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Biochemistry Flashcards

Lecture 1 - Glycolysis Lecture 2 - Lipid Catabolism Lecture 3 - Amino acid catabolism

1
Q

what is glycogenesis?

A

= synthesis of glycogen from glucose

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2
Q

what is glycogenolysis?

A

= breakdown of glycogen to form glucose

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3
Q

what is gluconeogenesis?

A

= de novo synthesis of glucose from metabolic precursors (lactate, amino acids, glycerol) is the way time

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4
Q

what is glycogen?

A

= main storage form of glucose in liver and muscle cells.

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5
Q

when is liver glycogen broken down? and why is released?

A

= between meals and released to maintain blood glucose levels for red blood cells and brain

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6
Q

Yes or No.

Is muscle glycogen available for maintenance of blood glucose levels?

A

= NO.

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7
Q

what does muscle glycogen do?

A

= provides energy via glycolysis & TCA during bursts of physical activity

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8
Q

what are 3 sources of blood glucose?

A

1) dietary
2) glycogenolysis
3) gluconeogenesis

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9
Q

what fluctuates dependent upon meal times?

A

= glycogenolysis

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10
Q

what is the primary source of glucose overnight when hepatic glycogen is depleted?

A

= glyconeogenesis

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11
Q

is glycogen a polymer or monomer?

A

= polymer consisting of glucose molecules

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12
Q

what are the glucose molecules in glycogen joined by?

A

= alpha 1-4 glycosidic links

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13
Q

how are branches introduced to glycogen structure?

A

= alpha 1-6 glycosidic links

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14
Q

what can glucose residues only be added to?

A

can only be added to an existing glycogen chain

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15
Q

what is required for glucose residue to bind to glycogen chain?

A

= a glycogen ‘primer’ containing at least 4 glucose residues

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16
Q

what is the primer covalently attached to?

A

a protein called glycogenin

liver specific protein

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17
Q

GLYCOGEN SYNTHESIS

how is glucose converted to glucose-6-phosphate?

A

by ATP being hydrolysed to ADP
and
the enzyme hexokinase

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18
Q

GLYCOGEN SYNTHESIS

how is glucose-6-phosphate converted to glucose-1-phosphate?

A

by enzyme phosphoglucomutase

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19
Q

GLYCOGEN SYNTHESIS

how is glucose-1phosphate converted to UDP-glucose?

A

by UDP glucose pyrophosphorlyase
and
hydrolysis of ATP and addition of UTP

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20
Q

GLYCOGEN SYNTHESIS

how is UDP-glucose is converted to glycogen?

A

by glycogen synthase.

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21
Q

in UDP-glucose, what are simple precursors first converted to?

A

activated intermediates

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22
Q

what can UDP glucose be thought as?

A

an activated form of glucose

ATP and acetyl CoA are activated forms of phosphate & acetate

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23
Q

what does the phosphate ester linkage in a nucleotide sugar release?

A

releases free energy on hydrolysis

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24
Q

what does glycogen synthase do?

A

synthesises glucose from UDP-glucose

- it adds one glucose molecules to glycogen at a time

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25
Q

what can glycogen synthase only do?

A

only extend the chains of glycogen

it cant start new molecules

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26
Q

Yes or No.

Can glycogen synthase introduce branches?

A

= NO.

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27
Q

what is the rate limiting enzyme of glycogenesis?

A

= glycogen synthase

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28
Q

what is an example of a branching enzyme?

what does it do?

A

= transglycosylase

= introduces an Alph 1-6 glycosidic branches into glycogen
approximately every 10 glucose residues

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29
Q

what is glycogenolysis catalysed by?

A

= glycogen phosphorylase

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30
Q

describe the pathway of glycogenolysis?

A

[glucose]n + phosphate
INTO
glucose-1-phosphate + [glucose]n-1

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31
Q

what does glycogen phosphorylase do?

A

cleaves one glucose molecule of ends of glycogen at a time

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32
Q

what is glucose-1-phosphate converted to and what converts it?

