Module 2 Flashcards
(176 cards)
1
Q
What are the 5 main components of an amino acid?
A
An amino group, a carboxylic acid group, an alpha carbon, and a side chain
2
Q
What is the chemical formula for an amino group?
A
H2N
3
Q
What is the chemical formula for a carboxylic acid?
A
COOH
4
Q
How is electrostatic charge distributed in an amino acid at neutral pH?
A
The amino group is positively charged and the carboxylic acid is negatively charged.
5
Q
What does pH measure?
A
pH is a logarithmic scale which inversely indicates the concentration of hydrogen ions in a solution
6
Q
What are the properties of a solution with high pH?
A
A high pH solution is basic, meaning it has a low concentration of hydrogen ions.
7
Q
What are the properties of a solution with low pH?
A
A low pH solution is acidic, meaning it has a high concentration of hydrogen ions.
8
Q
Are acids proton donors, or proton acceptors?
A
Proton donors
9
Q
What are the 6 types of amino acid side chains?
A
Polar uncharged
Positively charged (basic)
Negatively charged
Aliphatic (Non-polar/hydrophobic)
Aromatic
H/Glycine
10
Q
How many protein amino acids are there?
A
20
11
Q
Which of the amino acids is actually an imino acid and what is the key impact this has on the protein?
A
Proline - it has an imino group rather than an amino group. The imino group is part of a cyclic structure. This limits the possible rotation between the nitrogen and the alpha carbon, which impacts the shape of the protein backbone.
12
Q
What are the 6 nonpolar/aliphatic/hydrophobic amino acids?
A
Girls Always Vote Left If Provoked OR
GLaciers in ALAska VALiantly Locate ISOlated PROwlers
Glysine (G)
Alanine (A)
Valine (V)
Leucine (L)
Isoline (I)
Proline (P)
13
Q
What are the 3 aromatic amino acids?
A
The AROma of fine Pine and yellow Timber is worth the TRYP
Phenylalanine (F)
Tyrosine (Y)
Tryptophan (W)
14
Q
What are the two alcoholic amino acids?
A
ALCOHOL is a SERious THREat
Serine (S)
Threonine (T)
15
Q
What are the three basic/positively charged amino acids?
A
BASICally, HIS Lost kid Always returned
Histidine (H)
Lysine (K)
Arginine (R)
16
Q
What are the two sulfur-containing amino acids?
A
METhodically Check the path for SULFUR.
Methionine (M)
Cystine (C)
17
Q
What bonds determine the primary structure of a protein?
A
Covalent bonds (aka dipeptide bonds or amide linkages)
18
Q
What are the two ends of a protein called, and how do they differ?
A
The N terminus is at the amino group of the first amino acid added to the protein chain. The C terminus or carboxy end is at the free carboxyl group of the last amino acid
19
Q
Which colour is the N terminus and which is the C terminus? At which end would you find the most recently added amino group?
A
Red is N terminus, blue is C terminus. The most recent amino group is at the C terminus.
20
Q
***List 8 functions of proteins
A
Catalysis
Transport
Structure
Motion
Antibodies
Hormones
Messenger proteins
Genetic information stored in DNA
21
Q
**Give two examples of proteins involved in catalysis
A
DNA polymerase (DNA replication)
Enolase (glycolysis)
22
Q
**Give two examples of proteins involved in transport
A
Haemoglobin (oxygen transport)
Lactose permease (transports lactose across cell membrane)
23
Q
**Give two examples of proteins involved in structure
A
Keratin (hair, nails, horns)
Collagen (connective tissue)
24
Q
**Give two examples of proteins involved in motion
A
Myocin (muscle tissue)
Actin (muscle tissue and cell motility)
25
What is a dipeptide?
A polymer made up of 2 amino acids
26
What is a tripeptide?
A polymer made up of 3 amino acids
27
What is an oligopeptide?
A polymer made up of a few amino acids
28
What is a polypeptide?
A polymer made up of many amino acids
29
What kind of reaction occurs to form a peptide bond?
Condensation reaction
30
Draw the formation of a peptide bond
31
32
What is a chiral carbon?
A carbon linked to four distinct functional groups (none the same as each other)
33
What are enantiomers?
The two mirrored configurations of a molecule containing a chiral centre
34
An enantiomer is one of two kinds of:
Stereoisomers
35
You can obtain a mirror image of a ______ but not a _______ molecule without breaking covalent bonds
Achiral, chiral
36
What is the difference between conformation and configuration?
Conformation refers to the different shapes a molecule can take based on free rotation of its single bonds.
