Lipid & Protein Metabolism Flashcards
1
Q
What do amino acids and nucleotides contain that carbohydrates & fats don’t?
A
They contain nitrogen!
2
Q
Where does nitrogen come from?
A
Air contains approx 80% nitrogen.
However we don’t really use the nitrogen we breathe in!
Instead, we get nitrogen from our diet (which comes from nitrogen fixing bacteria (the diazotrophs)).
3
Q
The Nitrogen Cycle
A
NOTION 1.1
4
Q
Simplified sets of reactions involved in the nitrogen cycle
A
Fixation stage:
N2 => NH4+ =>
Assimilation stage:
Glutamate => Other amino acids => Proteins/ nucleotides
Degradation stage:
=> Amino acids => Glutamate => NH4+ => N2
5
Q
Why is nitrogen unreactive?
A
It has a triple bond between nitrogen atoms.
6
Q
Abiotic process involved in fixation of Nitrogen
A
N2 + O2 + Lightning => NO or NO2
7
Q
How can nitrogen be fixed using high pressure chemistry?
A
The Haber-Bosch process is used:
N2 + H2 + 400-450*C + 200 atm + Iron Catalyst => NH4+
8
Q
What are 2 examples of nitrogen fixing bacteria?
A
Cyanobacteria (found in high abundance in particular locations e.g Lake Atitlan (Guatemala)).
Root nodules on legumes also contain Rhizobium bacteria.
9
Q
N2 fixed per different processes:
- Industrial
- Lightning
- Biological - sea
- Biological - farmland
A
NOTION 1.2
10
Q
What enzyme is required for fixation of nitrogen, within bacteria?
A
Nitrogen fixation requires enzyme nitrogenase and a lot of energy!
11
Q
General equation for fixation of nitrogen, within bacteria
A
NOTION 1.3
12
Q
How is nitrogenase inactivated?
A
Nitrogenase is inactivated by oxygen.
Therefore nitrogen fixing bacteria live anaerobically.
Some uncouple mitochondria - Increase electron flow and “burns” off O2 in cell.
13
Q
How do cyanobacteria stop O2 entry?
A
Some cyanobacteria form heterocysts whose “cell wall” prevents O2 entry.
14
Q
How do leguminous plants keep O2 concentration low?
A
Leguminous plants produce leghemoglobin which binds to O2 and keeps the concentration low enough to allow nitrogenase work.
This is an example of the symbiotic relationship between the bacteria and the plant!
15
Q
What happens after nitrogen is fixed?
A
Fixation:
N2 => NH4+ =>
Nitrification:
NO2- => NO3- =>
Nitrate taken up by plants:
NO2- => NH4+
16
Q
What does the flow of N from NH4+ to other biomolecules occur through?
A
Flow of N from NH4+ to other biomolecules occurs through glutamate.
17
Q
How is glutamate formed?
A
Alpha-ketoglutarate + NH4+ + NADPH + ATP
|
Glutamate + NADP+ + ADP + Pi
NOTION 1.4
18
Q
What 4 amino acids can be found in much higher concs in cells compared to other amino acids?
A
- Alanine
- Glutamine
- Glutamate
- Aspartate
19
Q
What can glutamate and aspartate be used for?
A
They are used as excitatory neurotransmitters.
20
Q
Why is glutamate important?
A
Glutamate is also important in taste (mono sodium glutamate). And is used in the breakdown of amino acids.
21
Q
How can nitrogen be conserved in humans?
A
By transferring amino groups between different molecules - transamination
NOTION 1.5
22
Q
General principles of transamination
A
There is no loss or gain of nitrogen!
The reaction is readily reversible.
One of the 2 substrate pairs is often glutamate.
NOTION 1.6
23
Q
What is the product of glutamate (amino acid) + pyruvate (keto acid)?
A
Glutamate + Pyruvate -> Alpha ketoglutarate + Alanine
NOTION 1.7
24
Q
What do all aminotransferases rely on?
A
All aminotransferases rely on the pyridoxal phosphate cofactor.
25
1. What ketoacid typically accepts amino groups?
2. What acts as a temporary storage of nitrogen?
1. Typically, alpha-ketoglutarate accepts amino groups.
2. L-Glutamine acts as a temporary storage of nitrogen.
It can donate the amino group when needed for amino acid biosynthesis.
26
What is the abbreviation for pyridoxal phosphate?
How is this cofactor made?
What is its function?
PLP = pyridoxal phosphate
- Cofactor made from vitamin B6 (essential vitamin)
- Transfers the amino group during the reaction
27
What is the diagnostic value of plasma aminotransferases?