A

= glucose-6-phosphate

converted by
= phosphoglucomutase

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33
Q

in the liver, as a continuation of glycogenolysis what happens to glucose-6 phosphate?

A

de-phosphorylated

and resulting glucose released into blood stream via GLUT2 transporter

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34
Q

in skeletal muscles, as a continuation of glycogenolysis, what happens to glucose-6 phosphate?

A

CANNOT be de-phosphorlyated but instead provides energy via glycolysis & TCA cycle

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35
Q

Yes or No.

Does de-branching require additional enzymes?

A

YES

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36
Q

what is gluconeogenesis?

A

= synthesis of glucose within body from precursor substrates

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37
Q

what are 3 examples of precursors of gluconeogenesis?

A

1) lactate = synthesised by skeletal muscles under anaerobic conditions
2) amino acids = derived form muscle proteins by proteolysis
3) glycerol = derived from triglycerides by lipolysis in adipose tissue

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38
Q

where does the energy come from in gluconeogenesis?

A

= from oxidation of fatty acids released from adipose tissue

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39
Q

where does gluconeogenesis occur?

A

= in liver, small amounts in kidney

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40
Q

REMIDNER

- what are 3 irreversible reactions in glycolysis?

A
  • hexokinase
  • phosphofructokinase
  • pyruvate kinase
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41
Q

what is required for gluconeogenesis?

A

= four unique liver enzymes

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42
Q

what does gluconeogenesis proceed?

A

= proceeds via synthesis of oxaloacetate in mitochondria

- the TCA cycle intermediate which accepts acetyl groups

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43
Q

does gluconeogenesis consume energy?

A

yes it consumes energy

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44
Q

in gluconeogenesis, how is pyruvate converted to glucose?

A

2pyruvate + 4ATP + 2GTP + 2NADH + 4H+ + 6H20
GOING TO
glucose + 4ADP + 2GDP + 6Pi + 2NAD+ + 2H+

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45
Q

what does ATP hydrolysis drive?

A

an unfavourable reaction

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46
Q

what is the name of the cycle which converts lactate to glucose?

A

= cori cycle

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47
Q

what transport lactate to liver?

A

blood

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48
Q

what does the liver do?

A

= converts lactate back to glucose

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49
Q

what does the Cori cycle do?

A

buys time and shift metabolic burden from muscle to other organs

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50
Q

what is glycolysis and gluconeogenesis known as?

A

reciprocal regulation

meaning, when one is highly active, the other is inhibited

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51
Q

what 5 things are involved in reciprocal regulation?

A

1) hormonal regulation (glucagon, insulin)
2) high AMP or ADP (means low energy)
3) high ATP (high energy)
4) fructose 2,6-biphosphate
(high in fed state, low in starved state)
5) citrate, alanine and acetyl Co-A
(high when intermediates or building blocks are abundant)

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52
Q

LECTURE 2 - LIPID CATABOLISM

A

LECTUURE 2 - LIPID CATABOLISM

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53
Q

what does increased fat intake without appropriate energy expenditure leads to?

A

1) increased number of adipocytes
2) more fat in adipocytes
= obesity

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54
Q

what 2 factors does control of energy balance depend on?

A

1) genetically linked factors
e,g. protein messengers regulating appetite

2) environmental factors
e. g. food abundance, fashionable foods

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55
Q

what are fats required?

A

1) as energy source

2) for essential fatty acids
- some polyunsaturated fatty acids can’t be made by body
- deficiencies can lead to membrane disorders, increased skin permeability, mitochondrial damage

3) for fat soluble vitamins
- vitamins A, D, E, K
absorption of these vitamins is closely linked to that of fat
stored in body fat

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56
Q

what happens if fat intake or absorption is inadequate?

A

= secondary deficiencies occur

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57
Q

what are 3 different types of lipids?

A

1) simple lipid
- fatty acids
- triglycerides
- waxes

2) compound lipids
- phospho
- glyco-lipids
- lipoprotein

3) steroids
- cholesterol
- steroid hormones

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58
Q

what are lipids predominantly?