Configuration is the relative position of the atoms in a molecule and can only be changed by cleaving and forming new chemical bonds.
37
Molecular conformations with lower potential energy display _____ stability
Higher
38
\_\_\_bolism generates energy and waste
Catabolism
39
\_\_\_\_bolism uses energy
Anabolism
40
Metabolism is the combination of _______ and \_\_\_\_\_\_\_\_
Catabolic and anabolic biochemical reactions
41
All life on earth uses at least one of these two potential sources of energy:
Sunlight
Potential energy stored in food
42
Anabolism \_\_\_\_\_creases entropy
decreases
43
What is the first law of thermodynamics?
The universe contains a constant amount of energy.
Energy is not created nor destroyed, but it can change form.
44
What is the second law of thermodynamics?
Energy is transferred in a way that increases the randomness (entropy) of the universe.
45
How does a molecule contain potential energy?
In its bonds.
46
Increased entropy mostly occurs through the transformation of various forms of energy into \_\_\_\_\_\_\_\_\_\_\_\_\_
Thermal energy
47
Give the two versions of the Gibbs free energy equation (including definitions)
G = H - TS
ΔG = ΔH - TΔS
G = Free energy
H = Enthalpy
T = Temperature
S = Entropy
Δ = Change (delta)
48
Define enthalpy
Enthalpy is the total energy of a system.
In the case of a biochemical reaction, it includes all the energy stored in the chemical bonds of all the molecules involved in the reaction, as well as the environment around the reaction.
49
How is the T in the Gibbs free energy equation measured?
Degrees Kelvin
50
Why does temperature amplify the entropy term in the Gibbs free energy equation?
Because raising the temperature intensifies random molecular motion, leading to an increased disorder.
51
Define free energy
The portion of energy in a system that is available to do work
52
Define phototroph and name its alternative
A living organism using sunlight as a source of energy
Chemotroph
53
Define chemotroph, and name its alternative
A living organism that extracts energy from chemical molecules
Phototroph
54
Name and define the two types of chemotroph
Lithotrophs extract energy from inorganic molecules
Organotrophs extract energy from organic molecules.
55
Define autotrophs and heterotrophs
To obtain carbon for building biomolecules, autotrophs fix carbon dioxide, while heterotrophs rely on organic molecules.
56
Describe the cyclical relationship between autotrophs and heterotrophs
Autotrophs generate organic molecules and oxygen that will be used by heterotrophs.
Heterotrophs produce water and carbon dioxide used by autotrophs.
57
The flow of energy is irreversible because living organisms cannot convert _____ into \_\_\_\_\_.
Heat, chemical energy
58
Which goes with which?
Phototroph and Chemotroph
Autotroph and Heterotroph
There are autotrophs and heterotrophs within both phototroph and chemotroph categories.
59
A system rich in free energy is _______ and _______ evolves towards a more ______ state with ______ free energy.
Unstable
Spontaneously
Stable
Lower
60
61
When the entropy of a system increases, how does this affect the free energy of the system?
The free energy decreases
62
Describe a spontaneous process
A spontaneous process is characterized by a decrease of free energy as the system evolves toward a more stable state.
63
A spontaneous biochemical reaction - also called ___________ - is thermodynamically \_\_\_\_\_\_\_\_\_\_.
an exergonic reaction
favourable
64
In a spontaneous reaction, the substrate - with a ____ potential energy - is converted into reaction products with a _____ potential energy.
High
Lower
65
A spontaneous biochemical reaction is characterized by _____ of free energy
a decrease
66
What does ΔG refer to?
The change in free energy
67
What kind of reaction does this equation describe?
A spontaneous reaction
68
69
If change of enthalpy is negative, the reaction \_\_\_\_\_\_\_
and is said to be \_\_\_\_\_\_\_\_.
If change of enthalpy is positive, the reaction _______ heat and is said to be \_\_\_\_\_\_\_\_.
releases, exothermic
consumes, endothermic
70
71
What is the carbon in an amino acid called?
The alpha carbon
72
True or false: There are twenty amino acids
False. 20 amino acids are found in proteins, however there are others present in living organisms but not as constituents of proteins. Some Some residues can also be modified after a protein has been synthesized.
73
How many of the amino acids are chiral and what are the exceptions?
19 are chiral - only glycine is the exception as the alpha carbon is bound to 2 hydrogens
74
Which amino acids do not conform to this general structure, and why?
Proline, where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring - this limits the structural flexibility of proteins containing proline
75
How are the bonding orbitals arranged around the alpha-carbon of an amino acid?
