Session 4.1a - Pre-Reading [Book] Flashcards
Lippincott's Illustrated Reviews Biochemistry Chapter 1 pp1-12 https://meded.lwwhealthlibrary.com/content.aspx?sectionid=49716372&bookid=774 http://www.uobabylon.edu.iq/eprints/paper_11_9137_715.pdf (186 cards)
1
Q
What are the most abundant and functionally diverse molecules in living systems?
A
Proteins
2
Q
What does virtually every life process depend on?
A
The class of macromolecules known as proteins.
3
Q
Give an example of a function of enzymes and polypeptide hormones?
A
They direct and regulate metabolism in the body.
4
Q
What can direct and regulate metabolism in the body?
A
Enzymes and polypeptide hormones.
5
Q
What do contractile proteins in muscles do?
A
Permit movement
6
Q
What proteins permit movement in muscle?
A
Contractile proteins
7
Q
What type of molecule is collagen?
A
A protein
8
Q
What is the function of collagen in bone?
A
It forms a framework for the deposition of calcium phosphate crystals, acting like the steel cables in reinforced concrete.
9
Q
What proteins can you find in the bloodstream?
A
- Haemoglobin
- Plasma albumin
10
Q
Where can you find haemoglobin and plasma albumin and what do they do (broadly)?
A
In the bloodstream, shuttle molecules essential to life
11
Q
What is the function of immunoglobulins?
A
To fight infectious bacteria and viruses
12
Q
What proteins fight infectious bacteria and viruses?
A
Immunoglobulins
13
Q
What is the role of a protein?
A
They display an incredible diversity of functions!
14
Q
What is common to all proteins?
A
Their structure; they are linear polymers of amino acids
15
Q
What are linear polymers of amino acids called?
A
Proteins
16
Q
What are proteins made up of?
A
Amino acids
17
Q
How are proteins formed?
A
Simple building blocks (amino acids) join to form proteins that have unique 3D structures, making them capable of performing specific biological functions.
18
Q
How many amino acids are found in nature?
A
More than 300 different amino acids have been described in nature
19
Q
How many amino acids code for mammalian proteins?
A
Only 20 are commonly found as constituents of mammalian proteins
20
Q
How are amino acids coded for in humans?
A
There are only 20 amino acids that are coded for by DNA in mammalian proteins
21
Q
What is the genetic material in the cell?
A
DNA
22
Q
What does DNA code for in humans?
A
20 amino acids which join to form proteins
23
Q
What does each amino acid have?
A
- A carboxyl group,
- A primary amino group, and
- A distinctive side chain (“R-group”)
bonded to the - a-carbon atom
(Figure 1.1A).
24
Q
Which is the only amino acid that doesn’t have a carboxyl group?
A
Proline, which has a secondary amino group
25
What is the side chain of an amino acid often known as?
The "R-group"
26
What is the "R-group"?
The amino acid side chain
27
What are the carboxyl, amino group and side chain bonded to in amino acids?
The a-carbon atom
28
What is physiological pH?
Approximately pH 7.4
29
What is the significance of pH 7.4?
It is (approximately) physiological pH
30
What are the electrochemical properties of amino acids at physiological pH?
(~ pH 7.4)
- carboxyl group is dissociated
- amino group is protonated
31
What happens to the carboxyl group of amino acids at physiological pH?
It is dissociated, forming the negatively charged carboxylate ion (COO-)
32
What is dissociated in amino acids at physiological pH?
The carboxyl group
33
Is the carboxyl group negatively or positively charged at physiological pH?
Negatively charged
34
What is the carboxylate ion?
COO-
35
What is COO- known as?
The carboxylate ion
36
What happens to the amino group of amino acids at physiological pH?
It is protonated (NH3+)
37
What is protonated in amino acids at physiological pH?
The amino group
38
Is the amino group negatively or positively charged at physiological pH?
Positively charged
39
Describe the chemical formula of the amino group in an amino acid at physiological pH.
NH3+
40
How are the carboxyl and amino groups combined in proteins?
Almost all of these are combined through peptide linkage
41
Where does peptide linkage occur in amino acids?
Between the carboxyl and amino groups
42
Carboxyl and amino groups of _____ _____ combine to form ________
amino acids, proteins
43
Although at physiological pH, the carboxyl group of amino acids is negatively charged and the amino group positively charged. Why (in general) do these not react?