What do they usually contain?

Are lipids soluble in water?

A

Predominantly hydrocarbon.

Usually contain long chain fatty acids.

Insolube in water.

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59
Q

where are triglycerides the main energy storage from?

A

adipose tissue

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60
Q

are triglycerides hydrophobic or phillic?>

A

hydrophobic

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61
Q

are triglycerides high or low energy yield per gram?

A

high energy yield per gram

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62
Q

what dot triglycerides consist of?

A
  • glycerol

- 3 fatty acids

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63
Q

what are fat acids usually in terms of their chain appearance and rings?

A

= straight chains

= aliphatic (no rings)

  • usually contain an even number of C atoms.
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64
Q

what are the 3 things that fatty acids can be?

how do double bonds in fatty acids usually form?

A

1) saturated (no double bonds)
2) unsaturated (one double bond)

3) polyunsaturated (several double bonds)
- occur in small amounts

cis configuration

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65
Q

what are the 3 common main natural fats acids?

A

1) palmitic acid
2) stearic acid
3) oleic acid

66
Q

can polyunsaturated fatty acids be synthesised by the body?

what are polyunsaturated fatty acids usually?

A

many cannot be synthesised by body.

  • essential fatty acids
    e. g. linoleum acid
67
Q

what do fatty acids have on their carbon 1?

Note - what is an alpha carbon?

A

carboxyl group
OR
- carbon adjacent to carboxyl group is an alpha carbon
- C furthest away is Pi carbon

  • carbon adjacent to a carboxyl group
68
Q

when are fatty acids liquid at room temperature?

A

fatty acids with up to 8 carbon atoms.

- longer ones are solid

69
Q

what lowers melting point in fatty acids?

A

= double bonds

70
Q

what sort of fat contains a large proportion of unsaturated fatty acids = liquids?

A

= plant fats

71
Q

what do animal fats contain?

A

= mostly palmitic and stearic acid = solid

72
Q

what are 3 main products of fat digestion?

A

1) glycerol (absorbed by intestinal epithelial cells)
2) fatty acids
3) mono-glycerides

73
Q

where is the fat absorbed into?

A
  • into mucosal cells of intestine
    = Short and medium length fatty acids enter portal blood
    = longer chain FAs and monoglycerides are re-synthesised to triglycerides
74
Q

what are chylomicrons?

A

= products of fast digestion that are coated with a layer of protein, phospholipid, cholesterol

75
Q

what do chylomicrons enter?

what happens when chylomicrons at muscle and adipose tissue?

what happens to the free fatty acids at this point?

A

lymph then blood stream.

at muscle and adipose tissue chylomicrons are attacked and cleaved by lipoprotein lipases.

Free fatty acids are;

  • resynthesised into triaclyglycerols
  • oxidised to provide energy
  • depends on amount available
76
Q

what is lipolysis?

A

= breakdown of lipids

77
Q

where is fat stored?

A

in adipose tissue

78
Q

in lipolysis of stored fats, how are they initially cleaved?

A

by hormone sensitive lipase (e.g. adrenaline sensitive)
= releases free fatty acids and glycerol
= occurs when energy is needed

79
Q

what do fatty acids need to be converted to before they can be oxidised to generate energy?
an d where does this conversion take place?

A
  • converted to CoA derivates

= conversion takes place in cytoplasm

80
Q

describe the pathway of fatty acid conversion to acyl-CoA?

and what does this conversion required?

A

Fatty acids + CoA = acyl-CoA

required 2ATP

81
Q

where can further oxidation of fatty acids occur?

A

in mitochondrial matrix

- needs to be transported in mitochondria by special carrier mechanism

82
Q

what happens in the cytoplasm in the carnitine shuttle?

A
  • fatty acids are transferred from acyl-CoA to carnitine
83
Q

what does the acyl-carnitine transporter do in the inner membrane of the carnitine shuttle?

A

= facilities anti port of acyl-carnitine into mitochondrion and carnitine out

84
Q

what is the net result in the carnitine shuttle?

