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Principles 2018 > Biochemistry > Flashcards

Biochemistry Flashcards

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1
Q

What is oxidation?

A

Loss of electrons

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2
Q

What is reduction?

A

Gain of electrons

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3
Q

What is the most oxidisable state of carbon?

A 
Alkane 
Alcohol
Aldehyde
Carboxylic acid
Carbon Dioxide
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4
Q

What are some functions of biomolecules?

A 
Information storage
Structural
Energy generation
Energy currency/storage
Recognition/communication/specificity
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5
Q

What are the four major classes of biomolecules?

A

Peptides and proteins
Lipids
Nucleic acids
Carbohydrates

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6
Q

What is the first law of thermodynamics?

A

Energy is neither created nor destroyed

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7
Q

What is the second law on thermodynamics?

A

When energy is converted from one form to another, some of that energy becomes unavailable to do work

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8
Q

What changes are involved in reactions?

A

Enthalpy

Entropy

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9
Q

What is enthalpy?

A

Heat content

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10
Q

What is entropy?

A

Randomness, disorder

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11
Q

What is the equation for free energy change?

A

(energy of the products) – (energy of the reactants)

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12
Q

What is an exergonic reaction?

A

total free energy of the product(s) is less than the total free energy of the reactant(s)
Delta G is NEGATIVE

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13
Q

What is an endergonic reaction?

A

otal free energy of the product(s) is more than the total free energy of the reactant(s)

Delta G is POSITIVE

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14
Q

What is delta G?

A

Change in free energy under standard conditions

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15
Q

What reactions can occur spontaneously?

A

Exergonic reactions

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16
Q

Describe the stability of ATP?

A

negative charges close together in ATP put a strain (electrostatic repulsion) on the molecule that makes it less stable than ADP

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17
Q

Do cells store ATP?

A

No not really, constantly regenerated

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18
Q

Define metabolism?

A

all the reactions taking place in the body, divided into catabolism and anabolism

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19
Q

Describe glycolysis?

A

Initial breakdown of glucose for the generation of ATP

Early steps use two ATP molecules

Later steps generate four ATP molecules

Net gain of two ATP molecules per glucose molecule

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20
Q

Describe gluconeogenesis?

A

Making new glucose from non-carbohydrate precursors, e.g. pyruvate

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21
Q

What are control points in metabolic pathways?

A

Reactions with large delta G values

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22
Q

How is flux through control points controlled?

A

Altering the activity of the enzyme

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23
Q

What is significant about the structure of water?

A

Water is polar;

  • electrons are shared unequally
  • depends on electronegativity of atoms

Water molecule is bent

  • forms a dipole
  • tetrahedral shape
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24
Q

Which substances dissolve in water?