What are 2 aminotransferases that are particularly useful?
How is Liver disease followed?
Aminotransferases are intracellular enzymes: presence in plasma indicates cell damage.
Aspirate aminotransferase (AST - catalyses aspartate to oxaloacetate) and alanine aminotransferase (ALT - catalyses alanine to pyruvate) are particularly useful.
Liver disease followed by by measuring serum levels of ALT or AST (NOTION 1.8)
28
Do organisms use amino acids as an energy source?
- Not all organism use amino acids as the source of energy
- About 90% of energy needs of carnivores can be met by amino acids immediately after a meal
- Only a small fraction of energy needs of herbivores are met by amino acids
- Microorganisms scavenge amino acids from their environment for fuel
29
What 3 circumstances do amino acids undergo oxidative catabolism?
Amino acids undergo oxidative catabolism under three circumstances:
1. Leftover amino acids from normal protein turnover are degraded
2. Dietary amino acids that exceeds the body’s protein synthesis needs are degraded
3. Proteins in the body are broken down to supply amino acids for catabolism when carbohydrates are short supply (starvation, diabetes mellitus)
30
What is pepsin?
What are Trypsin’s & chymotrypsins?
What are Aminopeptidases and Carboxypeptidases?
• Pepsin cuts protein into peptides in the stomach
• Trypsin and chymotrypsin cut proteins and larger
peptides into smaller peptides in the small intestine
• Aminopeptidase and carboxypeptidases A and B
degrade peptides into amino acids in the small
intestine
31
The specificity of some common methods for fragmenting polypeptide chains
NOTION 1.9
32
Enzymatic degradation of dietary proteins
NOTION 1.10
33
What does digestion of dietary proteins in the intestine provide?
Digestion of dietary proteins in the intestine and degradation of proteins within cells provide a steady supply of amino acids.
34
How are proteins digested in the stomach?
What about in the intestine?
• Stomach – acidic environment + enzymes → free amino acids and di- or tri-peptides
• Intestine – membrane bound proteins (aminopeptidases)
degrade proteins further
NOTION 1.11
35
Cellular proteins can be targeted for destruction, why might they be targeted? What is the end product? What is involved?
The following proteins may be destroyed:
- Misfolded proteins
- Foreign proteins
- Unwanted proteins
Same end point as dietary proteins:
- Individual amino acids
NOTION 1.12
36
Overview of Protein Turnover
NOTION 1.13
37
What are some functions of lipids in the metabolism?
Lipids have different functions in the metabolism
• Energy stores
• Part of Lipoproteins
• Essential and major component of membranes
• Precursor of signalling molecules
→Prostagladine
→Leukotriene
→Thromboxane
Are all derivates of arachidonic acid (/\4 derivate
of eicosanoic acid
38
How are fatty acids used in the human body?
Fatty acids: Building block for triglycerides/ phospholipids/ precursor of eicosanoids
39
How are triglycerides used in the human body?
Triglycerides: Energy storage (fat)
40
How are phospholipids used in the human body?
Phospholipids: Major component of cell membranes
41
How is cholesterol used in the human body?
Cholesterol: Component of cell membranes, precursor for bile acids, precursor for steroid hormones, involved in fat transport
42
What are lipids, and what are their structure?
- Lipids are carboxylic acids
- They contain long hydro-carbon chains with terminal carboxy groups
- Chain length normally between 14 and 20 carbons but up to 36
- Normally even number of carbons → formed from C2 bodies
43
Properties of lipids
- The ‘heads’ are charged and polar
- The tails are uncharged and unpolar
→‘heads’ are hydrophile
→Tails are lipophile
44
Common straight chain saturated fatty acids
NOTION 2.1
45
What stereoisomer is more common in fatty acids?
Cis-conformation is more common in fatty acids.
46
Omega 3 and Omega 6 fatty acids
ω-3 fatty acids (FAs) have a terminal carbon-carbon double bond in the omega three-position, the third bond from the methyl end of the acid, whereas, ω-6 acids have it in the omega six-position, the sixth bond from the methyl end of the fatty acid, respectively.
47
Common straight chain unsaturated fatty acids
NOTION 2.2
48
Effects of chain length & double bonds on physical properties of fatty acids
Increased chain length = Increased melting point
Increased Unsaturation = Decreased melting point
49
Why does increasing the degree of unsaturation of fatty acids, decrease the melting point?
