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Biomolecules > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is an anomeric carbon?

A

The carbon on a carbonyl group

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2
Q

What is the carbohydrate equilibrium?

A

Linear to Cyclic, cyclic is dominating

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3
Q

What causes a cyclic form of carbohydrates?

A

The angle of attack of the OH on the anomeric carbon.

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4
Q

General rule with carbohydrate bonding?

A

Alpha+beta= alpha….
Beta+alpha= beta…
They are not the same.

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5
Q

Which sugar is naturally occurring and which one is synthetic?

A

Naturally: D sugar where group on penultimate carbon points right
Synthetic: L sugar where group points to left

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6
Q

What is an epimer?

A

A change on the orientation of the group on the a carbon other than the chiral

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7
Q

What is a stereisomer?

A

Change on the orientation of the group on the chiral centre

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8
Q

What is a diastereisomer?

A

Change on the orientation of groups on more than one carbon

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9
Q

What is mutarotation?

A

Where anomeric carbon dictates which stereoisomer will be made in excess.

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10
Q

Which amino acids have basic side chains?

A

Lysine, arginine, histidine

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11
Q

Which amino aids have acidic side chains

A

Aspartic acid, glutamic acid

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12
Q

Which amino acid have uncharged and polar side chains?

A

Aspargine, glutamine, serine, threonine, tyrosine

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13
Q

Which amino acids have non polar side chains

A

Alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, glycine, cysteine.

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14
Q

What shape is the haem group?

A

Planar

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15
Q

What is the structure of myoglobin?

A

It has 8 major helical regions
It is water soluble because polar region outwards, non polar region inwards.
Haem groups present
Monomeric

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16
Q

What is the structure of haemoglobin?

A

It is a tetramer.
It has 2 alpha subunits, 2 beta subunits.

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17
Q

In Haemoglobin, what are the deoxygenated and oxygenated states called

A

Deoxygenated= T
Oxygenated= R

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18
Q

What happens between subunits when oxygen binds to subunits in deoxyhaemoglobin?

A

Binding of oxygen causes the affinity in neighbouring subunits to increase.

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19
Q

What is the meaning of allostery?

A

Where the binding of proteins/molecule causes the binding properties of other subunits in the molecule to change.

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20
Q

What is the meaning of cooperativity?

A

Where the binding of a protein/molecule causes the change of the affinity in other subunits.

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21
Q

Binding of oxygen to haemoglobin is both —- and—–

A

Allosteric and Cooperative.

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22
Q

What happens to histidine when oxygen binds to haemoglobin?

A

Because iron is pulled above the plane, histidine which is below it is pulled in the middle for haemoglobin.

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23
Q

What is the point of 2,3 bisphoshoglycerate?

A

It is important for haemoglobin to be efficient as an oxygen transporter. Only one molecule has to bind per deoxygenated haemoglobin tetramer and this reduces the affinity for oxygen and allows it to be released to respiring tissues.

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24
Q

What does BPG do in haemoglobin?

A

Makes beta subunits cross link via electrostatic forces. BGP is an allosteric effector.

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25
Q

Does fetal hameoglobin bind to BPG?

A

Binds BPG less than adult haemoglobin. Because BPG reduces affinity for haemoglobin, and fetal haemoglobin doesnt bind readily, it means fetal hameoglobin has higher affinity.
lower affinity for BPG= more affinity.

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26
Q

What is different about the structure of fetal haemoglobin

A

Fetal haemoglobin has 2 alpha subunits and 2 gamma subunits.
Y chain is 72% identical to B chain.

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27
Q

How does the binding of histidine work?

A

Histidine 143 has a positive charge and therefore binds to BPG well but fetal haemoglobin has Serine instead of histadine 143.

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28
Q

How does sickle cell anaemia occur?

A

Where there is single mutation in the code for the beta subunit causing glutamate to be substituted to valine. Valine reacts with phe85 and val88 on beta chain of neighbouring subunit when deoxygenated. This causes an insoluble fibre to be produced on deoxyhaemoglobin which causes rbc’s to sickle.

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29
Q

In the bohr shift what does CO2 addition to N terminal groups do?

A

It produces carbamate groups which is negative charge forms electrostatic interactions which stabilise T state which means oxygen affinity decreases.

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30
Q

How does CO poisoning work?

A

Binds to one subunit on R state so oxygen can be collected but not released.

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31
Q

What is the difference between a reversible and an irreversible inhibitor?

A

Irreversible: produces covalent interactions with the substrate and the inhibitor never comes off.

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32
Q

What do competitive inhibitors do?

A

Don’t affect the Vmax, high levels of substrate outcompete it. They also increase Km.