A

= acyl-CoA located in mitochondria matrix

85
Q

what is beta oxidation?

A

cycle of reactions in mitochondrial matrix

86
Q

how many steps are there in beta oxidation and describe the products of each step?

A

Four steps

= 1 acetyl Co-A
= 1 FADH2
= 1 NADH + H+
= 1 fatty acyl-CoA shortened by 2 carbon atoms

87
Q

in the yield of Beta oxidation, how many times is the cycle repeated?

A

8 times

88
Q

what are 3 additional pathways?

A

1) unsaturated fatty acids
- already partially oxidised
- yields less FADH2

2) odd-chain fatty acids
- yields propionyl CoA in last step
- converted to succinylcholine CoA
- enters TCA cycle directly

3) branched chain fatty acids
- C1 carbon oxidised to CO2
- acetyl and propionyl CoA released in equal numbers

= requires several additional enzymes

89
Q

describe the breakdown of glycerol?

A

1) Activated to glycerol-3-phosphate by glycerol kinase
- present in liver and kidney but absent from adipose tissue, skeletal and heart muscle

2) Dehydrogenated to dihydroxyacetone phosphate
- normal intermediate of carbohydrate metabolism

90
Q

where are ketone bodies formed?

A

in liver mitochondria

from acetyl CoA from B oxidation

91
Q

where do ketone bodies diffuse into?

A

into blood stream and to peripheral tissues

92
Q

why are ketone bodies important?

A

important molecules of energy metabolism for heart muscles and renal cortex
- converted back to acetyl CoA which enters TCA cycle

93
Q

what happens normally in ketosis?

A

fatty acid oxidation yields acetyl-CoA
enters citrate cycle if fat and carbohydrate degradation are balanced
depends on oxaloacetate (C4 compound) for formation of citrate
oxaloacetate can be provided as a side-product of glycolysis

94
Q

what happens in ketosis in starvation and diabetes?

A
  • oxaloacetate is consumed for gluconeogenesis
  • fatty acids are oxidised to provide energy
  • acetyl-CoA is converted to ketone bodies
  • high levels of ketone bodies in blood, too much for extrahepatic tissue (i.e. heart, brain, etc.) as ketone bodies are moderate acids
    and so accumulation leads to severe acidosis (blood can’t buffer any more)
  • impairs tissue function, particularly central nervous system
  • smell of acetone can be detected in breath
95
Q

LECTURE 3 - LIPID ANABOLISM

A

LECURE 3 - LIPID ANABOLISM

96
Q

what is lipogenesis?

A

fatty acid synthesis

97
Q

where does de novo synthesis of fatty acids occur?

A

mainly in liver, kidney, mammary glands, adipose tissue and brain

98
Q

when does de novo synthesis of fatty acids mainly take place?

A

during excess energy intake

99
Q

what happens when excesss carbohydrate is taken in?

A
  • conversion to fatty acids and triglycerides ini liver
  • free fatty acids are transported in plasma bound to albumin
  • triglycerides formed in liver are transported ti adipose tissue by VLDL for storage
100
Q

Is lipogenesis reductive or oxidative?

A

reductive process

- energetically unfavourable s electrons are required

101
Q

what is the pathway for lipogenesis?

A 
Dietary starch 
Glucose
Pyruvate 
Acetly CoA
Fatty acids = triglycerides
  • acetyl CoA is converted to fatty acids by FA synthesis and B-oxidation (lipolysis)
102
Q

where does the synthesis of fatty acids from acetyl CoA occur?

A

occurs in cytoplasm of liver cells.

103
Q

where is acetyl CoA generated?

A

in mitochondria

- by pyruvate dehydrogenase co[lex

104
Q

is the mitochondria membrane permeable to acetyl CoA?

True or false?

A

FALSLE

IMPERMEABLE

105
Q

what does citrate transport?

A

acetyl groups into the cytoplasm

106
Q

how is citrate formed?

What happens with citrate is present at high concentrations?

