L1: Amino Acids Flashcards
(138 cards)
1
Q
What are the three-letter abbreviations for all 20 mammalian amino acids? And the classification
A
Non-polar: Gly (Glycine), Ala (Alanine), Val (Valine), Leu (Leucine), Ile (Isoleucine), Met (Methionine), Pro (Proline), Phe (Phenylalanine), Trp (Tryptophan)
Uncharged polar: Ser (Serine), Thr (Threonine), Tyr (Tyrosine), Asn (Asparagine), Gln (Glutamine), Cys (Cysteine)
Acidic: Asp (Aspartic acid), Glu (Glutamic acid)
Basic: Lys (Lysine), Arg (Arginine), His (Histidine)
2
Q
How many amino acids are commonly found in mammalian proteins?
A
20
These amino acids are referred to as residues.
3
Q
What are the four components bound to the α-Carbon atom of an amino acid?
A
- Carboxyl group
- Hydrogen
- Primary amino group
- Distinctive side chain (R-group)
4
Q
What is the physiological pH of mammalian proteins?
A
~pH 7.4
5
Q
What is a zwitterionic amino acid?
A
A neutral molecule with both positive (-NH3+) and negative (-COO-) charges at physiological pH.
6
Q
What happens to the carboxyl group at physiological pH?
A
A H+ is lost to form a negatively charged carboxylate (-COO-) ion.
7
Q
What happens to the amino group at physiological pH?
A
A H+ is added to form a positively charged amino (-NH3+) group.
8
Q
What determines the role of an amino acid in a protein?
A
The properties of the R-group side chain.
9
Q
What characterizes amino acids with non-polar side chains?
A
- Oil-like
- All Carbon-Hydrogen side chains (hydrocarbons)
- Hydrophobic or nonpolar
10
Q
What occurs to non-polar R-groups in aqueous, polar environments?
A
They cluster in the interior of a protein due to hydrophobic interactions.
11
Q
Where do nonpolar R-groups arrange in hydrophobic environments?
A
At the exterior of a protein in contact with the non-polar lipid environment.
12
Q
What is unique about glycine’s R-group?
A
It has no hydrocarbon R-group (only H).
13
Q
Where is glycine often found in proteins?
A
On the exterior of proteins in β bends to provide flexibility.
14
Q
What makes proline unique among amino acids?
A
It has a secondary amino group that forms a rigid, five-membered ring structure.
Adds rigidity
15
Q
How does proline affect protein structure?
A
It imparts rigidity to proteins (e.g., collagen) and disrupts secondary structure (i.e., α-helices).
16
Q
What is the term for amino acids with uncharged polar side chains?
A
Zwitterionic
Zwitterionic refers to molecules that have both positive and negative charges but are overall electrically neutral.
17
Q
What can side chains of amino acids serve as sites for?
A
Attachment for other compounds
This includes post-translational modifications such as phosphorylation or glycosylation.
18
Q
Which amino acids are targets of phosphorylation by kinase enzymes?
A
Serine, threonine, and tyrosine
These amino acids can have phosphate groups added to them, affecting protein function and activity.
19
Q
What do phosphatase enzymes do?
A
Remove phosphate groups
Phosphatases play a crucial role in reversing the action of kinases.
20
Q
Why are amino acids with uncharged polar side chains considered hydrophilic?
A
They participate in hydrogen bonding
The strong attraction of hydrogen to highly electronegative elements like oxygen contributes to this property.
21
Q
What elements are strongly attracted to hydrogen due to high electronegativity?
A
Fluorine, Oxygen, and Nitrogen
These elements can form hydrogen bonds, contributing to the hydrophilic nature of certain molecules.
22
Q
What is the net charge of amino acids with acidic polar side chains?
A
Net negative charge (anionic)
These amino acids are typically negatively charged at physiological pH.
23
Q
Which amino acids donate protons (H+) from their side chains at physiological pH?
A
Aspartic acid and glutamic acid
These amino acids form fully ionized, negatively charged carboxylate groups (aspartate and glutamate).
24
Q
Fill in the blank: Aspartic acid and glutamic acid form _______ groups at physiological pH.
A
Negatively charged carboxylate groups (-COO-)
This ionization contributes to their acidic properties.
25
What type of side chains do amino acids with basic polar characteristics have?
Cationic, net positive charge
## Footnote
These side chains accept protons (H+s)
26
Which amino acids are fully ionized and positively charged at physiologic pH?
Lysine and arginine
## Footnote
Their side chains contain -NH3+ groups
27
How does the charge of histidine's side chain vary?
Can be positively charged or neutral depending on the ionic environment
## Footnote
This occurs when histidine is incorporated into a protein
28
What type of bonds are disulfide bonds?