They are combined with each other through peptide linkage and are therefore not available for chemical reaction. (Fig. 1.1B)
44
In general, carboxyl and amino groups of proteins are not available for chemical reaction because they are bonded together by peptide linkage. What bonding is the exception to this?
Hydrogen bond formation (Fig. 1.1B)
45
Which part of the amino acid dictates the role an amino acid plays in a protein?
It is the nature of the side chains
46
What is the role of the side chain in amino acids?
It is their nature that dictates the role an amino acid plays in a protein.
47
Why is the side chain that dictates the role of an amino acid plays in a protein?
- The carboxyl group and amino groups are constant in amino acids so they do not dictate the unique role of amino acids.
- Furthermore, they are bounded by peptide linkage so they do not have electrochemical properties that can react.
- The side chains are unique and convey different properties to the amino acid
- These are not electrochemically locked so they can react with other amino acids, and it is these individual reactions with unique amino acid sequences to perform unique conformations and therefore proteins
48
How are amino acids classified?
According to the properties of their side chains
49
Give an example of how amino acids can be classified.
Into nonpolar or polar
50
What is nonpolar?
An even distribution of electrons
51
What is polar?
An uneven distribution of electrons
52
How do you describe compounds with an even distribution of electrons?
Nonpolar
53
How do you describe compounds with an uneven distribution of electrons?
Polar
54
Give an example of polar molecules.
Acids and bases (Fig. 1.2 and 1.3)
55
Which molecules can react: polar or nonpolar?
Polar molecules (because they have an uneven distribution of electrons, so they have free electrochemical properties)
56
Draw the structural features of amino acids in their fully protonated form
+H3N, COOH, H, R, Ca
See Fig. 1.1
57
Fig. 1.1a
Label and caption this image
+H3N
58
Draw amino acids combined through peptide linkages (in their fully protonated form)
-NH-C(-R)H-CO-NH-C(-R)H-CO-
See Fig. 1.1B
59
Fig. 1.1B
Label and caption the image
R
60
Where are the dissociable hydrogen ions found in amino acids?
On the carboxyl and amino groups
61
What is the rough pK value for the carboxylate side chain in nonpolar amino acids?
2.3 (this is the value for glycine)
62
What is the approximate pK value for the amino group in nonpolar amino acids?
9.6 (this is the pK value for glycine)
63
What are the nonpolar amino acids?
```
Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline
```
64
What is the side chain for glycine?
H
65
What is the side chain for alanine?
CH3
66
What is the side chain for valine?
CH-CH3-CH3
67
What is the side chain for leucine?
CH2-CH-CH3-CH3
68
What is the side chain for isoleucine?
H-C-CH3-CH2-CH3
69
What is the side chain for phenylalanine?
CH2-benzene ring
70
What is the side chain for tryptophan?
CH2-C-CH-NH-benzene ring
71
What is the side chain for methionine?
CH2-CH2-S-CH3
72
What is the side chain for proline?
CH2-CH2-CH2-N2
73
Fig. 1.2
Label and caption the image
Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline
NONPOLAR SIDE CHAINS
Classification of the 20 amino acids commonly found in proteins, according to the charge and polarity of their side chains at acidic pH is shown here and continues in Figure 1.3.
Each amino acid is shown in its fully protonated form, with dissociable hydrogen ions represented in red print. The pK values for the a-carboxyl and a-amino groups of the nonpolar amino acids are similar to those shown for glycine. (Continued in Figure 1.3.)
74
Which amino acids have uncharged polar side chains?
```
Serine
Threonine
Tyrosine
Asparagine
Glutamine
Cysteine
```
75
What is the side chain for serine?
H-C(H)-OH
76
What is the side chain for threonine?
H-C(-CH3)-OH
77
What is the side chain for tyrosine?
CH2-benzene ring-OH
78
What is the side chain for asparagine?
CH2-C(-NH2)=O
79
What is the side chain for glutamine?
CH2-CH2-C(-NH2)=O
80
What is the side chain for cysteine?
CH2-SH
81
What are the pK values of tyrosine’s side chains?
COOH
82
What are the pK values of cysteine’s side chains?
COOH
83
What are the amino acids with acidic side chains?
Aspartic acid
| Glutamic acid
84
What is the side chain of aspartic acid?
CH2-COOH
85
What is the side chain for glutamic acid?
CH2-CH2-COOH
86
What are the pK values for aspartic acid?
COOH
87
What are the pK values for glutamatic acid?
COOH
88
What are the amino acids with basic side chains?