A

by condensation of acetyl CoA with oxaloacetate (first step in TCA)

  • citrate is transported into cytoplasm
107
Q

what is the direct precursor of lipolysis?

A

Malonyl CoA

108
Q

what is the vital first step involved in lipolysis?

A
  • activation of acetyl CoA to malonyl CoA by acetyl CoA carboxylase
109
Q

where is acetyl CoA carboxylase mainly expressed?

A

in liver and adipose issue

110
Q

wha is acetyl CoA carboxylase essentially?

A

essentially a regulatory enzyme

111
Q

what does malonyl CoA donate to new lipids?

A

carbon atoms

112
Q

what does fatty acid synthase do?

A

catalyses synthesis of saturated long chain fatty acids from malonyl CoA, acetyl CoA and NADPH

113
Q

is fatty acid synthase a single or multi enzyme complex?

A

MULTI-enzyme complex

- exists as a single polypeptide chain with 7 distinct enzyme activities

114
Q

what are the 4 steps involved in fatty acid synthesis when using the enzyme fatty acid synthase?

A

1) condensation
2) reduction
3) dehydration
4) reduction and release

115
Q

what is the name of the protein that fatty acid synthase contains?

A

acyl carrier protein (ACP)

116
Q

are fatty acids synthesised in a single reaction or a cycle of reactions?

A

in a cycle of reactions

117
Q

if you use acetyl CoA and malonyl CoA as precursor, what does one cycle of reactions add to the growing acyl chain?

A

adds 2 carbons

  • derived from malonyl- CoA
  • growing acyl chain is attached to ACP
  • requires NADPH as electron donor
118
Q

what length does the chain of carbons need to be in order for the fatty acid to be released?

A

needs to be C-16

e.g. palmatic acid (C16) is the longest fattty acid created by fatty acid synthase

119
Q

what is required to elongate the chain further or add unsaturated bonds?

A

further enzymes

120
Q

when is synthesises of fatty acid maximal?

A

when carbohydrates and energy are plentiful, and when fatty acids are scarce

121
Q

what has an essential role in regulating fatty and synthesis and degranulation?

A

acetyl CoA carboxylase

122
Q

what signals the fed state in acetyl CoA carboxylase regulation?

A

insulin

= stimulates storage of fuels and synthesis of proteins

123
Q

what signals the starved state?

what signals the requirement for energy?

A

starved - glucagon

  • epinephrine signals requirement for energy
    = mobilse glycogen stores
124
Q

what stimulates allosterically in acetyl CoA carboxylase regulation?

A

citrate

125
Q

when are citrate levels high?

A

high when acetyl CoA and ATP are abundant

126
Q

what is acetyl CoA carboxylase regulation antagonised by?

A

palmitoyl CoA

127
Q

when is palmitoyl CoA abundant?

A

when fatty acids are in excess

128
Q

what does the synthesises of triglycerides require?

A

glycerol-3-phosphate(G3P)

129
Q

what produces G3P from GLYCEROL?

A

liver

130
Q

what produces G3P from GLUCOSE?

A

adipose tissue

131
Q

when does adipose tissues only produce triglycerides?

A

only during the fed state

- insulin stimulates adipose tissue uptake of glucose

132
Q

what does triglyceride formation involve?

A

esterification

133
Q

what other 3 things does the liver also synthesise?

A

(i) phospholipids
(ii) cholesterol
(iii) lipoproteins

134
Q

AMINO ACID CATABOLISM

A

AMINO ACID CATABOLISM A

135
Q

when amino acids are not used as building blocks, what happens to them?

A

they are degraded

= no storage for amino acids

136
Q

what is the main site for amino acid degradation?

A

liver

137
Q

what produces single amino acids and di and tai-peptides?

A

proteolytic enzymes in stomach and intestine

138
Q

what happens to the single amino acids and di tri-peptides?

A

= absorbed into intestinal cells and released into blood for absorption by other tissue

139
Q

describe protein turnover.