Covalent bonds
## Footnote
Formed between sulfhydryl (-SH) groups of cysteine residues
29
What is the role of cysteine in disulfide bond formation?
Contains a sulfhydryl (-SH) group which can form covalent cross-links
## Footnote
This produces cystine through linkage of two cysteine residues
30
In what configurations can cysteines form disulfide bonds?
Adjacent, separated by many amino acids, or on different polypeptide chains
## Footnote
This arrangement helps maintain protein stability
31
What do disulfide bonds help maintain in proteins?
Stability of 3-dimensional shape and prevent denaturation (unfolding of proteins)
## Footnote
Important for proteins like immunoglobulins and insulin
32
What type of interactions do hydrogen bonds represent?
Non-covalent interactions
## Footnote
Occur between hydrogen side chains and electron-rich atoms
33
What enhances solubility in an aqueous environment?
Hydrogen bonds
## Footnote
They occur between –OH, -NH3+ and other side chains
34
What type of interactions occur between negatively and positively charged groups?
Ionic interactions
## Footnote
Examples include –COO- with –NH3+
35
What phenomenon describes the repulsion of like net charges?
Electrostatic repulsion
## Footnote
This principle is fundamental in molecular interactions
36
What type of interactions do nonpolar amino acid side chains participate in?
Hydrophobic interactions
## Footnote
They associate on the interior of globular proteins in aqueous environments
37
Where are polar or charged amino acid side chains typically located in globular proteins?
On the surface of the protein
## Footnote
This is opposite to the arrangement in lipid environments
38
What are proteins comprised of?
20 proteinogenic amino acids linked together by peptide bonds
39
What information does the linear amino acid sequence contain?
All information required to generate a protein molecule with the correct three-dimensional shape and biochemical properties
40
What is the hierarchy of protein folding?
Primary → Secondary → Tertiary → Quaternary (for multisubunit proteins)
41
What can cause many diseases related to proteins?
DNA mutations that alter a protein’s primary amino acid sequence, folding, and function
42
Define primary structure in proteins.
Linear sequence of amino acids linked by peptide bonds and encoded by the nuclear genome (DNA)
43
What is peptide bonding?
Covalent linkages between the α-carboxyl group of one amino acid and the α-amino group of another during translation
44
What are the characteristics of peptide bonds?
* Rigid and planar due to partial double-bond
* Generally in trans configuration
* Almost all α-carboxyl and α-amino groups are combined through peptide bonding
45
What ends does a polypeptide chain contain?
A free amino group (N-terminal end) and a free carboxyl group (C-terminal end)
46
Define secondary structure in proteins.
Non-random, regular repeating periodic arrangements of amino acids near each other in a linear amino acid sequence
47
How do hydrogen bonds stabilize protein secondary structures?
The -NH and –C=O groups of peptide bonds are polar and can be involved in hydrogen bonding
48
Describe the α-helix structure.
Polypeptide takes on a spiral structure with a tightly packed, coiled polypeptide core and side chains extending outward
49
What stabilizes the α-helix structure?
Intrachain hydrogen bonds between the –C=O of one peptide bond and the –NH of another 4 amino acids ahead
50
What is the twist direction of the α-helix?
Right-handed
51
What is the number of amino acids per turn in an α-helix?
3.6 amino acids per turn
52
Define β-sheets or β-pleated sheets.
Hydrogen bonding occurs between peptide bonds of at least two β-strands running perpendicular to the strand axis
53
How are β-strands oriented?
From N-terminal to C-terminal end and arranged either in parallel or anti-parallel
54
What is the twist direction of β-sheets?
Right-handed
55
What percentage of globular protein structure is comprised of nonrepetitive secondary structures?
Approximately 50%
## Footnote
Nonrepetitive secondary structures are not α-helix or β-sheet and include less regular loop or coil conformations.
56
What is the role of bends in protein structure?
Bends are composed of four amino acids, including proline and often glycine
## Footnote
Proline causes a kink, while glycine has the smallest R-group.
57
What are motifs in protein structure?
Multiple secondary structures combined to make recognizable structural forms
## Footnote
Motifs have a tightly packed interior hydrophobic core joined by less compact loops.
58
What determines the tertiary structure of a protein?
Folding of a protein into independent domains, determined by its primary amino acid sequence
## Footnote
Tertiary structure involves the compact arrangement of amino acids in aqueous environments.
59
What are domains in protein structure?
Basic units of protein structure that fold, function, and evolve independently
## Footnote
The core of a domain is a combination of structural motifs.
60
How does correct protein folding occur?
Within seconds to minutes, based on the cumulative mix of interactions between amino acids
## Footnote
Attractive interactions must outweigh repulsive interactions, such as electrostatic repulsion among positively charged amino acids.