Tetrahedral
76
How many stereoisomers can amino acids have, of what kind, and what are they called?
Two - enantiomers - L and D configurations
77
What are these two configurations of an amino acid called?
The first is L configuration and the second is D configuration. You can remember the L configuration because, with the carboxyl group at the top, the L configuration has the amino group to the LEFT of the alpha carbon.
78
Which stereoisomer of amino acids naturally occurs in proteins?
L configuration
79
Where can amino acids in the D configuration be found?
D-Amino acid residues have been found only in a few, generally small peptides, including some peptides of bacterial cell walls and certain peptide antibiotics.
80
How are cells able to specifically synthesize the L isomers of amino acids?
The active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereospecific.
81
Which four aliphatic non-polar side-chains tend to cluster together, and why?
The side chains of alanine, valine, leucine, and isoleucine
tend to cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions.
82
Which two amino acids contain sulfur?
Methionine and cysteine
83
Which functional group of tyrosine tends to form hydrogen bonds?
The hydroxyl group
84
Describe which aromatic R groups hydrophobic or hydrophilic?
They are all hydrophobic (non-polar) - Tyrosine and tryptophan are significantly more polar than phenylalanine, because of the tyrosine hydroxyl group and the nitrogen of the tryptophan indole ring.
85
At which wavelength do most proteins absorb light?
280 nm
86
Among amino acids, what is unique about histidine and what functions does this allow?
Histidine is the only common amino acid having an ionizable side chain with a pKa near neutrality. In many enzyme-catalyzed reactions, a His residue facilitates the reaction by serving as a proton donor/acceptor.
87
Which amino acids are amides?
What change would be made to create an amide of the amino acid pictured?
Aspartate and asparagine
Glutamate and glutamine
The carbon of the carbonyl group binds with a nitrogen and two hydrogens (and forms a double-bond with the remaining oxygen)
88
An acid is a proton \_\_\_\_\_\_\_\_
A base is a proton \_\_\_\_\_\_\_\_\_
Donor
Acceptor
89
A zwitterion can act as either ______ or \_\_\_\_\_\_\_
Acid
Base
90
What is a zwitterion?
A dipolar ion: a molecule or ion having separate positively and negatively charged groups.
91
Under what conditions do amino acids predominantly occur as zwitterions?
In aqueous solutions at neutral pH.
92
What do "amphoteric" and "ampholyte" describe?
Amphoteric - the ability to act as an acid or a base
Ampholyte - a substance that is amphoteric
93
What does pKa indicate?
The pH at which 50% of the functional groups exist in their protonated state and 50% exist in their deprotonated state.
Therefore if the pH is below the pKa of a functional group, protonate it!
94
What are the protonated and deprotonated forms of the amine functional group?
Protonated: NH3+
Deprotonated: NH2 + H+
95
What are the protonated and deprotonated forms of the carboxyl functional group?
Protonated: COOH
Deprotonated: COO- + H+
96
The _____ the pKa value, the stronger the acid
Lower
97
What is the difference between Ka and pKa
Ka is the acid dissociation constant of a solution
pKa is the negative base-10 logarithm of Ka. This makes the Ka values larger and therefore easier to interpret, and means that the tendency of a group to give up a proton decreases tenfold as the pKa increases by one unit
98
The tendency of a functional group to give up a proton decreases by ______ as the pKa _______ by one unit
tenfold
increases
99
What is the normal pH of intracellular fluid and blood?
7.4
100
Define isoelectric point
The characteristic pH at which the net electric charge of the molecule is zero
101
Where is the isoelectric point on this titration curve?
102
What do the blue boxes indicate in this titration curve?
The pH regions of greatest buffering power for the molecule
103
In an aqueous environment, only _____ has an R group (pKa = 6.0) providing significant buffering power near the neutral pH usually found in the intracellular and extracellular fluids of most animals and bacteria
Histidine
104
What is the reference molecule for the L and D configurations?
glyceraldehyde
105
Draw the formation of a peptide bond
106
Under standard biochemical conditions, does the equilibrium favour 2 amino acids or formation of a dipeptide?
2 amino acids
107
What is the difference between a polypeptide and a protein?
Although the terms “protein” and “polypeptide” are sometimes used interchangeably, molecules referred to as polypeptides generally have molecular weights below 10,000, and those called proteins have higher molecular weights
108
Peptide bonds in proteins are quite _stable/unstable_, with an average half-life (t1/2) of about ____ under most intracellular conditions.
