Unit 1 Flashcards
(83 cards)
1
Q
What is a proteome?
A
Entire set of proteins expressed by a genome
2
Q
Give two reasons why the proteome is larger than the genome?
A
- Alternative RNA Splicing
- Post Translation Modification
3
Q
Describe the structure of an amino acid
A
- Central Carbon Group
- NH2 Amine Group
- COOH Carboxylic Group
- H
- Variable R group
4
Q
What are the two main groups present in all amino acids?
A
Amine Group(NH2) Carboxylic Acid Group(COOH)
5
Q
What are the four classifications of R groups?
A
Acidic
Basic
Polar
Hydrophobic
6
Q
Describe the features of an Acidic R group
A
Contains a COOH
Negatively charged
7
Q
What classification of R groups contains an amide group and is positively charged?
A
Basic
8
Q
How are amino acids joined together?
A
Peptide Bonds
9
Q
What is the primary structure of a protein?
A
Order of amino acids in a peptide chain
10
Q
What causes secondary structure?
A
Hydrogen Bonds
11
Q
What are the two main folding motifs?
A
Alpha Helix
Beta Sheet
12
Q
Describe the Alpha Helix
A
Helical structure with four residues per turn
13
Q
Describe the Beta Sheet
A
Polypeptide chain linked together side by side, can be parallel or antiparallel
14
Q
Name some of the possible interactions that can cause tertiary structure of the protein
A
- Hydrophobic
- Ionic
- Hydrogen
- Van der Waals
- Disulphide
15
Q
Where are hydrophobic interactions typically found?
A
Towards the inside of the polypeptide
16
Q
What two molecules do ionic bonds occur between?
A
COO- and NH3+
17
Q
What bonds occur between covalent bonds between R groups of Cysteines
A
Disulphide Bridges
18
Q
What prosthetic group does Myoglobin contain?
A
Haeme
19
Q
Give an example of a protein that contains a carbohydrate prosthetic group?
A
Glycoprotein
20
Q
What prosthetic group does Lipoprotein contain?
A
Lipid
21
Q
Give an example of a protein that contains a nucleic acid prosthetic group?
A
Nucleoprotein
22
Q
What effect does PH have on a protein?
A
- Affects the concentration of H+ and OH- Ions in solution
- Changes charge of protein
- Places stress on polar interactions such as hydrogen and ionic bonding
- Denature the protein
23
Q
Give an example of a protein which contains Quaternary structure
A
Haemoglobin
24
Q
Describe Quaternary Stucture of a protein
A
Different subunits of polypeptide chains joined together
25
What is a Cytoplasmic Protein?
Proteins found in the cytoplasm
Hydrophyllic R groups on the surface
Globular proteins
Example: Enzymes and Hormones
26
What are the two classifications of proteins at the membrane?
Integral
| Peripheral
27
What is the function of Integral Proteins?
Found within the membrane, act as channels or transporters
28
How are integral proteins held in the protein?
Strong Hydrophobic Interactions
29
What is a Ligand?
A substance which can bind to a protein
30
What charge is the DNA sugar phosphate backbone?
Negatively Charged
31
What is the name of proteins that can bind to DNA and stimulate or inhibit the transcription of genes
Transcription Factors
32
What is a Modulator?
Substances which can bind to an enzyme at a site remote from the active site
33
What type of modulators increase the affinity for the substrate?
Positive Modulators
34
Describe Polar R groups
Hydrophyllic
| Example: C=O, N-H
35
What causes the increase in kinetic energy of a protein molecule?
Temperature
36
What effect can increasing the kinetic energy of a protein have?
Places stress on the bonds, breaking them, causing the protein to be denatured
37
What part of the protein determines the location in a cell?
R groups at the surface of the protein
38
Where are the hydrophobic R groups found in cytoplasmic proteins?
Clustered towards the middle
39
How are Peripheral proteins more associated with the heads of the phospholipids?
They contain more hydrophyllic R groups
40
Where are the R groups not involved in folding found and what is their purpose?
Form areas on the surface
| Ligands can bind to them
41
What is the function of positively charged histomes?
Bind to DNA to form Nucleosomes, allowing the DNA to be packaged in chromosomes
42
Give an example of how ligand binding can influence the activity of a protein
Induced fit in enzymes
43
What is Co-operativity?
Co-operativity occurs in proteins with more than one subunit. It is when ligand binding at one subunit alters the conformation of other sub units.