Histidine
Lysine
Arginine
89
What is the side chain of histidine?
CH2-C=CH-NH-CH-NH
90
What is the side chain of lysine?
CH2-CH2-CH2-CH2-NH3
91
What is the side chain of arginine?
CH2-CH2-CH2-NH-C(-NH2)=NH2
92
What are the pK values of histidine?
COOH
93
What are the pK values of lysine?
COOH
94
What are the pK values of arginine?
COOH
95
Which amino acids have hydrogen in their side chain that will dissociate?
ALL ACIDIC side chains
- Aspartic acid
- Glutamic acid
ALL BASIC side chains
- Histidine
- Lysine
- Arginine
SOME UNCHARGED POLAR side chains
- Tyrosine
- Cysteine
NO NONPOLAR side chains
96
Fig. 1.3
Label and caption the image
Classification of the 20 amino acids commonly found in proteins, according to the charge and polarity of their side chains at acidic pH (continued from Figure 1.2).
UNCHARGED POLAR SIDE CHAINS
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine
ACIDIC SIDE CHAINS
Aspartic acid, Glutamatic acid
BASIC SIDE CHAINS
Histidine, Lysine, Arginine
97
What are the properties of amino acids with nonpolar side chains?
Each of these amino acids has a nonpolar side chain that does not gain or lose protons or participate in hydrogen or ionic bonds (Figure 1.2).
98
What happens to the protons in amino acids with nonpolar side chains?
They are not gain or lost
99
What is the bonding of amino acids with nonpolar side chains?
They do not participate in hydrogen or ionic bonds (Figure 1.2).
100
How can the side chains of nonpolar amino acids be thought of as?
“Oily” or lipid-like
101
What interactions do amino acids with nonpolar side chains make?
Hydrophobic interactions
102
Describe the interactions of nonpolar amino acids and explain why they occur?
Nonpolar side chains do not:
- Gain or lose protons
- Participate in hydrogen or ionic bonds
They can be thought of as:
- “Oily” or lipid-like
- Promote hydrophobic interactions
(Figure 2.10)
103
What sort of environment is an aqueous solution?
A polar environment
104
Give an example of a polar environment
In aqueous solutions
105
Where are nonpolar amino acids found in aqueous solutions?
Aqueous solutions are polar, so the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein (Figure 1.4).
106
What is the hydrophobic effect?
Nonpolar amino acids clustering together in the interior of the protein in a polar environment e.g. aqueous solution
107
Nonpolar amino acids tend to cluster together in the interior of a protein in nonpolar amino acids. What is this effect known as?
The hydrophobic effect
108
What is the hydrophobic effect the result of?
The hydrophobicity of the nonpolar R-groups
109
Why does the hydrophobic effect occur in aqueous solution?
The hydrophobicity of the nonpolar R-groups act like droplets of oil that coalesce in an aqueous environment.
110
Where do nonpolar R-groups lie in proteins found in aqueous solutions?
They fill up the interior of the folded protein, to help give it its three-dimensional shape.
111
Where are nonpolar amino acids found in hydrophobic environments?
The nonpolar R-groups are found on the outside surface of the protein (Fig. 1.4)
112
Give an example of a hydrophobic environment.
A membrane
113
A membrane is an example of what type of environment?
A hydrophobic environment
114
Why are nonpolar R-groups found on the outside surface of the protein in membranes?
Membranes are hydrophobic environments, so the R-groups interact with the lipid environment (Fig. 1.4).
115
What are the hydrophobic interactions of nonpolar amino acids important for?
These hydrophobic interactions are important in stabilising tertiary protein structure
116
What is the location of nonpolar amino acids in proteins?
The NONPOLAR amino acid side chains interact with HYDROPHOBIC environments.
Therefore, in AQUEOUS solutions, a POLAR environment, nonpolar amino acids cluster together on the INSIDE of the protein,
Whereas in MEMBRANES, a HYDROPHOBIC environment, they cluster together on the OUTSIDE of the protein.
117
Fig. 1.4
Label and caption the image
Soluble protein
- Nonpolar amino acids cluster in the interior of soluble proteins.
- Polar amino acids cluster on the surface of soluble proteins.
Membrane protein
- Nonpolar amino acids cluster on the surface of membrane proteins. (Cell membrane)
Location of nonpolar amino acids in soluble and membrane proteins.
118
Draw the location of nonpolar and polar amino acids in a soluble protein (aqueous solution) and a membrane protein.
