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Biochem 1 > Test 1: A. A.'s, proteins, etc. > Flashcards

Test 1: A. A.'s, proteins, etc. Flashcards

1
Q

What is h-bonding?

A

Dipole interaction between H (+) and O, N, F (-).

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2
Q

What kind of substances does water dissolve readily?

A

Polar

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3
Q

What kind of molecules are sparingly soluble in water?

A

Nonpolar

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4
Q

In a cation hydration sphere, in what direction do the h atoms face?

A

Outward

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5
Q

In an anion hydration sphere, in what direction do the h atoms face?

A

Inward

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6
Q

Nonpolar:

A

Not water soluble b/c water must form a cage around the structure.

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7
Q

Amphipathic:

A

Molecule that contains both polar and nonpolar components.

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8
Q

What is the orientation of the polar and nonpolar groups from their interaction with water critical to?

A

The overall structure of many biomolecules

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9
Q

What are the 3 points that form the big picture for hydrophobic bonding?

A

Polar out.
Nonpolar in.
Away from water.

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10
Q

What are the 3 interactions in hydrophobic bonding?

A

1) Polar grp interacting with water.
2) Water excludes nonpolar grps.
3) Van der Waals attractions (inside, nonpolar grps.)

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11
Q

What are the 3 functions of a.a.?

A

1) Monomer unit of protein.
2) Precursor to certain hormones and neurotransmitters.
3) Fuel source (starvation, low carbohydrate diet)

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12
Q

What are the 3 structural grps. of aa’s?

A

1) Carboxyl (Sometimes -COOH)
2) NH2 (acts as a base at pka 9-10)
3) R-grps (20 coded for in DNA)

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13
Q

What is the pH of most amino acids?

A
  1. (aka zwitterion form)
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14
Q

Isoelectric (pI):

A

When (+) = (-). At this point it is least soluble in water.

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15
Q

What are the 4 types of side chain residues?

A

1) Nonpolar
2) Polar (uncharged)
3) Acidic (negatively charged)
4) Basic (positively charged)

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16
Q

How many amino acids are coded for in DNA?

A

20

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17
Q

Alanine

A

ala

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18
Q

aspartic acid

A

asp

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19
Q

cysteine

A

cys

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20
Q

glutamic acid

A

glu

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21
Q

glycine

A

gly

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22
Q

phenylalanine

A

phe

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23
Q

proline

A

pro

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24
Q

serine

A

ser

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25
Q

tyrosine

A

tyr

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26
Q

What are the 9 amino acids in the nonpolar group?

A

glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, proline

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27
Q

What are the 6 polar (uncharged) amino acids?

A

serine, threonine, cystein, tyrosine, asparagine, glutamine

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28
Q

What are the 2 acidic (negatively charged) amino acids?

A

aspartic acid, glutamic acid

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29
Q

What are the 3 basic (positively charged) amino acids?

A

lysine, arginine, histidine

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30
Q

What kind of amino acids send to compete with tryptophan for uptake across the blood/brain barrier?

A

Other nonpolar branched chain a.a.’s.

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31
Q

The availability of serotonin is significantly dependent on the uptake of what amino acid into the CNS?

A

Tryptophan

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32
Q

How is tryptophan uptake into the brain effected by exercise? (as related to increased mood/decreased depression)

A

When exercising there is an increased uptake of other nonpolar a.a.’s. With this increase there is less competition for tryptophan to get across the blood/brain barrier.
Increased trp uptake –> Increased serotonin production –> decreased depression and increased sense of well being.

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33
Q

What is glutamate (glutamic acid) used for?

A

Protein synthesis

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34
Q

What is glutamate (glutamic acid) a precursor to?

A

Glutamine (among other things)

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35
Q

What is the primary excitatory neurotransmitter in the CNS?

A

Glutamate

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36
Q

Changes in neuronal activity over time:

A

Plasticity

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37
Q

What is Long Term Potentiation (LTP)?