44
Give an example of a protein where co-operativity occurs
Haemoglobin
45
Explain the effect of binding of oxygen to one of the sub units in Haemoglobin
- - Changes its confirmation
- - In turns changes the conformation of the remaining subunits
- -Increasing their affinity for oxygen
- - Maximises the O2 uptake in lungs
46
What is the effect of the release of oxygen from Haemoglobin?
Reduces the affinity of the other subunits
47
What is a benefit of reducing the affinity of other subunits when oxygen is released from Haemoglobin?
Helps to release oxygen in oxygen depleted environments
48
Give an example of an oxygen depleted environment
Respiring Tissue
49
What two conditions can further reduce affinity of haemoglobin subunits for oxygen
```
Low pH (caused by presence of CO2)
High Temperature
```
50
What can be added or removed from particular R groups to cause reversible conformational change in proteins?
Phosphate
51
What type of modification is Phosphorylation an example of?
Covalent modification and post translation modification
52
What can Phosphorylation help to regulate?
The activity of many cellular proteins
53
What is the function of a Kinase?
Catalyse Phosphorylation, by transferring phosphate from ATP to the protein
54
What is the name for the enzymes that catalyse de-phosphorylation?
Phosphatase
55
Where are ATPases found?
Membrane, as are membrane bound
56
What and how do ATPases use phosphate for?
ATPases use phosphate to phosphorylate themselves, and they use it to change their confirmation and alter their activity
57
What is a use of transmembrane ATPases?
Active transport of ions and the sodium potassium pump
58
What triggers the movement of Myosin?
Conformational changes due to ligand binding
59
What does movement of Myosin cause?
The movement of finer actin filaments
60
Describe the process of Muscle Contraction
1. Myosin heads are bound to the actin, forming cross bridges
2. Binding of ATP occurs, causes a conformational change, myosin heads detach from the actin and swing forward
3. ATP is broken into ADP + Pi. They remain bound to the myosin and cause a second conformational change. The myosin acts as an ATPase
4. Myosin rebinds to the actin but at a further position along the filament. A third conformational change occurs.
5. ADP + Pi are released. Myosin head returns to original confirmation, dragging the actin filament along
61
What type of substances are able to diffuse directly through the bilayer in a membrane?
Hydrophobic
62
Give an example of a molecule that can diffuse directly through the membrane bilayer
Oxygen, Carbon Dioxide, Water, Steroid Hormones
63
Give an example of a molecule that requires a membrane protein to move it across the membrane
Glucose, Charged Molecules such as Na+, K+ and Ca2+
64
Can membrane proteins create/maintain concentration gradients?
Yes
65
What are the two types of membrane proteins?
Channels, Transporters
66
Describe Channel Proteins
Transmembrane proteins, passage is always passive through them
They can be gated or ungated
67
Give an example of an ungated protein
Aquaporin
68
What are the two ways gated channels can be controlled?
Ligand Gated
| Voltage Gated
69
Describe Ligand Gated Channel Proteins
Binding of a ligand triggers conformational change
Example: Neurotransmitters act as ligands when binding to receptors in post synaptic neurons, which open to allow sodium ions in
70
How are voltage gated channels opened and closed?
Changes in Ion Concentration across the membrane
71
Explain the difference between transporters and channels
Channels - molecule binds to channel to allow other molecules to move through
Transporters - molecule binds to transporter so it can move through
72
Are transporters specific?
Yes, very
73
If a transporter moves molecules passively what is this known as?
Facilitated Diffusion
74
Give an example of a transporter and where it can be found
GLUT 4 transporter
| Found in Fat and Muscle Cells
75
Define 'Coupled Transport'
The movement of two molecules together across a membrane
76
What is the difference between a symport and an antiport?
A symport moves both molecules in the same direction, and antiport moves them in opposite directions
77
Give an example of coupled transport and state the two molecules, the name of the transporter and whether the transporter is an antiport or a symport
Glucose Symport
- Transfers Na+ and Glucose
- Symport
- Found in cells lining small intestine
78
In the glucose symport, does sodium move up or down its concentration gradient?
Down
79
What happens when Na+ binds to the Glucose Symport?
causes a conformational change which pushes both sodium and glucose across the membrane
80
How do cells maintain the gradient of sodium required for the glucose symport?
Using an active transport protein, known as the sodium potassium pump(Na+/K+ ATPase)
81
Where does the Sodium Potassium ATPase get its energy from?
The hydrolysis of ATP
82
Describe the direction of the Sodium Potassium Pump
Sodium out, Potassium In
83
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