A
  • tightly regulated
  • takes place at different rates
  • damaged proteins have to be removed
140
Q

what do some amino acids also contain in the side chain?

A

nitrogen

141
Q

what does amino acid breakdown produce?

A 
ammonia (NH3) & 
ammonium ions (NH4+)
142
Q

Yes or NO.

Is NH4+ toxic at high concentration?

A

Yes

- build up leads to severe problems

143
Q

what are 4 major nitrogen containing excretory molecules?

A 
1) Urea
80%
2) uric acid 
3) creatinine 
4) ammonium ion (NH4+)
144
Q

where is urea formed?

A

in liver NOT kidneys

145
Q

what are the 3 steps involved in synthesises of urea?

A

1) transamination
= transfers an amino group to a ketoacid to form new amino acids.

2) de-amination
= removal of an amine group from a molecule of amino acid to eventually form ammonia
(( = converting nitrogen to ammonia ))

3) urea/ornithine cycle
= biochemical reactions that produces urea (NH2)2CO from ammonia (NH3).

146
Q

what moves the amino group from alpha amino acids to alpha keto acids in transamination?

A

amino-transferases

147
Q

what is a common alpha kept acid?

A

alpha-ketogluterate, a TCA intermediate

= give glutamate
occurs in all tissues

148
Q

in order for it to be transported to liver, what happens to the amino group of glutamate?

A

= transferred to pyruvate, giving alanine.
OR
= glutamin synthase adds NH4+ to glutamate giving glutamine

149
Q

what are 2 major carriers of nitrogen in blood to liver?

A

1) alanine

2) glutamine

150
Q

where does de-amiantion/urea cycle occur?

A

in liver

151
Q

what happens in the de-amminatiton / urea cycle?

A

= amino group of glutamate is converted to free ammonium ion.

152
Q

what are 3 examples of complex reactions that synthesises urea?

A

1) urea/ornithine cycle
2) 1 nitrogen from free ammonium, other form aspartic acid
3) carbon from CO2

153
Q

describe the equation in which urea is synthesised?

A

CO2 + NH4+ + 3ATP + aspirate + 2H20
INTO
Urea + 2ADP + 2PI + AMP + PPi + fumerate

154
Q

what is an intermediate in the citrate cycle?

A

fumarate

155
Q

what happens after removal of alpha amino group?

A

= the remaining carbon skeletons are converted into major metabolic intermediates
= can be converted to glucose or oxidised in TCA cycle

156
Q

what are 2 examples of family of amino acids that will eventually break down and describe each?

A

1) ketogenic amino acids
- degraded to acetyl CoA or acetoaceyl CoA
- can give rise to ketone bodies or fatty acids

2) glycogenic amino acids
- degraded to pyruvate or TCA cycle intermediates
- can be converted into phosphoenolpyruvate and then into glucose

157
Q

what are 3 examples of inherited disorders that arise from amino acid degradation?

A

1) alcaptonuria
2) maple syrup urine disease
3) phenylketonuria

158
Q

what is alcaptonuria?

A

= degradation of phenylalanine and tyrosine is blocked

159
Q

what is maple syrup urine disease?

A

= degradation of valine, isoleucine and leucine is blocked

  • urine smells like maple syrup
  • mental and physical retardation
  • prevented by appropriate diet
160
Q

what is phenylketonuria?

A

= pheynlalanine accumulates in all body fluids

  • leads to severe mental retardation if untreated
  • therapy = low phenylalanine diet
161
Q

what 4 defects could there be in urea cycle disorders?

A

1) acc1umulation of urea cycle intermediates
2) glutamine levels increase in the circulation
3) alpha -ketoglurarate is no longer regenerated

4) alpha-ketoglurarate levels become too low to fix more free ammonium ion
- elevated levels of ammonia in the blood are toxic for the nervous system

162
Q

how would you treat urea cycle disorders?

A

= treatment with low-protein diet
= drugs which remove nitrogen
- e.g. forming complexes with amino acids which are excreted
- gene therapy in hepatocytes

GI (43 decks)

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