Double bonds disturb the alignment of fatty acids, reducing the number of intermolecular forces that can be formed
50
Nomenclature of fatty acids
C_n:x
Where:
n = number of carbons &
x = number of double bonds
Example:
16:0 = 16 carbons & no double bonds
18:2 /\^5,8 = 18 carbons & 2 double bonds (at position 5, 8)
Note : we always count from the carboxylic acid carbon!
51
What are triglycerides?
Lipids that occur in fat or oil of plants and animals are
mixtures of triacylglycerols
→ Fatty acid triesters of glycerol
→ Only suitable form of lipids for ingestion for human
NOTION 2.3
52
Properties of triglycerides
• Non Polar
•Hydrophobic
•Form lipid droplets in cells
•Fatty acid COOH forms an ESTER link with glycerol OH groups
53
Where does the energy come from in triglycerides?
Glycerol – 5% energy
Fatty acids – 95% energy
54
Energy content of fatty acids vs glucose
Average fatty acid = 38kJ/g vs glucose = 14.8kJ/g
55
Affinity of triglycerides vs glycogen to water
Triglycerides are insoluble – different phase of cell
stable and compact store of fuel.
Glycogen ~2/3 of weight is associated water
56
Stores of glycogen vs triglycerides
Glycogen -> Glucose -> Blood (Last 12 hrs)
Triglycerides -> Fatty Acids -> Blood (Lasts 12 wks)
57
Where are triglycerides used as an energy source?
Triglycerides:
- Liver
- Heart
- Skeletal muscle (resting)
However the brain can’t use triglycerides! This is due to the Blood Brain Barrier.
58
What are ketone bodies?
Ketone bodies are water-soluble molecules or compounds that contain the ketone groups produced from fatty acids by the liver.
Brain uses glucose (priority) in hypoglycemia, but if these stores run out they will use ketone bodies.
59
What is the sole energy source during hibernation
Triglycerides
60
Structure of phospholipids vs cholesterol
NOTION 2.4
61
Different kind of head groups in phospholipids
NOTION 2.5
(Phosphatidylcholine is also known as Lecithin!)
62
Before fatty acids can be oxidised they must be _________
Before fatty acids can be oxidized the must be:
1. Activated
2. Transported to the mitochondria
63
How are fatty acids activated?
Fatty acids are activated by linking them to Coenzyme A.
This happens in the cytosol.
NOTION 3.1
64
How are fatty acids transported to the mitochondria?
To transport fatty acids to the mitochondria they are transferred to Carnitine.
Acyl-Carnitine is transported through the mitochondria membrane by the carnitine carrier protein.
NOTION 3.2
65
What are the 4 reactions involved in Beta-Oxidation?
1. Dehydrogenation
2. Hydration
3. NAD+ dependent dehydrogenation
4. Cleavage of C(alpha)– C(beta) bond and formation of Acetyl-CoA and a 2 carbon shorter fatty acid chain
→ Beta-oxidation reduction equivalents NAD+ and
FAD are regenerated by RBC.
→ Acetyl-CoA transfers the acetyl residue to the TCA-cycle where it is oxidized completely.
NOTION 3.3
66
Is Beta-Oxidation aerobic?
Yes, the pathway depends on oxygen.
67
Beta-oxidation usually takes place in the mitochondria, what is an exception?
Additional to mitochondrial Beta-oxidation, peroxysomal Beta-oxidation is important to oxidize fatty acids with more than 22 carbons
→ Same reactions but different enzymes
68
How is Beta-oxidation mainly regulated?
Mainly regulated by the availability of free fatty acids in the blood, cytoplasm and in the mitochondria.
69
What is the amount of FFA in the blood controlled by?
The amount of FFA in the blood is hormonally controlled by influencing the activity of hormone sensitive triacylglycerol lipases in the adipose tissue
→ Insulin inhibits the lipases
→ Glucagon, adrenalin or noradrenalin increase the
activity
70
How can the transport of fatty acids in the mitochondria be inhibited?
Transport of fatty acids in the mitochondria is inhibited by Malonyl-CoA.
71
What are 2 important reactions for the synthesis of fatty acids?
Two important reactions to remember:
1. Acetyl-CoA carboxylase reaction.
2. Fatty acid synthase
72
What are fatty acids synthesised by?
Where are fatty acids synthesised?
What happens in principle?
How is Acetyl CoA activated?
