Biochemistry Review Booklet 1
Biochemistry Review Booklet 1
Biochemistry Review Booklet 1
I.
Carbohydrate Structure
one glycogen molecule may contain 1,000,000 glucose molecules but only counts as 1
particle for osmosis best way to store glucose without affecting significantly osmotic
intracellular properties
Hexosans polyssacharides made up of 6 carbon monossacharides
Pentosans polyssacharides made up of 5 carbon monossacharides
Isomers same structural formula different configuration (Glucose with 4 asymmetric carbons can
form 16 isomers
Epimers isomers differing as a result of variations in configuration of the OH and H atoms at only
one asymmetric carbon ex. Glucose and Galactose at the 4th carbon, Glucose and Mannose at
the 2nd carbon.
Enantiomers a pair of stereoisomers that are non-superimposable mirror images of each other
Asymmetric (chiral) carbon centers = must have a carbon atom connected to 4 different
atoms or groups of atoms bonded in a tetrahedral structure
Type of monosaccharide is based on alcohol (OH) group bonded to only or last asymmetric
carbon atom (adjacent to last alcohol carbon) D = right and L = left (mirror images)
Biomedical and clinical importance of monosaccharide:
1. Glyceraldehyde and dihydroxyacetone important intermediates in glycolysis; branching points
in metabolism
2. Ribose and 2-deoxyribose are important in RNA, DNA, and nucleotide (ATP) structures. Ribose in
RNA is synthesized via the Pentose Phosphate Pathway and the deoxyribose is produced from
ribonucleotide diphosphates by ribonucleotide reductase. Structural component of coenzymes,
including ATP, NAD(P), and flavin coenzymes.
3. Glucose (hexose or blood sugar) (D(+)) important in cellular energy production. Derangement in
the metabolism of glucose is the main issue in Diabetes mellitus.
4. Galactose (D(+) readily metabolized to Glucose. Precursor for the synthesis of lactose and
important in glycoproteins and lipids that are involved with nerve and brain function. Hereditary
galactosemia as a result of failure to metabolize galactose leads to cataracts
5. Fructose (laevulose or fruit sugar) is extremely sweet. Has fewer calories per gram than other
sugar. Hereditary fructose intolerance leads to fructose accumulation and hypoglycemia
Amino Sugars
D-glucosamine constituent of hyaluronic acid
D-galactosamine (Chondrosamine) constituent of chondroitin important component of the
extracellular matrix.
Acidic sugars
Oxidation will result to gain of oxygen and loss of Hydrogen (electrons) Oxidation of glucose (6th
carbon OH is oxidized COO- forming Glucoronic Acid). This is important in the
biosynthesis of GAG.
II.
Carbohydrate Metabolism
Glucose Metabolism
A. Glycolysis
-
three regulatory steps are involved (rate limiting steps) catalyzed by the following
enzymes:
1). Hexokinase Phosphorylate Glucose intracellularly. (Hexokinase is
nonspecific with high affinity and low Km for glucose) Glucokinase is an isozyme of
hexokinase with low affinity and high Km for glucose found in the liver and pancreas.
Phosphorylation of glucose is irreversible.
Reduce the coenzymes NAD, FAD to be used as electron carriers to the Electron
Transport Chain for ATP synthesis. 3 NADH + H and 1 FADH2 are produced per turn of
the cycle. One ATP is produced by substrate level phosphorylation per turn of the cycle
glucose (acetyl CoA produced from the oxidation of the final product of
glycolysis which is Pyruvate),
amino acids (acetyl CoA from pyruvate the degradation product of glucogenic
amino acids and acetyl CoA the degradation product of ketogenic amino acids).
Fatty acid synthesis acetyl CoA a substrate of TCA cycle is a precursor for fatty
acid synthesis. Pyruvate dehydrogenase is a mitochondrial enzyme thus acetyl
CoA is formed in the mitochondria. Fatty acid synthesis occurs in the cytosol so
the acetyl CoA formed in the mitochondria should be available in the cytosol.