Stable
7 years
109
Which parts of a peptide contribute to the overall acid-base properties of the molecule
The _terminal_ amino and carboxyl groups and ionizable side chains
110
The pKa value for an ionizable R group _changes/remains the same_ when an amino acid becomes a residue in a peptide
Changes - due to the loss of charge in the alpha-carboxyl and alpha-amino groups which have formed peptide bonds, the interactions with other peptide R groups, and other environmental factors
111
What relationship exists between the molecular weights of biologically active peptides and proteins and their functions.
There is no generalizable relationship
112
What do oligomeric and protomer mean when describing a protein
When describing a multi-subunit protein, oligomeric indicates that at least 2 of the subunits are identical. Protomer is the name for each identical subunit
113
True or false: the different polypeptide chains in multi-unit proteins are always linked by non-covalent bonds
False - they are usually linked with non-covalent bonds but in some cases they can be linked with disulfide bonds
114
How do you calculate the approximate number of amino acid residues in a simple protein?
Divide the molecular weight of the protein by 110
115
What process breaks polypeptides back down into free amino acids?
Hydrolysis
116
Define a simple protein, and name and define the alternative
Simple proteins contain only amino acid residues and no other chemical constituents.
Conjugated proteins proteins contain permanently associated chemical components in addition to amino acids - these are called prosthetic groups
117
Name and define six classes of conjugated protein
118
Amino groups on an amino acid are weakly _acidic/basic?_
Basic
119
What kind of side chains do the non-polar aliphatic amino acids have?
Alkyl side chains
120
Which amino acid is present in proteins much less frequently than others?
Methionine
121
What does the ring structure of aromatic amino acid side chains allow them to do?
Absorb UV light
122
Which positively charged amino acid could also be considered aromatic?
Histidine
123
What kind of side-chain does cysteine have?
Thiol side-chain
124
Describe the formation and function of cystine
Two cysteines can be oxidised to form cystine
Cystine can form covalent cross-links within proteins
Cystine is hydrophobic
125
What kind of reactions is cysteine often involved in within cells?
Redox reactions
126
What kind of bonds can amide amino acids form?
They can form hydrogen bonds as H donors or H acceptors
127
What kinds of bonds can hydroxy amino acids form?
Hydrogen bonds with water or other H-acceptor groups on the protein
128
What defines a hydroxy amino acid and what does this allow?
The presence of a hydroxy group (-OH) - these can form phosphate esthers
129
What are peptide-hydrogen bonds?
hydrogen bonds between the carbonyl oxygen of one peptide bond and the amide hydrogen of another peptide bond within the same protein
130
Membrane proteins are more ________ than globular proteins
Hydrophilic
131
How are peptide bonds formed (what conditions are needed)?
Peptide bonds between amino acids are formed on the catalytic site of the ribosome, by peptidyl transferase
132
Is haemoglobin water soluble?
Yes
133
What defines an alpha amino acid?
Has the amino group and carboxyl group both bonded to the same alpha carbon. (Beta amino acids have the carboxyl group bonded to a carbon adjacent to the alpha carbon)
134
Are basic amino acids positively or negatively charged at low pH?
Positively charged
135
A protein with more acidic amino acids than basic amino acids will have a pI that is _____ 7
Below
136
Which amino acids are dissolved in water at neutral pH?
Those without an ionizable side-chain
137
At low pH, an amino acid will be _______ charged
positively
138
What is another name for aromatic side chain rings?
Benzene rings
139
Which two aliphatic amino acids are NOT usually found in the centre (away from water) of protein structures
Glycine and proline
140
What are the aromatic amino acids used to synthesize?
Tryptophan: serotonin
Tyrosine: thyroid hormones
Phenylalanine: dopamine
141
Which of the aromatic amino acids is not as good at absorbing UV light?
Phenylalanine
142
What causes sickle cell anemia?
Glutamate 6 (polar0 is replaced by valine (non-polar) in the beta subunit of haemoglobin. The creation of a new hydrophobic region causes multiple subunits to attract by hydrophobic forces, meaning the haemoglobin is polymerised beyond its usual tetramer quarternary structure. The polymerized hemoglobin distorts red blood cells into an abnormal sickle shape.
143
State the main functions and level of conservation of cytochrome c and cytochrome p450
Cytochrome c is mainly found in the mitochondria and acts as an electron transporter between membranes. It's primary structure is highly conserved across related species.
Cytochrome p450 is a liver enzyme needed for detoxification pathways, include metabolism of medications. Cytochrome p450 shows polymorphisms between individuals within a species.
144
Describe the evolution of myoglobin and haemoglobin
(see module 2 lecture 2)
145
What bonds stabilise secondary structure?
