cell anemia (Hb S) - glutamate is substituted with valine

Hemoglobin C (Hb C)- glutamate substituted with lysine

Hemoglobin SC - (Hb S + Hb C)

81
Q

Fibrous proteins tend to be mainly for what?

A

Structure

82
Q

Fibrous protein examples

A

Collagen
Elastin
a-keratin
Silk fibroin

83
Q

Most abundant protein in the human body

A

Collagen

84
Q

Composition of collagen…

A

Right handed triple helix, each individual helix itself is Left handed

85
Q

Type of collagen found in teeth, bone, skin and tendons

A

Type 1

86
Q

AA composition of collagen

A

~33% glycine
Up to 30% proline and 4-hydroxyproline
3-hydroxyproline and 5-hydroxylysine also occur

87
Q

A high % of hydroxyproline and hydroxylysine suggest the presence of…

A

Collagen

88
Q

Where does collagen synthesis occur?

A

Both inside and outside the cell

89
Q

Main steps of Collagen Biosynthesis

A
  • after transcription
    1. selected proline and lysine residues are hydroxylated
    2. Selected hydroxylysine residues are glycosylated with glucose and galactose
    3. A triple helix is formed and procollagen is produced
    4. The N-terminal and C-terminal propeptides are cleaved by procollagen peptidases, producing tropocollagen
    5. Self-assembly of tropocollagen into fibrils with cross-linking to form mature collagen fibers
90
Q

Defects in collagen

A

Ehlers-Danlos syndrome (EDS)- fragile stretchy skin and loose joints

Osteogenesis imperfecta (OI)- bones that easily bend and fracture

91
Q

Where are elastin fibers found?

A

Lungs
Walls of large arteries
Elastic ligaments

92
Q

Where is keratin found?

A 
Hair
Wool
Skin
Horns
Fingernails
93
Q

Nonpolar amino acids

A 
Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline
94
Q

Uncharged polar amino acids

A 
Serine
Threonine
Tyrosine
Cysteine
Glutamine
Asparagine
95
Q

Acidic amino acids

A

Aspartate

Glutamate

96
Q

Basic amino acids

A

Lysine
Arginine
Histidine

Biochem (8 decks)

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