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Biochem Exam 1 > Chapter 5 - Amino Acids and Proteins > Flashcards

Chapter 5 - Amino Acids and Proteins Flashcards

1
Q

Describe the general structure of an amino acid.

A

Alpha Carbon bonded to a carboxyl group (COO-), and amine group (most commonly primary:NH3+), hydrogen atom, and an R side chain

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2
Q

Why is the middle carbon of an amino acid assigned as “alpha” carbon?

A

It’s the carbon directly adjacent to the carboxyl group

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3
Q

The alpha carbon is chiral in all 20 amino acids except for 1. Which one?

A

Glycine

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4
Q

Virtually all amino acids are present in the D or L form??

A

L

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5
Q

What are the acidic amino acids?

A

Aspartate (Asp, D), glutamate (Glu,E)

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6
Q

Which are the basic amino acids?

A

Lysine, arginine, histidine

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7
Q

Which amino acid can act both as an acid AND a base?

A

Histidine

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8
Q

What are the 3 amino acids with hydroxyl groups? Which is primary, which is secondary, and which is aromatic?

A

Primary hydroxyl - Serine
Secondary hydroxyl-Threonine
Aromatic hydroxyl - Tyrosine

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9
Q

When going from serine to threonine to tyrosine, do rates of dephosphorylation increase or decrease?

A

Increase

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10
Q

Are primary, secondary or tertiary alcohols more reactive?

A

Tertiary is the most reactive

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11
Q

Sulfur appears in 2 amino acids. Which ones and explain how they are incorporated into the structure.

A

Cysteine - sulfhydryl
Methionine - thioether

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12
Q

What is a thioether?

A

S bonded to 2 R groups

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13
Q

What is a sulfhydryl?

A

S bonded to an H and an R group

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14
Q

Why is Sulfur considered a SOFT nucleophile?

A

Its valence electrons are more shielded and distant from the nucleus. Thus, it will readily reverse its nucleophilic additions

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15
Q

What is significant about 2 cysteine molecules interacting in the protein structure?

A

-HS and -SH can form a DISULFIDE BRIDGE -S-S-.
This further stabilizes protein structure

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16
Q

Why do alterations in pH affect amino acids??

A

Changes in pH affect the charges of the dissociable acid and base groups.

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17
Q

At a minimum, how many dissociable groups will an amino acid have and what are they?

A

2 - Carboxyl group is a weak acid and will lose its H, NH2 (amine) is a base and will accept a proton

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18
Q

How many common amino acids are there that are used as the building blocks of proteins?

A

20

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19
Q

How many amino acids have an L conformation?

A

19 - Glycine is neither not chiral

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20
Q

What are the 2 acidic amino acids??

A

Aspartate (Asp,D)
Glutamate (Glu, E)

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21
Q

Which 2 amino acids contain sulfur in the side chain??

A

Methionine (Met,M)
Cysteine (Cys, C)

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22
Q

What is the largest amino acid??

A

Tryptophan

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23
Q

Which 3 amino acids can be an O glycosylation site?? (Oxygen attached to sugar)

A

Serine, Threonine, tyrosine

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24
Q

Which is more reactive to N glycosylation - R or Q??

