MGD Session 1 Flashcards
1
Q
What are the main organelles in a mammalian cell?
A
Golgi Apparatus Cytoplasm Lysosome Mitochondria Endoplasmic Reticulum Nucleus Nucleolus Plasma membrane Ribosome
2
Q
Briefly outline the function of the golgi apparatus
A
Glycosylation and Export of proteins
3
Q
Briefly outline the function of the cytoplasm
A
Metabolism of cabohydrates, amino acids and nucleotides, fatty acid synthesis
4
Q
Briefly outline the function of the lysosomes
A
Cellular digestion
5
Q
Briefly outline the function of the mitochondria
A
ATP Synthesis
6
Q
Briefly outline the function of the endoplasmic reticulum
A
Export of proteins, membrane synthesis, protein synthesis, detoxificiation
7
Q
Briefly outline the function of the nucleus
A
DNA synthesis and repair
8
Q
Briefly outline the function of the nucleolus
A
RNA processing and ribosome assembly
9
Q
Briefly outline the function of the plasma membrane
A
Cell morphology and movement
10
Q
Briefly outline the function of the ribosomes
A
Protein synthesis
11
Q
List the features that a eukaryotic cell has where a prokaryote does not.
A
A nucleus Chromosomes Endoplasmic Reticulum Lysosomes Golgi complex The potential to have a vacuole Mitochondria Cytoskeleton
12
Q
List the features that a prokaryotic cell has where a eukaryote does not.
A
Cell Wall
Circular DNA/RNA strand
Flagellum
13
Q
What are the 4 levels of structure of the nucleus in a eukaryotic cell?
A
Nucleotides
DNA
Chromatin
Nucleusow are monomeric units joined?
14
Q
How are monomeric units joined together and what do they form when they join?
A
They are joined by covalent bonds to form macromolecules
15
Q
How are macromolecules held together?
A
Non-covalent interaction
16
Q
What is a hydrogen bond?
A
A bond that forms between a hydrogen atom bound to an electronegative atom and another electronegative atom.
17
Q
What is an ionic interaction?
A
Attraction or repulsion between ions.
18
Q
What does solubility depend on?
A
Ability to form hydrogen bonds
19
Q
What are hydrophobic interactions?
A
Non polar interactions i.e. they do not interact with water
20
Q
When do Van der Waals interactions occur?
A
When two atoms are in close proximity.
21
Q
Define hydrophobic
A
When a molecule will not interact with water and can pass through lipid bilayers.
22
Q
Define hydrophillic
A
Polar. They interact with water and cannot pass through lipid bilayers unassisted
23
Q
Define amphipathic
A
When a molecule has both a hydrophilic (polar) and a hydrophobic (non polar) end
24
Q
What is an alpha helix?
A
a type of regular protein secondary structure. It is a right handed helix with 3.6 residues per turn.
25
What is a beta sheet?
A secondary structure of a protein where the polypeptide chains are in an extended conformation.
26
What is a micelle?
A sphere of amphipathic molecules with hydrophobic parts are on the inside away from water and the hydrophilic heads face outwards, interacting with water.
27
Define pH
A measurement of the concentration of H+ ions in a solution.
28
How does the dissociation of strong acids in water differ to that of weak acids?
Strong acids (and bases) dissociate completely in solution whereas weak ones only partly dissociate.
29
What is pK
The tendency of an acid to dissociate.
30
If the pK value is low, what does this mean?
That the acid is more likely to dissociate in solution.
31
What is a buffer a mixture of?
A weak acid and its conjugate base.
32
What do buffers do?
Resist pH changes
33
When pH > pK ....
the deprotonated form dominates
34
When pH < pK ...
the protonated form dominates.
35
When pH = pK ...
There is an equal amount of acid and its conjugate base
36
How do you calculate pH from pK?
pH = pK + log([A-]/[HA])
37
What is the structure of a simple amino acid?
alpha-C in centre with 4 groups;
- R group
- H group
- COOH group
- NH2 group
38
Which group on the C are amino acids classified by?
Their R group
39
Amino acids are classified on 3 levels. What are these?
- Non polar / polar
- Aromatic / Aliphatic
- Positive / Negative charge
40
What is a zwitterion?
A neutral molecule that has positive and negative charge
41
What is pI?
The isoelectric point. The pH at which the protein has no overall charge.
42
If pI is lower than 7, what does this say about the protein?
It is acidic and it contains many negatively charged amino acids.
43
Name 4 biological reasons why proteins are important.
```
Enzymes (catalysts)
Transporters
Structural support (collagens)
Machines (muscle contraction)
Immune protection (immunoglobulins)
Ion channels
Receptors (hormones, neurotransmitters)
Ligands in cell signalling (growth factors)
```
44
How does a peptide bond form?
Dehydration reaction (condensation)
Bond forms between the Carboxyl group of one amino acid and the Amino group of the second.