- Fatty acids are synthesised by fatty acid synthase (FAS)
- Fatty acids are synthesised in the cytoplasm
- In principle many Acetyl-CoA are linked
- Acetyl-CoA is linked to the growing Acyl- chain
- Acetyl-CoA must be activated to allow the addition of the acyl-CoA residue
- Acetyl-CoA is activated by Carboxylation
NOTION 3.4
73
How is Acetyl-CoA activated?
- Irreversible two-step reaction
- Animal cells - one multifunctional polypeptide
- Require a biotin prosthetic group
NOTION 3.5/ 3.6
74
Overall reaction involved in carboxylation of Acetyl-CoA
NOTION 3.7
75
Reaction overview of fatty acid synthesis
1. Acyl- and Malonyl- residues linked to the FAS and then with each other
2. After elongating the Acyl chain by one acetyl residue the reactions are reverse to the Beta-oxidation
Important difference:
1. NADPH + H+ is used as electron source instead of NADH + H+ and FADH2
2. All reactions are catalysed by the dimeric multi-activity Enzyme Fatty acid synthase
NOTION 3.8
76
What are the two binding sites on the fatty acid synthase complex?
NOTION 3.9
77
Step 1 of fatty acid synthesis
NOTION 3.10
78
Step 2 of fatty acid synthesis
NOTION 3.11
79
Step 3 of fatty acid synthesis
NOTION 3.12
80
Step 4 of fatty acid synthesis
NOTION 3.13
81
What is the lengthened fatty acid then translocated to?
Lengthened fatty acid chain is then translocated to KS.
Another malonyl group is added to the SH group of ACP.
82
Summary of fatty acid synthesis
NOTION 3.14
83
Where is the glycerol part of triglycerides derived from?
The glycerol part of TG is derived from
• The glycolysis pathway: DHA -> G3P
• Or direct use of glycerol (liver/kidney) G -> G3P
84
How is G3P formed from DHAP?
Dihydroxyacetone phosphate is reduced to form glycerol 3 phosphate.
85
How are triglycerides synthesised?
Triglycerides are synthesised via Phosphatidic Acid.
NOTION 3.15
86
How are triglycerides formed from phosphatidic acid?
NOTION 3.16
87
How can nitrogen be removed from the body?
Remember transamination reaction & fact that only glutamate can “lose” its nitrogen by this route.
So, like nitrogen assimilation, glutamate is central to this process.
NOTION 4.1
88
What do many aquatic vertebrates release to their environment?
Does this process involved passive or active transport?
Many aquatic vertebrates release ammonia to their environment
– Passive diffusion from epithelial cells
– Active transport via gills
89
What do many terrestrial vertebrates and sharks excrete nitrogen in the form of?
Many terrestrial vertebrates and sharks excrete nitrogen in
the form of urea
– Urea is far less toxic that ammonia
– Urea has very high solubility
90
What do some animals, such as birds and reptiles excrete nitrogen as?
Some animals, such as birds and reptiles excrete nitrogen as uric acid:
– Uric acid is rather insoluble
– Excretion as paste allows to conserve water
91
What do humans and great apes excrete nitrogen as?
Humans and great apes excrete both urea (from amino acids) and uric acid (from purines).
92
What is uric acid the cause of?
The cause of gout.
93
What is ammonia transported in the bloodstream as?
Where does the excess get processed?
Ammonia is Transported in the Bloodstream Safely as Glutamine. Excess glutamine is processed in intestines, kidneys and liver.
NOTION 4.2
94
What is produced when glutamate donates an ammonia to pyruvate? Why might this occur?
Glutamate can Donate Ammonia to Pyruvate to Make Alanine:
• Vigorously working muscles operate nearly anaerobically and rely on glycolysis for energy
• Glycolysis yields pyruvate that muscles cannot metabolize aerobically; if not eliminated lactic acid will build up
• This pyruvate can be converted to alanine for transport into liver
95
What is involved in the glucose-alanine cycle?
• Proteins are broken down in exercising muscle if required
• Transported to the liver as alanine (or glutamine)
• Carbon skeleton → pyruvate
• Nitrogen excreted as ammonia (ammonium ion) and converted to urea by the urea cycle.
NOTION 4.3
96
Why is nitrogen metabolism so complicated?
Why make glutamate, then convert it to glutamine or alanine only to convert it back in the liver?
What charge does glutamate have? -ve charge
What charge do alanine and glutamine have? NO charge
Charged molecules don’t pass through membranes easily;
hence convert to uncharged molecule to allow easy transport.
97
How is glutamate metabolised in the mitochondria of the hepatocytes?
NOTION 4.4
98
How is ammonia recaptured?
Ammonia is Re-captured via Synthesis of Carbamoyl Phosphate (First nitrogen acquiring reaction).