```
Soluble protein (i.e. aqueous solution - polar environment)
- Nonpolar inside; polar outside
```
```
Membrane protein (hydrophobic environment)
- Nonpolar inside the cell membrane
```
119
[Clinical]
What is sickle cel anaemia?
A sickling disease of red blood cells
120
A sickling disease of red blood cells is known as?
Sickle cell anaemia
121
[Clinical]
What is the pathophysiology of sickle cell anaemia?
The substitution of polar glutamate by nonpolar valine at the sixth position in the beta subunit of haemoglobin
122
[Clinical]
What amino acid is substituted in sickle cell anaemia?
Glutamate for valine
123
What is the significance of the glutamate to valine substitution in sickle cell anaemia?
Glutamate - polar
| Valine - nonpolar
124
At which structural position is valine substituted for glutamate in sickle cell anaemia (a haemoglobinopathy)?
The sixth position in the b subunit of haemoglobin
125
How does proline differ from other amino acids?
Proline’s side chain and a-amino N form a rigid, five-membered ring structure (Figure 1.5).
126
Which amino acid has a rigid, fibre-membered ring structure?
Proline (via its side chain and a-amino N)
127
Describe proline’s amino group.
Proline has a secondary (rather than a primary) amino group (due to its five-membered ring structure).
(The N is bound to two R groups - the central carbon atom and a methane group to form a ring)
128
What is the classification of amino groups?
Primary, secondary, tertiary
The number relates to the amount of R groups bound to the N
```
Primary = R1-NH2
Secondary = R1-R2-NH
Tertiary = R1-R2-R3-N
```
129
What is proline an example of?
An imino acid
130
Which of the 20 amino acids made from DNA is frequently referred to as an imino acid?
Proline
131
What is an imino acid?
A molecule that contains both imino (>C=NH) and carboxyl (COOH) functional groups.
132
What is the difference between an amino and imino acid?
Amino acids have amines: a functional group that contain a basic nitrogen atom with a lone pair
Imino acids have imines: a functional group containing a carbon-nitrogen double bond
133
What is the biological relevance of the unique geometry of amino acid proline?
- Contributes to the formation of the fibrous structure of collagen
- Interrupts the a-helices found in globular proteins
134
What amino acid contributes to the formation of the fibrous structure of collagen?
Proline
135
What amino acid often interrupts the a-helices found in globular proteins?
Proline
136
Fig. 1.5
Label the secondary and primary amino group. Name the amino acids and caption it.
Comparison of the secondary amino group found in proline with the primary amino group found in other amino acids, such as alanine.
Secondary amino group - Proline
Primary amino group - Alanine
137
Draw the structure of an amino acid with a secondary amino group and the structure of an amino acid with a primary amino group.
Secondary - proline R2-NH2
Primary - alanine R1-NH3
138
Describe the properties of amino acids with uncharged polar side chains.
These amino acids have zero net charge at neutral pH
139
Which uncharged polar amino acids can lose a proton from their side chains?
Cysteine and tyrosine (at alkaline pH)
140
At what pH can cysteine and tyrosine can lose a proton at what pH?
Alkaline (see Figure 1.3).
141
What do serine, threonine and tyrosine have in common?
They are amino acids with uncharged polar side chains, which each contain a polar hydroxyl group
142
Which amino acids contain a polar hydroxyl group?
Serine, threonine and tyrosine
143
What are the reactive properties of serine, threonine and tyrosine?
They have a polar hydroxyl group, so they can participate in hydrogen bond formation (Figure 1.6)
144
What do the side chains of asparagine and glutamine contain?
A carbonyl (C=O) and an amide (-NH2) group
145
Which amino acids contain a carbonyl and an amide group?
Asparagine and glutamine
146
What are the electrochemical properties of asparagine and lgutamine?
They both contain a carbonyl group and an amide group - both of which can also participate in hydrogen bonds.
147
What are the electrochemical properties of nonpolar uncharged amino acids?
These can either lose a proton (at alkaline pH) or participate in hydrogen bonds.
148
Fig. 1.6
Label and caption the diagram.
Hydrogen bond between the phenolic hydroxyl group of tyrosine and another molecule containing a carbonyl group.
Tyrosine
Hydrogen bond
Carbonyl group
149
Draw a hydrogen bond between the side chain of tyrosine and another molecule containing a carbonyl group.