- No rotation about the peptide bond
- All atoms in the same plane (horizontally drawn)
- Carbonyl Oxygen and amide hydrogen are in the trans orientation
45
Name the charged amino acids and note their charge.
Glutamate & Aspartate (positive)
| Histidine, Arginine, Lysine (negative)
46
What are the four levels of protein structure?
Primary
Secondary
Tertiary
Quarternary
47
What is the primary structure?
The amino acid sequence
48
What is the secondary structure? Name the two conformations and state the bond type involved.
Local spatial arrangement of the polypeptide backbone (alpha helix or beta sheet). Bonds on either side of the peptide bond can rotate freely and when the angles remain the same, a regular secondary structure is adopted. Hydrogen bonds maintain this structure.
49
What is the tertiary structure?
The 3D structure of the protein by folding of secondary structure.
50
What is a domain?
Regions of the polypeptide that have distinct structures and often serve particular roles.
51
What is a motif?
Folding patterns containing 1 or more secondary structure elements.
52
What is the quarternary structure?
Interaction between different polypeptide subunits within the same protein.
53
What is "homomeric"?
Proteins made up of the same kind of polypeptide.
54
What is "heteromeric"?
Proteins made up of different polypeptide chains.
55
What kind of bonds are involved in the tertiary structure of a protein?
Hydrogen bonds, Van der Waals, Hydrophobic interactions, Disulphide bonds and Ionic interactions
56
What is the quarternary structure?
Hydrogen bonds, Van der Waals, Hydrophobic interactions, Disulphide bonds and Ionic interactions
57
What a globular protein? Give an example
Several structures of secondary structure. Enzymes and regulatory proteins. Example: Haemoglobin
58
What is a fibrous protein? Give an example
A protein with one repeating primary structure. They are useful for structure, support and protection. Example : Collagen.
59
What are the properties of an alpha helix?
Right handed helix, with 3.6 amino acids per turn.
60
What are the properties of a beta sheet?
Parallel or antiparallel conformation (or mixed)
| Extended chain of amino acids with multiple interstrand h-bonds
61
Why does proline act as a helix breaker?
Proline breaks the helix because there is no rotation around the N-C bond.
62
Where do disulphide bonds form when maintaining tertiary structure?
Between Cys residues
63
What is denaturation?
Disruption of protein structure by heat, pH, solvents etc.
64
What is a molecular chaperone?
Something that helps a protein fold if it does not fold spontaneously.
65
What are amyloidoses?
Improper folding of proteins.
66
What can be the result of misfolding?
Disease as the protein is no longer able to function effectively e.g. transmissable spongiform encephalopathies
67
What are the main organelles in a mammalian cell?
```
Golgi Apparatus
Cytoplasm
Lysosome
Mitochondria
Endoplasmic Reticulum
Nucleus
Nucleolus
Plasma membrane
Ribosome
```
68
Briefly outline the function of the golgi apparatus
Glycosylation and Export of proteins
69
Briefly outline the function of the cytoplasm
Metabolism of cabohydrates, amino acids and nucleotides, fatty acid synthesis
70
Briefly outline the function of the lysosomes
Cellular digestion
71
Briefly outline the function of the mitochondria
ATP Synthesis
72
Briefly outline the function of the endoplasmic reticulum
Export of proteins, membrane synthesis, protein synthesis, detoxificiation
73
Briefly outline the function of the nucleus
DNA synthesis and repair
74
Briefly outline the function of the nucleolus
RNA processing and ribosome assembly
75
Briefly outline the function of the plasma membrane
Cell morphology and movement
76
Briefly outline the function of the ribosomes
Protein synthesis
77
List the features that a eukaryotic cell has where a prokaryote does not.
```
A nucleus
Chromosomes
Endoplasmic Reticulum
Lysosomes
Golgi complex
The potential to have a vacuole
Mitochondria
Cytoskeleton
```
78
List the features that a prokaryotic cell has where a eukaryote does not.
Cell Wall
Circular DNA/RNA strand
Flagellum
79
What are the 4 levels of structure of the nucleus in a eukaryotic cell?
Nucleotides
DNA
Chromatin
Nucleusow are monomeric units joined?
80
How are monomeric units joined together and what do they form when they join?
They are joined by covalent bonds to form macromolecules
81
How are macromolecules held together?
Non-covalent interaction
82
What is a hydrogen bond?
A bond that forms between a hydrogen atom bound to an electronegative atom and another electronegative atom.
83
What is an ionic interaction?
Attraction or repulsion between ions.
84
What does solubility depend on?
Ability to form hydrogen bonds
85
What are hydrophobic interactions?
Non polar interactions i.e. they do not interact with water
86
When do Van der Waals interactions occur?
When two atoms are in close proximity.
87
Define hydrophobic
When a molecule will not interact with water and can pass through lipid bilayers.