Hydrogen peptide bonds
146
Describe the properties of peptide bonds as they relate to secondary structure
They are rigid and planar from alpha-carbon to alpha-carbon (usually trans).
They have a partial double bond character.
Rotation of the planes is possible around the phi and psi bonds linking the amino and carboxyl groups respectively to the alpha carbon.
This rotation is limited by steric hindrance.
147
How are the peptide-hydrogen bonds aligned in an alpha-helix?
Roughly parallel with the helical axis
148
How are R-groups arranged in an alpha-helix?
They protrude outwards and slightly towards the N terminus
149
Which direction of alpha-helix is found in proteins?
Right handed - as if you were going up a spiral staircase and the outside rail was in your right hand
150
Which protein amino acids can participate in the alpha-helix structure?
All of them to some extent, although proline disrupts the structure by limiting rotation around the phi angle bond and glycine because its side-chain supports other conformations.
151
Which four amino acids are most often found in alpha-helices?
Alanine, Glutamate, Leucine, and Methionine
152
What kinds of bonds stabilise beta-sheets?
Peptide hydrogen bonds between strands
153
Which is stronger - parallel or antiparallel beta sheet - and why?
Antiparallel is stronger as the peptide-hydrogen bonds are better aligned (more linear)
154
How are R groups arranged in a beta-sheet?
They protrude above and below the sheet, perpendicular to the hydrogen bonds. On each strand, they alternate between above and below.
155
How are beta-turns stabilised?
Hydrogen bonds from a carbonyl oxygen to an amide nitrogen three residues down the sequence
156
Over how many residues is a beta turn formed, and which amino acids are commonly found in beta turns?
A 180 degree turn is achieved over four amino acids
Proline is often found in position 2, or glycine in position 3.
157
Where in a protein to beta turns often occur?
Near the surface, and in crevices between domains.
158
What is the difference between a type 1 and type 2 beta turn?
Type 1 contains proline at position 2
Type 2 contains glycine at position 3
159
Which amino acids can participate in peptide-hydrogen bonds?
All except proline
160
How many amino acid residues are in each turn of an alpha-helix?
3.6
161
Where are beta sheets most often found in a protein?
At its core
162
What types of R-groups are more likely to participate in beta sheets?
Hydrophobic R-groups e.g. valine and isoleucine
163
What is another name for a negatively charged carboxyl group?
A carboxylate
164
Which is the strongest and which is the weakest non-covalent bond?
Strongest - ionic
Weakest - van der Waals
165
Which non-covalent bond is directional?
Hydrogen bond - is strongest when the two dipoles are aligned
166
Is a disulfide bond more likely to occur in extracellular or intracellular space?
Extracellular - disulfide bonding is an oxidisation reaction and requires an oxidising environment which is found extracellularly
167
How many conformations can the peptide bond take and what greek letter represents this bond?
Two only - cis and trans (defined by position of the alpha carbon) - due to the planar nature of the bond, aka its partial double bond character
It is represented by omega (ω) and is either 180 degrees or 0 degrees.
168
Which conformation does the peptide bond usualy take, why, and what is the exception?
Trans - meaning the alpha carbons are on opposite sides. This is because when the carbons are in cis conformation, their side chains tend to clash.
The exception is the peptide bond on the n-terminal side of a proline, which can be cis or trans.
169
What is the geometric term to describe the phi and psi bonds on the amino acid backbone?
Dihedral
170
Hydrogen bonds between what and what stabilise alpha helices?
Between the carbonyl of residue N, and the amino group of residue N+4
171
Which of the three types of secondary structure often contributes to the actives sites of a protein and why?
Beta loops/turns as they have a lot of conformational flexibility to shape themselves around ligands
172
Why does a proline often break an alpha helix?
Because of the imino ring, it has no free hydrogen to bond with a carbonyl group
173
What motif is this?
Beta alpha beta - two beta strands joined by an alpha helix
174
Define a domain
This is an independent folding unit within a single polypeptide, usually comprised of several motifs. It can form and maintain its tertiary structure independent to the rest of the protein.
175
Describe the quarternary structure of alcohol dehydrogenase
It is a homodimer of two polypeptides, each containing two domains. It has two active sites - one at the intersection of the two domains in each subunit.
176
If protein folding reduces entropy, why is it thermodynamically favourable?
Because when water molecules encounter hydrophobic surfaces, this limits their possible movements and reduces entropy. When the hydrophobic elements of a protein are folded away into the protein's core, more water molecules can move freely, so overall system entropy is increased.