61
What role do chaperone proteins play in protein folding?
Aid in the proper folding of proteins
## Footnote
Chaperone proteins are also known as 'heat shock' proteins.
62
Fill in the blank: The core of a domain in protein structure is a combination of ______.
structural motifs
63
True or False: Hydrophobic amino acids are found on the surface of globular proteins.
False
## Footnote
Hydrophobic amino acids are buried in the interior, while hydrophilic groups are on the surface.
64
What type of conformations allow proteins to fold into compact structures?
Less regular loop or coil conformations
65
What type of protein structure includes α-helices and β-sheets?
Repetitive secondary structures
66
What is the quaternary structure of a protein?
Arrangement of multiple independent polypeptides into a multimeric protein complex
## Footnote
Example: hemoglobin
67
How are polypeptide subunits in a multimeric protein held together?
By noncovalent interactions such as hydrogen bonds, ionic bonds, and hydrophobic interactions
68
What are the two possible functions of subunits in a multimeric protein?
Subunits may function independently or cooperatively
69
What are enzymes?
A type of protein that can bind substrate and increase the rate of a given reaction without being utilized or consumed
70
What is the active site of an enzyme?
A special pocket formed by folding of the protein that contains amino acids participating in substrate binding and catalysis
71
What forms when a substrate binds to an enzyme?
An enzyme-substrate (ES) complex
72
What happens to the enzyme upon substrate binding?
Induces a change in enzyme conformation that allows catalysis and conversion of substrate to product
73
How do enzymes regulate their activity?
Increased or decreased in response to cellular needs
74
How much faster are enzymatic reactions compared to uncatalyzed reactions?
Enzymatic reactions are 10^3 to 10^8 times faster
75
What is the specificity of enzymes?
An enzyme usually interacts with one or very few substrates and catalyzes only one type of reaction
76
Where do many enzymes function within the cell?
Within specific organelles to isolate substrates or products from competing reactions
77
What are cofactors?
Nonprotein molecules required by some enzymes to enhance their activity, often ions like zinc or iron
78
What are coenzymes?
Nonprotein molecules that are small organic molecules, often derived from vitamins (e.g., NAD+ contains niacin)
79
What is a holoenzyme?
An active enzyme with its nonprotein component
80
What is an apoenzyme?
An inactive enzyme without its nonprotein component
81
What does an enzyme provide during a reaction?
A more energetically favorable reaction path than an uncatalyzed reaction
82
What is the free energy of activation?
The energy barrier that separates substrates from products
83
What is the transition state in a reaction?
A high-energy intermediate formed prior to the formation of the product
84
What must molecules contain to complete a reaction?
Enough energy to overcome the energy barrier of the transition state
85
How does the free energy of activation affect reaction rates?
If low, more molecules will have sufficient energy to reach the transition state, and the reaction will proceed more quickly
86
What characterizes uncatalyzed reactions?
They have a slow reaction rate
87
What characterizes enzymatic reactions?
They have a more rapid reaction rate
88
What is the rate or velocity of a reaction (V)?
The number of substrate molecules converted to product per unit of time, measured in µmol of product formed per minute (µmol/min).
89
What factors influence reaction rates of enzymatic reactions?
* Substrate concentration
* Temperature
* pH
90
How does substrate concentration affect the rate of an enzyme-catalyzed reaction?
The rate increases with substrate concentration until Vmax is reached.
91
What happens at high substrate concentrations in enzyme-catalyzed reactions?
Saturation of all active sites occurs, leading to a plateau in reaction rate (Vmax).
92
Can the reaction rate increase after Vmax is reached?
No, the rate cannot increase further by adding more substrate if enzyme concentration is constant.
93
What are the two types of curves that describe enzyme kinetics?
* Hyperbolic (M-M kinetics)
* Sigmoidal (allosteric regulation)
94
How does temperature affect enzymatic reaction velocity?
Velocity usually increases with temperature until a peak is reached; cold temperatures can render enzymes nonfunctional.
95
What occurs if the temperature rises above a certain point during enzyme reactions?
A decrease in velocity and eventual temperature-induced enzyme denaturation.
96
What role does pH play in enzymatic reactions?
Enzymes require specific concentrations of [H+] to function optimally; extreme pH can cause denaturation.
97
Fill in the blank: The rate of an enzyme-catalyzed reaction increases as substrate concentration increases until a maximum velocity known as _______ is reached.
Vmax
98
What does the Michaelis-Menten model describe?
The relationship between reaction velocity and substrate concentration in enzyme-catalyzed reactions.
99
In the Michaelis-Menten model, what forms when the enzyme combines with its substrate?
An enzyme-substrate (ES) complex.
100
What are the rate constants in the Michaelis-Menten model?
k1, k-1, and k2.