Tyrosine (H3N-C(-COOH)-H)
-CH2-benzene ring-OH
H hydrogen bonded to O=C (carbonyl group)
See Figure 1.6
150
What is special about the amino acid cysteine?
The side chain contains a sulfhydryl group (-SH)
151
Which amino acid contains a sulfhydryl group (-SH)?
Cysteine
152
Why is cysteine biological important?
Its side chain contains a sulfhydryl group (-SH), which is an important component of the active site of many enzymes.
153
Which amino acid is an important component of the active site of many enzymes and why?
Cysteine, because it contains a sulfhydryl group (-SH).
154
What can occur to two cysteines in proteins?
The -SH groups of two cysteines can become oxidised to form a dimer (cystine).
155
What happens when two -SH groups from two cysteines become oxidised to form a dimer?
This creates a covalent cross-link called a disulfide bond.
156
What type of bond is a disulfide bond?
Covalent bond between two sulfurs (-S-S-)
157
Which amino acid can form disulfide bonds?
Cysteine (because it has an -SH group)
158
What is the biological significance of disulfide bonds?
Many extracellular proteins are stabilised by disulfide bonds.
159
Give an example of extracellular protein stabilisation.
Disulfide bonds (from cysteine residues; -S-S-).
160
What is albumin?
A blood protein that functions as a transporter for a variety of molecules
161
What blood protein is stabilised by disulfide bonds?
Albumin
162
Which amino acids can be phosphorylated?
Serine, threonine and rarely, tyrosine.
163
What is phosphorylation?
Addition of a phosphate group
164
Why can serine, threonine and (rarely) tyrosine be phosphorylated?
Due to their polar hydroxyl group on their side chain, acting as a site of attachment
165
Which amino acids can serve as sites of attachment for oligosaccharide chains in glycoproteins?
Asparagine, serine or threonine
166
How do asparagine, serine or threonine act as a site of attachment for oligosaccharide chains in glycoproteins?
Asparagine - amide group
Serine or threonine - hydroxyl group
167
Define oligosaccharide chains in glycoproteins.
Oligosaccharide - "few sugars" - a small amount of monosaccharide units forming a carbohydrate
Glycoproteins - proteins with carbohydrate groups attached to the polypeptide chain
168
Which amino acids are proton donors?
Aspartic and glutamic acid (acidic side chains).
169
Amino acids with acidic side chains are proton ______
donors
170
Amino acids that are proton donors have ______ side chains
acidic
171
How are aspartic and glutamic acid found at physiologic pH?
The side chains are FULLY IONISED, containing a NEGATIVELY charged carboxylate group (-COO-)
172
How do aspartic and glutamic acid appear in their fully ionised form?
Negatively charged carboxylate group (-COO-)
173
When are aspartic and glutamic acid found with a negatively charged carboxylate group?
At physiologic pH (side chains fully ionised).
174
What is the name of aspartic and glutamic acid at physiologic pH?
Aspartate and glutamate, respectively
| this emphasises that these amino acids are negatively charged at physiologic pH - see Figure 1.3
175
Which amino acids accept protons?
Basic amino acids (see Figure 1.3)
176
Amino acids with basic side chains are proton ______
acceptors
177
Amino acids that are proton acceptors have ______ side chains
basic
178
How do lysine and arginine appear at physiologic pH?
Their side chains are fully ionised and positively charged
179
Which amino acids have fully ionised and positively charged side chains at physiologic pH?
Arginine and Lysine
180
How does histidine appear at physiologic pH?
It is weakly basic, so the free amino acid is largely uncharged
181
Which amino acid is weakly basic?
Histidine
182
What are the properties of a weakly basic amino acid?
E.g. histidine; its free amino acid is largely uncharged
183
What form does histidine take when incorporated into a protein?
This depends on the ionic environment provided by the polypeptide chains of the protein; so can be positively charged or neutral.
184
Why can histidine be positively charged or neutral?
Because it is weakly basic, so it depends on the ionic environment surrounding it
185
What is the biological relevance of histidine?
Histidine is weakly basic so can have a positively charged or neutral status depending on its environment.
This is significant because it contributes to the role it plays in the functioning of proteins such as haemoglobin (see Mechanisms of the Bohr effect).
186
Why is histidine important in haemoglobin?
Histidine is weakly basic so can have a positively charged or neutral status depending on its environment.
This is significant because it contributes to the role it plays in the functioning of proteins such as haemoglobin (see Mechanisms of the Bohr effect).