88
Define hydrophillic
Polar. They interact with water and cannot pass through lipid bilayers unassisted
89
Define amphipathic
When a molecule has both a hydrophilic (polar) and a hydrophobic (non polar) end
90
What is an alpha helix?
a type of regular protein secondary structure. It is a right handed helix with 3.6 residues per turn.
91
What is a beta sheet?
A secondary structure of a protein where the polypeptide chains are in an extended conformation.
92
What is a micelle?
A sphere of amphipathic molecules with hydrophobic parts are on the inside away from water and the hydrophilic heads face outwards, interacting with water.
93
Define pH
A measurement of the concentration of H+ ions in a solution.
94
How does the dissociation of strong acids in water differ to that of weak acids?
Strong acids (and bases) dissociate completely in solution whereas weak ones only partly dissociate.
95
What is pK
The tendency of an acid to dissociate.
96
If the pK value is low, what does this mean?
That the acid is more likely to dissociate in solution.
97
What is a buffer a mixture of?
A weak acid and its conjugate base.
98
What do buffers do?
Resist pH changes
99
When pH > pK ....
the deprotonated form dominates
100
When pH < pK ...
the protonated form dominates.
101
When pH = pK ...
There is an equal amount of acid and its conjugate base
102
How do you calculate pH from pK?
pH = pK + log([A-]/[HA])
103
What is the structure of a simple amino acid?
alpha-C in centre with 4 groups;
- R group
- H group
- COOH group
- NH2 group
104
Which group on the C are amino acids classified by?
Their R group
105
Amino acids are classified on 3 levels. What are these?
- Non polar / polar
- Aromatic / Aliphatic
- Positive / Negative charge
106
What is a zwitterion?
A neutral molecule that has positive and negative charge
107
What is pI?
The isoelectric point. The pH at which the protein has no overall charge.
108
If pI is lower than 7, what does this say about the protein?
It is acidic and it contains many negatively charged amino acids.
109
Name 4 biological reasons why proteins are important.
```
Enzymes (catalysts)
Transporters
Structural support (collagens)
Machines (muscle contraction)
Immune protection (immunoglobulins)
Ion channels
Receptors (hormones, neurotransmitters)
Ligands in cell signalling (growth factors)
```
110
How does a peptide bond form?
Dehydration reaction (condensation)
Bond forms between the Carboxyl group of one amino acid and the Amino group of the second.
- No rotation about the peptide bond
- All atoms in the same plane (horizontally drawn)
- Carbonyl Oxygen and amide hydrogen are in the trans orientation
111
Name the charged amino acids and note their charge.
Glutamate & Aspartate (positive)
| Histidine, Arginine, Lysine (negative)
112
What are the four levels of protein structure?
Primary
Secondary
Tertiary
Quarternary
113
What is the primary structure?
The amino acid sequence
114
What is the secondary structure? Name the two conformations and state the bond type involved.
Local spatial arrangement of the polypeptide backbone (alpha helix or beta sheet). Bonds on either side of the peptide bond can rotate freely and when the angles remain the same, a regular secondary structure is adopted. Hydrogen bonds maintain this structure.
115
What is the tertiary structure?
The 3D structure of the protein by folding of secondary structure.
116
What is a domain?
Regions of the polypeptide that have distinct structures and often serve particular roles.
117
What is a motif?
Folding patterns containing 1 or more secondary structure elements.
118
What is the quarternary structure?
Interaction between different polypeptide subunits within the same protein.
119
What is "homomeric"?
Proteins made up of the same kind of polypeptide.
120
What is "heteromeric"?
Proteins made up of different polypeptide chains.
121
What kind of bonds are involved in the tertiary structure of a protein?
Hydrogen bonds, Van der Waals, Hydrophobic interactions, Disulphide bonds and Ionic interactions
122
What is the quarternary structure?
Hydrogen bonds, Van der Waals, Hydrophobic interactions, Disulphide bonds and Ionic interactions
123
What a globular protein? Give an example
Several structures of secondary structure. Enzymes and regulatory proteins. Example: Haemoglobin
124
What is a fibrous protein? Give an example
A protein with one repeating primary structure. They are useful for structure, support and protection. Example : Collagen.
125
What are the properties of an alpha helix?
Right handed helix, with 3.6 amino acids per turn.
126
What are the properties of a beta sheet?
Parallel or antiparallel conformation (or mixed)
| Extended chain of amino acids with multiple interstrand h-bonds
127
Why does proline act as a helix breaker?
Proline breaks the helix because there is no rotation around the N-C bond.
128
Where do disulphide bonds form when maintaining tertiary structure?
Between Cys residues
129
What is denaturation?
Disruption of protein structure by heat, pH, solvents etc.
130
What is a molecular chaperone?
Something that helps a protein fold if it does not fold spontaneously.
131
What are amyloidoses?
Improper folding of proteins.
132
What can be the result of misfolding?
Disease as the protein is no longer able to function effectively e.g. transmissable spongiform encephalopathies