A

A persistent increase in synaptic strength following high frequency stimulation of a chemical synapse.

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38
Q

What is central sensitization?

A

An enhanced responsiveness of nociceptive neurons in the CNS to their normal afferent input.

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39
Q

What are the 2 things that effect the solubility of a side chain residue?

A

1) Polar > nonpolar

2) Size (smaller size is usually more soluble)

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40
Q

What is the isoelectric point (pI)?

A

The pH where amino acids are least soluble.
(it’s easier to precipitate when all s+ and s- balance out)
(-) = (+)

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41
Q

What is a stereoisomer?

A

Isomers that have atoms bonded in the same order, but with different arrangements in space.

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42
Q

What kind of isomers are the only ones used in protein biosynthesis?

A

L-isomers. (Glycine is the only exception).

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43
Q

What is located on the left side on an L-isomer?

A

The amine grp.

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44
Q

What are 2 categories of stereoisomers?

A

L-isomers (- ; Levarotary)

D-isomers (+ ; Dextrarotary)

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45
Q

What is necessary for a ninhydrin reaction?

A

alpha amino group

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46
Q

What is required in a disulfide bridge formation?

A

2 cysteines in a peptide chain.

Formed through oxidation (?)

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47
Q

What is an amide bonde?

A

When a carbonyl grp is attached to an amino grp or a substituted nitrogen atom.
(Peptide bond if it’s 2 amino acids).

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48
Q

To get a specific peptide, what needs to be done?

A

1) Activate the -COO (-) end

2) Protect the -NH3 (+) end

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49
Q

Ultimately, what determines shape and function of proteins?

A

The primary structure

50
Q

What is a Primary str?

A

Sequence of amino acids in order from the amine to carboxyl end.
(The sequence is dictated by the genes in the DNA).

51
Q

What does histidine do?

A

Physiological buffering.

52
Q

What is Substance P (SP)? What does it do?

A

It’s a neuropeptide that is used as a peptide transmitter in the CNS.

53
Q

What is the most common inhibitory CNS neurotransmitter?

A

Gamma-Aminobutyric Acid (GABA).

Comes from Glutamate

54
Q

What is the main function of peptides?

A

Signal molecule.
eg: Hormones, neurotransmitters
ADH (antidiuretic hormone) causes resorption of water in the kidneys.

55
Q

What are the 3 main types of opiates (endorphins)?

A

Enkephalins, b-endorphins, dynarphins.

all are peptides

56
Q

What are the 5 functional classes of proteins?

A

Enzymes, transport proteins, mechanical support, contractile, and control/signal.

57
Q

Enzymes:

A

Proteins that catalyze rxns (most diverse group).

ex: ribonuclease, myosin ATPase, pepsin.

58
Q

Transport Proteins:

A

Carriers, transporters.

ex: hemoglobin, lipoproteins

59
Q

Mechanical support proteins:

A

Fibrous (there for support).

ex: collagen and keratin

60
Q

Contractile proteins:

A

ex: actin and myosin

61
Q

Control/signal Proteins:

A

Ex: receptors, hormones, NT’s

62
Q

Primary Str.:

A

Sequence of amino acids.

63
Q

What are invariant positions?

A

The sequence has certain critical positions which must contain a given amino acid, any substitution will result in a non-functional protein.

64
Q

Conservative Change:

A

Less critical positions. Different amino acids are found when comparing homologous proteins, however, these are almost always similar types of side chains.
(eg: glu replaced by asp).

65
Q

What are the 3 3D views of proteins?

A

Secondary, tertiary, and quaternary.

66
Q

What are the 2 characteristics of a peptide bond?

A

1) Has delocalized electrons with 40% double bond character and no rotation.
2) Is found in the TRANS position. (no rotation around that peptide bond).

67
Q

What are the 4 types of protein secondary structures?

A

a-helix, B-sheeting, collagen triple helix, and random coil.