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33
Q

What do non competitive inhibitors do?

A

Vmax isn’t reached and it cannot be outcompeted. It doesn’t affect the Km.

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34
Q

What is the Km?

A

The substrate concentration at which the Vmax is halved.
When it is high, it means a high substrate concentration is required which means low affinity interaction.

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35
Q

What is Ki?

A

Dissociation constant of enzyme inhibitor complex. Smaller the Ki, the tighter the inhibitor binds.

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36
Q

What are the two types of assay for measuring enzyme activity?

A

Continuous: measure activity live and as reaction proceeds. You can also used couples reactions.
Discontinuous: Stop reaction at various time points and measure products and substate formed.

37
Q

What is the Michaelis-Menten equation?

A

V0= Vmax[S]/ (Km + [S])
Give the classic enzyme activity curve.

38
Q

What is a Linweaver-burkplot?

A

Inverts the Michaelis-Menten equation.
It mimics y=mx+c, giving a straight line. The y-intercept is the 1/Vmax, the X intercept is -1Km
X axis= 1/[S]
y axis= 1/V0

39
Q

How is ATP produced?

A

Glycolysis: glucose to pyruvate, produces 2 ATPS
Citric acid cycle: 1 ATP produced, oxidises carbon fuels, generates high energy transfer.
Oxidative phosphorylation.

40
Q

What is ATP?

A

It is a nucleotide containing adenine, 3 phosphates and a ribose sugar.
ATP is favoured as its more stable.

41
Q

What do kinases and phosphatases do?

A

Kinases: adds phosphates.
Phosphatases: removes phosphates.

42
Q

When does a reaction spontaneously occur?

A

When Gibbs free energy is negative.

43
Q

What can a glycerol backbone produce? Components of each product.

A
  1. Triglycerides/triacylglycerides- glycerol backbone, 3 fatty acids
  2. Phospholipids- Glycerol backbone, 2 fatty acids, one phosphate group
  3. Glyceroglycolipids- Glycerol backbone, 2 fatty acids, phosphate group, carbohydrate on phosphate group.
44
Q

What is the pathway for the cholesterol synthesis?

A
  1. -3 Acetyl CoA condensed to HMG CoA by HMG CoA synthase and acetoacyl CoA thiolase to produce HMG CoA.
    -Produces Mevalonate by HMG CoA reductase
    -Mevalonate to isopentenyl diphosphate by 2x phosphorylation and 1x decarboxylation.
  2. Isopentenyl diphosphate turns to dimethylallyl diphosphate with isopentenyl diphosphate isomerase (IDI). The two isomers are put together to produce it.
    -Prenyl transferase turns to c10 molecule, it goes to c15 molecule and the two together produces squalene through condensation reaction (C30)
  3. Addition of a hydroxyl group produces cholesterol.
  4. Acetyl CoA—> Isopentyl diphosphate—> squalene—> cholesterol c27
45
Q

What is pka?

A

The pH at which a molecule becomes protonated.

46
Q

What kind of lipid is most abundant in membranes?

A

Glycerophospholipid: basically whats in the phospholipid bilayer.

47
Q

What does phospholipase A1, A2, C and D do?

A

A1=digestive system
A2=pancreatic juice, venoms
C=liberates diacylglycerol
D=converts phospholipids to phosphotides

48
Q

Is sphingosine present in plant, animal and bacterial membranes? and what is the structure?

A

yes, yes , not generally.
The backbone is sphingosine, its trans double bond (trans: when double bond gives you straight chain).
It has an amine group and alcohol group.
Long chained alcohol joined to isoprene

49
Q

What is ceramide?

A

Fatty acyl group lined to sphingosine via amide bond.

50
Q

Where can you find gangliosides?

A

They are present on cell surfaces.

51
Q

What are cholesterol derived from?

A

Derived from squalene.

52
Q

Where does fatty acid synthesis occur?

A

occurs cytosol- adult mammals.

53
Q

How does fatty acid synthesis occur

A
  1. Acetyl ACP and malonyl ACP production
  2. They add to produce 3ketoacyl ACP
  3. They reduce to dehydrate
  4. Then when it gets to 16 carbons (Palmotyl)
  5. Thioesterase enzyme reduces fatty acid from ACP by using H2O hydrolysis.
54
Q

What can be used if a fatty acid longer than palmitate is needed?

A

Elongases.

55
Q

How is phosphatidate intermediate synthesised?

A
  1. Glycerol 3 phosphate is turned to 1 acyl glycerol 3 phosphate by acyl transferase.
  2. The it is turned into Phosphotidate by acyl transferase.
56
Q

How is triacylglycerol made

A
  1. Phosphatidate to 1,2 diacylglycerol by taking a phosphate off
  2. Then enzyme diacylglycerol acyl transferase produces triacylglycerol.
57
Q

How are phospholipids synthesised?

