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Biochemistry > Butler and Porter Lectures > Flashcards

Butler and Porter Lectures Flashcards

1
Q

Four major types of molecules

A

Proteins
Carbohydrates
Lipids
Nucleic Acids

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2
Q

Lactoferrin

A

Protein - when binding iron undergoes conformational change (can distinguish between iron bound and not)

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3
Q

alpha-carbon

A

next to carboxyl group
bonded to hydrogen group
bonded to side chain group (R)

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4
Q

Chiral

A

Distinguishable from mirror form

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5
Q

Four main groups of amino acids

A

Hydrophobic, polar, positive, negative

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6
Q

Glycine

A 
No chirality (R group is H)
Flexible
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7
Q

Proline

A

Imposes tight restraints on protein –> found in proteins that need to be rigid e.g. collagen

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8
Q

Histidine

A

Found in active site of many enzymes

Side chain near neutral pH –> side chain can alter it’s charge at physiological pH

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9
Q

Cysteine

A

Contains a free thiol group
High pKa –> found in active sites
Cysteine residues form a covalent bond in some proteins to form cystine

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10
Q

Zwitterionic

A

Amino acids are Zwitterionic (functional group where at least one has a positive and one has a negative electrical charge)

  • In neutral pH exist as dipolar ions –> In this form, the amino group is protonated (NH3+) and the carboxyl group is deprotonated (COO-)
  • As pH is raised - the carboxylic acid is the first group to give up a proton
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11
Q

Peptide bond formation: Amino Acids - how?

A

Loss of water molecule

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12
Q

Amino acids - direction?

A

Amino terminal –> carboxyl terminal

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13
Q

Hierarchy of Protein Structure

A

Primary structure – the sequence of the amino acids.
Secondary structure – simple, repetitive motifs that are found in almost all proteins.
Tertiary structure – the overall fold of a protein.
Quaternary structure – when several proteins fold together.

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14
Q

Phi

A

The angle of rotation about the bond between the nitrogen and the a-carbon atom

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15
Q

Psi

A

The angle of rotation about the bond between a-carbon and the carbonyl carbon atom

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16
Q

Ramachandran Plot

A

Possible combinations of phi or psi

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17
Q

Eg. Secondary Structures

A

Alpha helix, the beta sheet and turns and loops.

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18
Q

Myoglobin

A

An all alpha-helix protein

Binds heme

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19
Q

Concanavalin A

A

An all beta-sheet protein

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20
Q

Heteromultimers

A

Several different proteins can come together to make the mature protein

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21
Q

Homomultimers

A

Lots of the same protein coming together to make mature protein

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22
Q

Fibrous Proteins Example

A 
Alpha helix (hair)
Beta sheet (insect silk)
Collagen (three helices, polyproline helix)
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23
Q

Delta G depends on …

A

Free energy of the products - free energy of the reactants

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24
Q

Delta G provides no…

A

information about the rate of reaction

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25
Q

The rate of reaction depends on…

A

Free energy of activation (delta G double plus)

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26
Q

Activation energy

A

Energy that a molecule requires to overcome the transition state free energy barrier

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27
Q

How do enzymes increase the rate of reactions?

A

Reducing the transition state energy

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28
Q

How do enzymes reduce the transition state barrier?

A 
Stabilise the unfavourable intermediate
-Charge-charge interactions
-Hydrogen bonding
-Protecting hydrophobic groups
Make possible a less favourable reaction
-Provide acid/base-like conditions
-Allow oxidation/reduction
-Provide a small vacuum
-Provide an attacking group (covalent catalysis)
-Provide a metal ion
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29
Q

k

A

rate constant

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30
Q

Assumptions: enzyme kinetics

A

Release of product is very fast

The reverse reaction is sufficiently slow q

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31
Q

High KM indicates…

A

Weak binding

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32
Q

Low KM indicates ….

A

Strong binding

33
Q

Inhibitor

A

Reduces the rate of enzymatic reaction

34
Q

Competitive inhibitor: features

A

Resembles the substrate but differs

-Assumed that inhibitor binds reversibly to the enzyme and is in rapid equilibrium with it

35
Q

Non-competitive inhibitor: features

A

The inhibitor binds directly to the enzyme-substrate complex but not to the free enzyme
-The enzyme-substrate-inhibitor complex, is catalytically inactive

36
Q

Mixed Inhibition: features

A

A mixed inhibitor binds to enzyme sites that participate in both substrate binding and catalysis.

37
Q

Inactivator definition

A

If the inhibitor binds irreversibly to an enzyme

38
Q

Regulation of Enzyme activity

A
  1. Control of enzyme availability

2. Control of enzyme activity

39
Q

Allosteric effector definition

A

Any molecule that can bind to an enzyme away from the active site, and by so doing change the enzyme’s activity for its substrate
Increase the rate of the reaction (activator) visa versa

40
Q

Allostery Defintion

A

Situation where a chemical binds to an enzyme away from the active site
E.g. ATCase Allosteric Behaviour
-ATCase is allosterically inhibited by cytidine triphosphate (CTP), a pyrimidine nucleotide.
-ATCase is allosterically activated by adenosine triphosphate (ATP), a purine nucleotide.

41
Q

ATCase Two Forms

A

Relaxed (with substrate) and Tense (without)

42
Q

Glycolysis

A

Process: Glucose is converted to Pyruvate

43
Q

First Law of Thermodynamics

A

Energy can neither be created nor destroyed

44
Q

The Second Law of Thermodynamics

A

The total entropy of any isolated thermodynamic
system tends to increase over time, approaching
a maximum value

45
Q

Entropy

A

Measure of disorder in a system

46
Q

Entropy Formula

A

S = kB*ln W

47
Q

Isolated system: Entropy and enthalpy changes

A

Energy change = 0

Entropy change > 0

48
Q

Gibbs Free Energy

A

Entropy change of the isolated system

G = H - TS

49
Q

For any spontaneous process

A

Gibbs free energy is less than or equal to 0

50
Q

Forces which Stabilise the 3D Structure of Proteins

A

Hydrophobic interactions.