101
What does the Michaelis-Menten equation describe?
How reaction velocity (v0) varies with substrate concentration ([S]).
102
What are the two assumptions of the Michaelis-Menten equation?
* [S] >> [E]
* Rate of ES product formation equals rate of ES breakdown.
103
What is the formula for the initial reaction velocity (v0) in the Michaelis-Menten equation?
v0 = Vmax [S] / (Km + [S]).
104
What does Vmax represent in the Michaelis-Menten equation?
Maximal velocity of the reaction.
105
What is Km in the context of the Michaelis-Menten equation?
Michaelis constant = (k-1 + k2) / k1.
106
What does a small Km indicate about an enzyme's affinity for a substrate?
High affinity for the substrate; low [S] needed to reach ½ Vmax.
107
What does a large Km indicate about an enzyme's affinity for a substrate?
Low affinity for the substrate; high [S] needed to reach ½ Vmax.
108
What type of curve results when plotting v0 against [S] in the Michaelis-Menten model?
A hyperbolic curve.
109
What is the purpose of transforming the data to plot 1/v0 versus 1/[S]?
To create a straight line for easier calculation of Km and Vmax.
110
What is the Lineweaver-Burke plot also known as?
The double-reciprocal plot.
111
What is the equation of the Lineweaver-Burke plot?
1/v0 = Km / Vmax + 1/Vmax * 1/[S].
112
What does the x-axis intercept of the Lineweaver-Burke plot represent?
-1/Km.
113
What does the y-axis intercept of the Lineweaver-Burke plot represent?
1/Vmax.
114
What does the slope of the Lineweaver-Burke plot represent?
Km/Vmax.
115
What is an inhibitor?
Any substance that decreases the rate of an enzymatic reaction.
116
What types of bonds do irreversible inhibitors form with enzymes?
Covalent bonds.
117
What is the effect of irreversible inhibitors on enzyme activity?
Prevents the enzyme from interacting with the substrate again, resulting in a loss of enzyme activity.
118
What types of inhibitors form noncovalent bonds with enzymes?
Reversible inhibitors.
119
What are the two types of reversible inhibitors?
* Competitive inhibitors
* Noncompetitive inhibitors
120
How do competitive inhibitors affect Vmax and Km?
Vmax = unchanged, Km = apparently increased.
121
What can overcome the effect of competitive inhibitors?
Adding enough substrate.
122
What is an example of a competitive inhibitor?
Statin drugs that compete with HMG-CoA.
123
How do noncompetitive inhibitors affect Vmax and Km?
Vmax = decreased, Km = unchanged.
124
Do noncompetitive inhibitors compete for binding with the substrate?
No.
125
What is the clinical effect of antibiotics like penicillin?
Irreversible inhibition of enzymes required for bacterial cell wall synthesis.
126
What type of inhibition do vasodilators like captopril exhibit?
Competitive inhibition of angiotensin-converting enzyme (ACE).
127
What type of inhibition does aspirin cause?
Irreversible inhibition of COX-1 and COX-2 enzymes.
128
What is the effect of increased substrate concentration on reaction rates?
Leads to an increase in reaction rate.
129
What is the typical intracellular concentration range of substrates in relation to Km?
Normally in the range of the Km.
130
Name three ways enzyme activity can be regulated.
* Allosteric regulators
* Covalent modifications
* Altered rate of enzyme synthesis/degradation
131
What are allosteric enzymes regulated by?
Effector molecules that bind non-covalently at a site other than the active site
## Footnote
Allosteric regulation allows for fine-tuning of enzyme activity.
132
What is the typical structure of allosteric enzymes?
Usually multi-subunit proteins
## Footnote
They often catalyze the committed step of a metabolic pathway.
133
Where is the allosteric site located in allosteric enzymes?
On a subunit that is not itself catalytic
## Footnote
This allows for regulation independent of the active site.
134
What type of curve do allosteric enzymes typically show?
Sigmoidal curve
## Footnote
This is due to substrate binding at multiple sites.
135
What effects can effectors have on allosteric enzymes?
They can inhibit or stimulate enzyme activity and modify enzyme affinity or maximal catalytic activity
## Footnote
K0.5 refers to the affinity for substrate, and Vmax refers to maximal catalytic activity.
136
What is a homotropic effector?
The substrate itself serves as the effector, usually functioning as a positive effector
## Footnote
It enhances the catalytic properties of the enzyme at other substrate-binding sites.
137
What is a heterotropic effector?
The effector is different than the substrate
## Footnote
Often involved in feedback inhibition.
138
What role does feedback inhibition play in allosteric regulation?
A later product in the pathway serves as a negative effector for an earlier reaction
## Footnote
This helps regulate the appropriate amounts of a product needed by the cell.