A

1,2diacylglycerol turns to Phosphatidylethanolamine with phosphoethanolamine transferase enzyme

Phosphocholine transferase used on 1,2 diacylglycerol to make phosphatidylcholine.

3x methylation on Phosphatidylethanolamine produces phosphatidylcholine.

58
Q

How is ceramide made and what is the point of ceramide?

A
  1. Serine and palmotyl-coA
  2. 3ketosphinganine
  3. Sphinganine produced by reduction of 2.
  4. N-acetylsphinganine made by acetyl group taken off by acetyl-coA
  5. Ceramide produced y desaturation of N-acylsphinganine.

Ceramide is the source of other sphingosines.

59
Q

What is the difference between sterol synthesis and triglyceride synthesis

A

lipid isn’t derived by addition of fatty acid and glycerol

60
Q

How is cholesterol synthesised?

A

acetate (C2)–>Isoprenoid (C5)–>Squalene (C30)–> Cholesterol (C27).
All carbon atoms are from acetyl CoA.

61
Q

What is the principal site for cholesterol synthesis?

A

HMG- COA reductase

62
Q

What processes are controlled by cholesterol levels?

A

Phosphorylation, transcription, control of degradation.

63
Q

How do statins work?

A

Competitive inhibition of HMG-COA reductase.

64
Q

Why are fatty acids degraded?

A

To release energy and two carbons to produce acetyl coA for the citric acid cycle.

65
Q

Where does fatty acid beta oxidation degradation occur?

A

Occurs in mitochondria.

66
Q

What is the fatty acid degradation cycle?

A
  1. Fatty acyl coA —> trans-3-enoyl coA by hydratase (losing two carbons) oxidation
  2. trans-3-enoylcoA turned to alcohol by trans-3-enoylcoA hydratase.
  3. When oxidised, 3ketoacyl ACP
  4. Thiolysis where 2 carbons are lost
67
Q

What is an anomer?

A

It is a steroisomer but in cyclic sugars

68
Q

What does ACP stand for?

A

Acyl carrier protein

69
Q

Describe alpha keratin

A

Right handed alpha helix, wrap around each other to form left handed helix.
Every 7th residue is leucine which is hydrophobic.

70
Q

Describe the structure of silk fibroin

A

is in beta sheets and is stacked. It is rich in alanine and glycine which are two smallest side chains therefore allow close packing.

71
Q

Describe the structure of collagen

A

Left handed helix. Every third residue is glycine and there are many prolines in the structure. Also, they have many hydroxylated residues.

72
Q

What cofactors do hydroxylation enzymes need?

A

They need iron 2+ ,oxygen and vitamin C to work on residues after they’ve been added on the chain.

73
Q

What does proline cause in collagen?

A

Proline has an unusual structure and causes kinks in chains.

74
Q

What do GPI anchors do?

A

allow protein holding on the extracellular part of the chain.

75
Q

What types of integral proteins are there?

A

Monotonic: Only span lipid bilayer once
Polytopic: span the lipid bilyaer multiple times

76
Q

What is the most common transmembrane protein structure?

A

Alpha helical.
Beta barrels: mainly found in bacteria.

77
Q

What are the three main hexose sugars?

A

Glucose, galactose, fructose

78
Q

What is the textbook way of representing sugars?

A

Haworth

79
Q

When a cyclic carbohydrate is made, what are the orientations of OH referred to as?

A

OH is down: axial
OH is side ways: equatorial

80
Q

What bonds does maltose have? vs lactose?

A

Maltose: Alpha 1,4
Lactose: Beta 1,4

81
Q

What is an aldohexose vs ketohexose

A

Hexose with aldehyde or ketone group

82
Q

What is the main driving force for tertiary structure?

A

Hydrophobic, hydrophillic interactions

Other ones include: van der walls, electrostatic forces, hydrogen bonds

83
Q

What can disulphide bonds be broken down by?

A

Reducing agents

84
Q

What does co-translational mean?

A

Where the protein folds up into its shape whilst on the ribosome.

85
Q

What is renaturation of a protein?

A

When the detergent that temporarily denatured the protein is taken away and the protein regains its properties.

86
Q

Do amino acids protrude outside of alpha helix?

A

Yes.

87
Q

Are Beta sheets parallel and antiparallel?

A

Yes they can be both

88
Q

In Beta turns, what is the function of proline and glycine?

A

Proline has a unique structure so gives a tighter turn and glycine is small and flexible.

Biomolecules (3 decks)

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