Ionic interactions

Van der Waals interactions

Hydrogen bonds

Disulfide bonds – these are the only covalent interactions.

51
Q

Van der Waals distance

A

Optimal distance between the two atoms

52
Q

Disulfide Bonds

A

Covalent bond between two cysteine amino acids in the protein chain

53
Q

Arrhenius equation

A

Gives the relationship between activation energy and reaction rate constant

54
Q

Co-enzymes

A

Non-protein organic molecules required for catalysis e.g. biotin, NAD+, FAD

55
Q

Co-factors

A

Inorganic substances that are required for catalysis e.g. metal ions Fe2+, Zn2+ , Cu2+, Mg2+ etc.

56
Q

Holoenzyme

A

Combination of protein and co-enzyme/co-factor

57
Q

Apoenzyme

A

The protein alone without the co-enzyme/ co-factor

58
Q

Diseases result from deficiency in co-enzymes:

A

Megaloblastic anaemia for folic acid deficiency (used to make tetrahydrofolate) for B12 deficiency

Beriberi for thiamine (B1) deficiency

Pellagra for nicotinamide (B3) deficiency:

59
Q

Enzyme Mechanisms: Three Types

A

General Acid-Base Catalysts
Metal Ion Catalysis
Covalent Catalysis

60
Q

Protease Mechanism: Serine proteases use a combination of acid-base and covalent catalysis to hydrolyse proteins

A

This is a mixture of acid-base catalysis and covalent catalysis
-Serine residue acts as the nucleophile and is made more nucleophilic by the histidine and aspartic acid.

6 steps

  1. ES complex- Michaelis Complex
  2. First Transition State- Tetrahedral Intermediate
  3. Acyl Enzyme Intermediate
  4. Acyl Enzyme water Complex
  5. Second Transition State- Tetrahedral Intermediate
  6. Free Enzyme
61
Q

Functions of fatty acids

A

Energy storage and production

Structural components of membranes.

Some hormones are derived from fatty acids (prostaglandins/eicosanoids which have roles in inflammatory response, blood pressure regulation, clotting etc)

62
Q

Photosynthesis takes place in…

A

Chloroplasts

63
Q

Oxidative phosphorylation takes place in…

A

Mitochondria

64
Q

Photosynthesis overview:

A

Light photon is absorbed
Energy used to drive an electron from water to generate NADPH
Also drives protons across a membrane
These protons drive ATP synthesis.
The ATP and NADPH are used in the light independent reactions (Calvin cycle) to fix CO2

65
Q

Photosynthetic reaction centres example: plants

A 
Photosystem I (PS I) P700 (lambda <700nm)
Photosystem II (PS II) P680 (lambda < 680nm)
66
Q

Proton Gradient Experiment: Andre Jagendorf

A

Thylakoid membranes were soaked in pH 4 buffer for several hours.

Then rapidly submerged in pH 8 buffer containing ADP and Pi.

The pH inside the thylakoids initially remained at pH 4.

A burst of ATP production was noted that accompanied the disappearance of the pH gradient.

67
Q

The Calvin Cycle

A

Carbon dioxide fixation

  • Occurs in the chloroplast stroma
  • Uses the products of the light reactions (ATP and NADPH) to fix CO2
  • Requires 2 NADPH and 3 ATP per CO2 fixed
68
Q

Calvin Cycle: CO2 fixation

A

CO2 is fixed by the enzyme Rubisco, which reacts CO2 with ribulose bisphosphate to produce two molecules of 3-phosphoglycerate

69
Q

Calvin Cycle: C02 Reduction

A

3-phosphoglycerate is phosphorylated by ATP to 1,3 bisphosphoglycerate, which is then reduced to glyceraldehyde-3-phosphate by NADPH

70
Q

Calvin Cycle: CO2 Regeneration

A

Ribulose bisphosphate is regenerated and sucrose or starch is the byproduct

71
Q

Regulation of Calvin Cycle

A

-Does not occur in the dark

72
Q

Control of Rubisco, SBPase and FBPase activity

A

Light/dark
pH levels
Mg2+ activates all enzymes

73
Q

One molecule of triose-P is produced for…

A

Every 3 CO2 fixed

74
Q

Overall Calvin Equation

A

CO2 + 5-C intermediate –> [6-C intermediate] –> 2 x 3-PGA

75
Q

Oxidation of fatty acids: Three Steps

A

Step 1: Free fatty acids in the cytosol are activated forming fatty acyl-CoA (Activation costs the equivalent of 2 ATPs)

Step 2: Fatty acyl-CoA uptake into mitochondria.

Step 3: b-oxidation pathway in mitochondria

76
Q

Glyoxylate cycle

A

Allow plants and fungi to convert acetyl CoA to sugars

77
Q

Fatty acid synthesis occurs in…

A

Cytoplasm

  • Substrates are acetyl CoA and NADPH
  • The citrate shuttle is used to transport acetyl CoA from the mitochondria to the cytoplasm.
  • Sources of NADPH for fatty acid synthesis are the pentose phosphate pathway and the citrate shuttle.
78
Q

Lipids: Functions

A

Cell membranes
Energy storage
Cell signalling

79
Q

Fatty acid degradation (b-oxidation) occurs in …

A

Mitochondria

Biochemistry (2 decks)

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