99
What is the second nitrogen acquiring cycle?
Entry of aspartate into the urea cycle is the second nitrogen acquiring reaction.
100
How does nitrogen from carbomyl phosphate enter the urea cycle?
What is involved in the urea cycle?
NOTION 4.5
101
Summary of protein breakdown
NOTION 4.6
102
After removal of the amino group, carbon skeletons can be converted to?
How many intermediate compounds can the 20 amino acids be converted to, to enter the metabolic pathways?
List these 6 intermediates.
After removal of the amino group carbon skeletons are converted to glucose or oxidised as part of the citric acid cycle
20 amino acids enter metabolic pathways through only 6 intermediate compounds:
– Seven to acetyl-CoA: Leu, Ile, Thr, Lys, Phe, Tyr, Trp
– Six to pyruvate: Ala, Cys, Gly, Ser, Thr, Trp
– Five to alpha-ketoglutarate: Arg, Glu, Gln, His, Pro
– Four to succinyl-CoA: Ile, Met, Thr, Val
– Two to fumarate: Phe, Tyr
– Two to oxaloacetate: Asp, Asn
103
How many amino acids are non essential/ essential?
What are some of the essential amino acids?
Image displaying the essential, non essential & conditionally essential amino acids.
20 coded amino acids: 10 are “non-essential” (can be
synthesised in body)
9 are “essential” needed in diet:
(Histidine, Isoleucine, Leucine, Lysine, Methionine,
Phenylalanine, Threonine, Tryptophan, Valine)
NOTION 4.7
104
Diagram showing entry of amino acids into the CAC.
What amino acids are glucogenic vs ketogenic
NOTION 4.8
105
Protein turnover
NOTION 4.9
106
Where do the terms “glucogenic” vs “ketogenic” come from?
Some amino acids “feed in” to gluconeogenesis and so produce glucose or glycogen, in liver. These termed glucogenic.
Other amino acids “feed in” to acetoacetate or acetyl CoA. These termed ketogenic and cannot result in gluconeogenesis
107
Why can’t ketogenic amino acids feed into gluconeogenesis?
Remember, pyruvate dehydrogenase reaction (pyruvate to acetyl CoA) is irreversible and no NET synthesis of oxaloacetate through the citric acid cycle.
108
What 5 amino acids are both glucogenic and ketogenic?
Note that some amino acids are both glucogenic and
ketogenic – isoleucine, tyrosine, tryptophan, threonine and phenylalanine
109
Diagram of glucogenic amino acids
NOTION 4.10
110
Diagram of ketogenic amino acids
NOTION 4.11
111
What is Negative N Balance?
Negative N balance (N-flow_in < N-flow_out)
112
What is Kwashiorkor also known as?
What is it caused by?
What is its effect?
Kwashiorkor (“sickness of the displaced child”) = Caused by protein deficiency with adequate carbohydrate intake (i.e. weaned onto high starch, low protein diet).
Low N intake -> Low plasma albumin -> Low osmotic pressure -> Low entry interstitial water into plasma -> Oedema
113
What are the symptoms of Hyperammonaemia?
What is its cause?
Why does it have its effects?
Symptoms: Tremors, speech-slurring, coma & death
Cause: Hereditary defect in urea cycle enzymes.
Urea cycle is the only route for synthesis of urea (and thus removal of nitrogen from broken down proteins).
Decreased α-ketoglutarate:
= decreased TCA cycle
= decreased ATP production
114
What is phenylketonuria?
How prevalent is it?
What are some effects of this condition?
Deficiency of phenylalanine hydroxylase; hence build-up of phenylpyruvate (and metabolites) in blood (and urine).
Prevalence 1:11,000
Lack of tyrosine prevents melanin production -> hypopigmentation
Untreated -> intellectual disability
NOTION 4.12
115
How is phenylketonuria tested for?
How can it be treated?
Neonatal diagnosis through heel-prick test.
Treatment involves dietary restriction of Phe and… Need tyrosine in diet!
116
What is alkaptonuria?
What does it cause?
What is the cause of this condition?
How can it be treated?
- First ever recognized inborn error of metabolism (1859).
- Causes urine to turn black when exposed to air
- And black spots appear in various tissues e.g. eye
- Defect in enzyme involved in tyrosine breakdown so toxic tyrosine byproduct (homogentisic acid) accumulates.
- Treatment: Dietary restriction of tyrosine. Need to also restrict phenylalanine because Phenylalanine is converted into Tyrosine.