A

Ionic and polar substances

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25
What is a hydrogen bond?
Covalent bond between hydrogen and a more electronegative atom
26
Are hydrogen bonds stronger than covalent bonds?
Individually they are weaker, can be strong collectively
27
What is the hydrophobic effect?
Oil and water don't mix
28
Define amphipathic?
Hydrophilic and hydrophobic
29
Describe the structure of amphipathic molecules?
Polar (hydrophilic) head Non-polar (hydrophobic) tail
30
What do amphipathic molecules form in water?
Micelles
31
What lipids are found in cell membranes?
- structural (lipid bilayer) | - precursors of signalling molecules (DAG, IP3)
32
What is the roll of proteins in cell membranes?
confer selectivity involved in recognition and more
33
What does D and L polypeptides refer to?
stereochemistry of amino acids D and L forms are sterioisomers: non-superimposable mirror images
34
What do all amino acids contain?
``` -a-carbon group bonded to; >an amino group (-NH2) >a carboxyl group (-COOH) >a hydrogen (-H) >a side chain (-R) ```
35
What is the exception to the stereoisomer rule?
Glycine
36
How are peptide bonds formed?
by hydrolysis
37
Describe peptide bonds
- Partial double bond character - Planar - Strong and rigid
38
Describe an acid
Can donate a protein
39
Describe a base
Can accept a proton
40
What is pH?
Measurement of home many protons in a solution?
41
What is a buffer?
Solution to control the pH of a reaction mixture
42
What does a titration curve plot?
pH as a function of base added to an acid
43
What is a zwitterion?
Amino acids without charged side groups (no net charge)
44
How can proteins act as buffers?
Several of the amino acid side chains can be ionised
45
What can cause the ionisation of a protein?
A change in pH
46
Describe primary protein structure?
the sequence of amino acid residues
47
Describe secondary protein structures?
the localised conformation of the polypeptide backbone
48
Describe tertiary protein structure?
the three-dimensional structure of an entire polypeptide, including all its side chains
49
Describe quaternary protein structure?
the spatial arrangement of polypeptide chains in a protein with multiple subunits
50
How can polypeptides rotate?
Rotate around the angles between - the a carbon and the amino group - the a carbon and the carboxyl group
51
What are the three types of secondary protein structure?
Alpha helix Beta strands triple helix
52
Where is the collagen triple helix found?
Component of bone and connective tissue
53
Are collagen triple helices water soluble?
No
54
What bonds are involved in a collagen triple helix?
Repeating sequence of X-Y-Gly in all strands >X = any amino acid >Y = proline or hydroxyproline >also contains hydroxylysine Inter-chain H-bonds (no intra-chain) >involving hydroxylysine and hydroxyproline Covalent inter- and intra-molecular bonds
55
What changes in collagen structure with age?
Covalent cross linking increases
56
What is the basis of scurvy?
The enzyme which hydroxylates proline requires ascorbic acid (vitamin C) This results in weakened collagen
57
What are the two forms of tertiary structure?
Fibrous proteins | Globular proteins
58
Describe the structure of fibrous proteins?
polypeptide chains organized approximately parallel along a single axis >consist of long fibers or large sheets >tend to be mechanically strong >insoluble in water and dilute salt solutions
59
Give examples of fibrous proteins
Keratin of hair and wool | Collagen of connective tissue including cartilage, bones, teeth, skin, blood vessels
60
Describe the structure of globular proteins?
folded to a more or less spherical shape >soluble in water and salt solutions >polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions >nonpolar side chains are buried inside nearly all have substantial sections of alpha-helix and beta-sheet
61
Give examples of globular proteins?
Myoglobin | Haemoglobin
62
What forces stabilise tertiary structure?
-Covalent disulphide bonds -Electrostatic interactions = salt bridges -Hydrophobic interactions -Hydrogen bonds >backbone >side chain -Complex formation with metal ions
63
Where are polar side groups usually locates on proteins?
The outside
64
What hydrophobic interactions are present within proteins?
>Weaker attraction between water and hydrocarbon >Weaker attraction between hydrocarbon and hydrocarbon (van der Waals interactions) >Strong organizing influence – the hydrophobic effect Amino acids with hydrophobic side-chains tend to cluster in the centre of globular proteins
65
How does substitution of amino acids alter protein structure?
By changing the physiological pH you change interactions and bond formation
66
Describe the physiological changes involved in sickle cell anaemia
Single nucleotide sequence change in coding region of the B chain of haemoglobin A, resulting in altered protein (valine instead of glutamic acid)
67
What can misfolding of polypeptide chains cause?
Alzheimer's, parkinson's, CJD
68
What is the folding of polypeptide chains aided by?
Chaperones
69
What is mad cow disease caused by?
Caused by infection
70
What is cruetzfeldt-jacob disease caused by?
Spontaneous or inherited mutations
71
What are prion proteins?
Normal components of the brain
72
What types of physical condition or chemical agent sill disrupt the various protein structures?
``` -Heat (increase in vibrations) -Extremes of pH (electrostatic interactions interrupted) -Detergents, urea, guanidine hydrochloride (disrupt hydrophobic interactions) -Thiol agents, reducing agents (reduce and thereby disrupt disuplhide bonds) ```
73
Describe the structure of myoglobin?
Globular -contains a haem group > which contains an iron iron (prosthetic groups)
74
What is the haem in myoglobin responsible for?
Binding oxygen | Storing oxygen in muscle
75
Describe the structure of haemoglobin?
- Four subunits - two a and two B - each contains a haem group
76
What does binding of one oxygen to haemoglobin do?
Changes the affinity of the other subunits

Principles 2018 (34 decks)

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