68
Q

What determines the specific orientation of the peptide chain in a given section of a protein?

A

Secondary Structure.

It’s a myopic view of a protein since the total structure is ignored

69
Q

What greatly influences the common secondary structures found in most proteins?

A

Hydrogen bonds

70
Q

What is the most common protein secondary structure?

A

a-helix

71
Q

In an a-helix, the H-bonds are between the ___ and ___ amino acids along the peptide chain.

A

1st and 5th.

72
Q

In an a-helix, where are the R-groups located?

A

Roughly lined up on the outside (on one side).

73
Q

What are 2 characteristics of proteins with 100% a-helix arrangements?

A

They are linear and fibrous in nature.

This is also true for other types of secondary structures

74
Q

What amino acid is known as an a-helix breaker?

A

Proline.

75
Q

What are the 2 varieties of B-sheeting?

A

Parallel and Anti-Parallel.

76
Q

Which B-sheeting variety is stronger and why?

A

Anti-parallel b/c the H-bonds line up to make it stronger.

aka pleated B-sheets

77
Q

What is a random coil best for?

A

A denatured protein

78
Q

What is the body’s most prevalent protein?

A

Collagen.

1/3 of the total protein

79
Q

What are the 3 most important amino acids in the composition of collagen?

A

Glycine- Critical role in allowing 3 strands of helix to get close to each other.
Proline- Unique R-group limits orientation of peptide chain.
Hydroxyproline- Modified proline; done after the protein is made.

80
Q

What holds tropocollagen together?

A

Interchain h-bonds between the 3 separate strands of peptide chains.
(The triple helix is NOT an a-helix)

81
Q

What is the critical residue in the x-linking in collagen?

A

Lysine

82
Q

In the tertiary structure, where are the nonpolar grps located?

A

On the inside.

83
Q

In tertiary structure, where are the polar groups located?

A

On the outside.

84
Q

What are the 6 features of globular proteins?

A

1) Very compact
2) Polar side chains are on the outside
3) Nonpolar side chains are on the inside
4) All homologous proteins have the same basic structure
5) A.a. side chains greatly separated on the chain can sit very close together in the 3-D molecule
6) Active site (binding site) generalities

85
Q

Native form:

A

Functional state.

Lowest and most stable energy state.

86
Q

In the Native Form, the specific structure is due to what 2 things?

A

1) Hydrophobic bonding.
2) Specific side chain interactions.
(Ultimately determined by the primary structure).

87
Q

What are the 4 main tertiary interactions (side chain interactions)?

A

Disulfide bridges, kvan der waals forces, salt pairs, and side chain h-bonding.

88
Q

Van der waals forces:

A

Important on interior of protein.

modest contribution

89
Q

Salt pairs:

A

Ionic bonding.

Acidic + Basic.

90
Q

Side chain h-bonding:

A

Between polar uncharged groups and/or peptide bonds.

only with F, O, N

91
Q

What are the 3 types of quaternary structure?

A

Dimer (2 subunits)
Tetramer (4 subunits)
Large aggregate

92
Q

In quaternary structure, what are the 5 things that drive the subunits together?

A

1) hydrophobic bonding and side chain interactions (similar to tertiary str).
2) Van der Waals (eg: leucine zippers)
3) H-bonding
4) Salt pairs
5) Disulfide bridges (not very often)

93
Q

What are the 4 chemical reactions of proteins?

A

Denaturation
Biuret reaction
Hydrolysis
Electrophoresis

94
Q

What is denaturation?

A

The loss of the secondary, tertiary, and quaternary str, but not the primary. (The peptide chain stays intact).

95
Q

What are the 3 types of denaturation?

A

Heat (reversible or irreversible)
Chemical (ex: urea)
Detergents (interferes with hydrophobic effect and van der waals attraction; pH alters acid/base grps)

96
Q

What is a critical player in a Biuret Reaction?