A

R is more reactive. Arginine is a base

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25
Which are the 3 aromatic amino acids??
Phenylalanine (phe,F) Tyrosine (tyr, y) Tryptophan (trp, W)
26
Lysine gives ____plateaus when titrated. Why??
3 plateaus. It has 3 polarizable groups
27
What are the 3 base amino acids??
Lysine (Lys,K) Histidine (His,H) Arginine (Arg, R)
28
What could be the precursor of dopamine??
Tyrosine
29
What is the function of a disulfide bond in a protein??
Stabilizes protein structure
30
primary structure determines _________structure
3D
31
What are the 3 things that make up the secondary structure of a protein
Alpha helix Beta sheet Beta turns
32
Most proteins are ______soluble
water
33
Proteins embedded in the cell membrane are _______soluble
lipid
34
Is the main chain or side chain involved in Hydrogen bonding in alpha helix/beta sheet?
ALWAYS main chain
35
Since side chains do not engage in Hydrogen bonding, what is their role in secondary structure formation?
They might prevent it from forming. They can clash and prevent H bonds if the side chain is too big (ex: tryptophan)
36
What 4 intermolecular forces are involved in folding to form the 3D structure?
1. Disulfide bond (covalent) 2. Salt bonds 3. Hydrogen bonds 4. Van der Waals forces
37
Among the 4 intermolecular forces that fold a protein into its 3D structure, which is the strongest??
Disulfide bridge. The other forces are not covalent
38
Does protein folding involve absorbing or releasing heat????
releasing. folded structure is more stable (less energy)
39
Protein denaturation involves the _____ of heat
absorption
40
The enzyme Rnase can be unfolded by heating. When the solution is cooled slowly, the enzyme regains its function. What does this suggest??
Folded protein is at a low energy state Primary structure determines 3D structure
41
Which amino acid has a sulfhydrl (SH) functional grouo?
Cysteine
42
Which 3 amino acids have hydroxyl groups?
Tyrosine (Tyr, Y) Serine (Ser,S) Threonine (Thr, T)
43
What is the most reactive amino acid with a hydroxyl group?
Tyrosine
44
What are Zwitterions??
Molecule that has 2 charged groups but a net charge of zero
45
Most amino acids are _______at a physiological pH
zwitterions
46
Which has a better chance at penetrating the cell membrane?? COO- or COOH
COOH
47
What is isoelectric point??
pH at which the zwitterion has exactly a zero charge
48
How do we determine pI? (isoelectric point)
average the 2pka's
49
How is the peptide bond linked?
alpha amine of 1 amino acid linked by dehydration synthesis to alpha carboxyl group of another amino acid
50
What 2 things do we need to input before forming a peptide bond?
energy (ATP) and an enzyme
51
Amide bond in an amino acid is commonly referred to as a ___________
peptide bond
52
Which is on the left side?? N-terminus or C-terminus?
N terminus on the left, C terminus on the right (both carry a charge)
53
What is the amide (peptide) bond?
C-N
54
What is another name for N-terminus?
Amino
55
What is another name for C-terminus?
Carboxyl
56
What exists at the peptide bond which makes it very stable?
Delocalization (resonance) between O,C,N
57
Peptide bonds are more stable than _______
esters
58
C-N has partial _______ character. Why?
C-N has partial double bond character due to resonance. They can't freely rotate. Restricts 3D arrangement
59
Amino acids start being numbered at the __________side
N-terminus
60
Short chains have _____or less amino acids. They're called ________
short chains have 25 or less amino acids. They're called peptides
61
What is a LINEAR peptide that causes vasoconstriction and increased blood pressure?
Angiotensin II
62
2 cysteine molecules can form a _____bond. In which peptide does this occur??
can form a disulfide bond. occurs in vasopressin
63
Short peptides are often utilized as ______
hormones
64
Longer chains with ____or more amino acids are no longer called peptides, but _______
25 or more, proteins
65
Proteins can be broken down into smaller pieces by _______. Do they require ATP?
proteases,no
66
proteases break peptide bonds through....?
Hydrolysis - addition of water
67
What is the primary structure of a protein?
SEQUENCE and IDENTITY of amino acids in a linear protein chain
68
What is the secondary structure of a protein?
Regular, repeating structural element formed when a segment folds into 3D shape. (alpha helix,beta sheet)
69
What is the tertiary structure of a protein?
The entire 3D arrangement or conformation
70
Most proteins function in their ______structure
tertiary
71
What is the quaternary structure?
3D arrangement of multi subunit protein chains that associate NONCOVALENTLY
72
When is a protein in its lowest energy state?
in its 3D structure
73
What is the function of random coils?? What structure are they categorized under?
random coils link secondary structures together. THEY DO NOT BELONG TO A STRUCTURE
74
Alpha helices are joined by
N-O hydrogen bonds
75
The inner core of an alpha helix is _______
hydrophobic
76
Water solubility is determined by ____groups
R
77
Which 2 properties of amino acids PERMIT helix formation??
Hydrophobic amino acids Side chains have ISOLATED charges
78
Which property of amino acids PREVENTS helix formation?
Neighboring charges (electrical repulsion)
79
What are the 2 different alignments of beta pleated sheets?
parallel and antiparallel
80
What are beta sheets stabilized by?
Hydrogen bonds
81
Do amino acids hydrogen bond at the turn?
NO
82
Domains exist between _______ and ______levels of structure
secondary and tertiary
83
What is a domain?
a combination of secondary structural elements that has a specific finction
84
What is an example of a domain?
binding pocket in an enzyme
85
The core of an alpha helix is ________. Why?
Hydrophobic because there are already numerous hydrogen bonds between N and O , leaving nothing to interact with water
86
What are helix breakers??
amino acids with neighboring charges causing electrical repulsion, preventing alpha helices from forming
87
Domains often correspond to a certain ________
function
88
What are 2 names for domain structure?
motif, supersecondary structure
89
what is a prosthetic group
a small molecule which is bound to a protein to assist its function
90
what is an example of a prosthetic group
heme
91
explain the structure of heme
4 linked pyrrole rings each with a nitrogen attached to a central fe2+. fe2+ has a coordination number of 6
92
what 6 things is fe2+ bound to
4 nitrogen, 1 histidine residue of myoglobin. 6th is either occupied by oxygen (oxygen bound myoglobin) or unoccupied in free myoglobin
93
which binds oxygen more avidly??
myoglobin
94
myoglobin provided oxygen for ____use when the concentration is very ____.
intercellular, low. binds more tightly
95
what is the bohr effect?
diminished binding of oxygen to hemoglobin in response to an increase in concentration of protons
96
protons _____the binding of oxygen to hemoglobin and shift the curve to the ____
decrease, right
97
the oxygen saturation curve for hemoglobin is a ___shaped curve
s
98
in order to purify a protein what must happen first?
must be extracted from its natural environment
99
what is an assay
specific measure of a protein. must be easy to perform
100
what are some measures taken to prevent denaturation during extraction and purification?
cold room, buffers, inclusion of protease inhibitors to prevent hydrolysis, reagents to prevent oxidation of cysteine side groups
101
the methods of separation of molecules are based on what 3 differences?
solubility size charge
102
the main purification is usually achieved by a form of _____
chromatography
103
what is chromatography?
separation of components due to their different affinities towards 2 distinct phases - mobile phase and stationary phase
104
what is affinity chromatography?
attaching a molecule to the stationary phase known to strongly bind the protein
105
what is electrophoresis?
form of chromatography in which the mobile phase is driven by an electrical field imposed by electrodes. used to IDENTIFY proteins present
106
what do chaperones too?
they are proteins that assist and accelerate the process of folding
107
name 3 analysis methods applied to proteins
NMR, mass spectroscopy, X Ray crystallography

Biochem Exam 1 (7 decks)

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