A

Cu(2+). It reacts with the nitrogens in a peptide bond. (It needs 2 peptide bonds).

97
Q

What happens in hydrolysis?

A

Heat and acid is added and the peptide bonds in a protein break and you end up with an amino acid.

98
Q

What is electrophoresis?

A

A way to separate proteins.

Widely used in DNA testing and protein separation.

99
Q

What are the general principles of elextrophoresis?

A

Separation of molecules is based on charge (and size).
Get the movement of charged particles through a solvent in an electrical field.
(Smaller molecules tend to migrate faster)

100
Q

What are the purposes of special proteins?

A

They focus on structure and its connection to function.

eg: Hb, Mb, Antibodies

101
Q

Hemoglobin (HbA):

A

Key protein in O2 transport.

Found in RBCs

102
Q

How many subunits are in Hemoglobin and what are they?

A

4 Subunits;

2 alpha, 2 Beta

103
Q

How many O2 binding sites are in hemoglobin?

A

4

heme grps

104
Q

How much of hemoglobin is an alpha helix?

A

70%

105
Q

What is a heme grp?

A

Porphyrin ring + Fe(2+).
Heme is the non-protein grp.
It’s a prosthetic grp.

106
Q

Met Hb:

A 
contains Fe(3+) within the heme grp.
Doesn't bind O2
107
Q

How does Hb affect O2 binding?

A

Greatly increases oxygen solubility and transport.

S-shaped sigmoidal curve.

108
Q

What is the O2 binding under resting conditions?

A

25% of O2 is delivered to tissues.

109
Q

Myoglobin (Mb)O2 binding:

A

An oxygen carrier (binding protein) in tissues.
Has a single subunit (just one heme grp and 1 O2 binding site).
Has left shifted hyperbolic curve.

110
Q

What does the left shifted hyperbolic curve of Mb mean?

A

Mb binds O2 more tightly than Hb.

111
Q

What is the effect of CO on Hb?

A

CO displaces O2 at low concentration and interferes with O2 transport b/c it competes for the heme grp by binding to Fe(2+).

112
Q

What is the effect of CO2 on Hb?

A

CO2 does not hook up with the heme grps. It binds to the NH3 end of the different subunits. So CO2 does not bind to the heme grp. and simply replaces O2 b/c carboxyl Hb has a lower affinity for O2.

113
Q

What is the bohr effect/proton?

A 
Increased H(+) -> decreased O2 binding -> more O2 delivered to tissues.
(more O2 delivery with more H(+) around)
114
Q

What direction does the curve shift in the bohr effect/proton and in what direction?

A

The hyperbolic curve shifts right b/c of the increased H(+). This yields a decreased O2 binding affinity.

115
Q

Describe the graph of HbF (fetal):

A

There is a left shift O2 binding curve b/c the gamma chain doesn’t bind BPG. The left shift means there’s a higher O2 affinity. (Helps get O2 to the fetus).

116
Q

What is IgG?

A

It’s the antibody prototype for other antibodies. It has the highest plasma count which causes phagocytosis and activates the complement system.

117
Q

What is the structure of IgG?

A

There are 4 separate amino acid chains (2 Heavy and 2 Light). Each chain has a constant and variable section.
It is Y-shaped with bilateral symmetry. There are antigen binding sites on the upper ends of the “Y”

118
Q

What are the functions of antibodies?

A

Recognize non-self chemical groups (antigens).
Cause phagocytosis.
Initiate complement system, group of proteins including some degradative enzymes that can destroy bacterial walls (among other things).

119
Q

What are some general characteristics of antigens?

A

Can be proteins, polysaccharides, nucleic acids, lipids, and/or synthetic polymers.
Must have size (mw > 1000 g/m…usually larger)
Has non-self chemical group.

120
Q

What is a monoclonal antibody?

A

Ab from a single cell line that binds to 1 epitope (w/in a determinant). It is more exacting, but these have to be made artificially.

Biochem 1 (2 decks)

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