Acetyl CoA is provided for fatty acid synthesis when citrate (a product produced
from the condensation of axaloacetate and acetyl CoA) is transported to the
cytosol. In the cytosol citrate is cleaved to acetyl CoA and Oxaloacetate by ATPcitrate lyase. Citrate is transported out of the inner mitochondrial membrane
when aconitase is saturated with acetyl CoA.
TCA has functions of both oxidative (degradative) and synthetic processes thus, it is
amphibolic.
The reaction catalyzed by succinate thiokinase (synthetase) is the only reaction in TCA
that has phosphate level phosphorylation. It has 2 isozymes in gluconeogenic and nongluconeogenic tissues:
o
Gluconeogenic tissues (liver and kidney) has to isozymes, one is specific with
GDP and the other is ADP. The GTP formed is used in the decarboxylation of
oxaloacetate (phosphoenolpyruvate carboxykinase) to phosphoenolpyruvate. It
provides a regulatory link between citric acid cycle activity and the withdrawal
of oxaloacetate for gluconeogenesis.
o
-
Transamination to aspartate
Ten ATPs are formed per turn of the cycle (3 NADH ~2.5 ATPs , 1 FADH2 ~ 1.5 ATPs, 1
ATP in substrate level phosphorylation)
(1) riboflavin, in the form of flavin adenine dinucleotide (FAD), a cofactor for
succinate dehydrogenase;
(2) niacin, in the form of nicotinamide adenine dinucleotide (NAD), the electron
acceptor for isocitrate dehydrogenase, -ketoglutarate dehydrogenase, and
malate dehydrogenase;
C. Glycogen metabolism
-
Liver contains higher glycogen content by weight, however total glycogen is of the
total glycogen is in muscles (muscle mass is greater than that of the liver).
o
Muscle glycogen provides fuel for ATP synthesis. Muscle lacks glucose-6phosphatase so it cant produce glucose from glucose 6 phosphate a product of
the isomerization of Glucose-1-phosphate (G1P) from glycogenolysis.
1. Glycogenesis
- Occurs mainly in the liver and muscle
- One of the pathways in glucose metabolism that utilize glucose 6 phosphate (G6P). G6P
is isomerized to G1P by phosphoglucomutase the starting substrate for glycogenesis.
- Uridine diphosphates glucose phosphorylase catalyszes the reaction of G1P and uridine
triphosphate (UTP) to uridine diphosphate glucose (UDPGlc) the active nucleotide and
pyrophosphate.
- UDPGlc is the substrate of glycogen synthase which catalyzes the formation of a
glycoside bond between C-1 of the glucose of UDPGlc and C-4 of a terminal glucose
residue of glycogen. It is the source of glucose in the glycosylation of a tyrosine residue
of glycogenin.
o
In the muscle the glycogenin remains attached in the center of the glycogen
molecule
In the liver the number of glycogen molecules is more than the number of
glycogenin molecules
Degradation of glycogen to yield G1P the isomerized to G6P (in the liver G6P is
dephosphorylated by glucose 6 phosphatase releasing glucose to the circulation; in
the muscle G6P is metabolized in glycolysis).
glucan transferase transfers a trisaccharide unit from one branch to the other,
exposing the 1-6 branch point for the debranching enzme to act. The glucan
transferase and the debranching enzme is a characteristic of one complex enzyme.
Glucose 6 Phosphatase (deficiency can cause Von Gierkes disease) is in the lumen
of the smooth endoplasmic reticulum. Genetic defects involving Glucose 6
Phosphate transporters can cause a variant of type I glycogen storage disease.
Genetic defect in the isoform of glycogen synthase will have the following
manifestations;
Glycogen Storage Disease (Ex. Von Gierkes disease) genetic enzyme deficiencies
leading to accumulation of glycogen intracellularly with the following manifestations;
The first phase (oxidative nonreversible phase) of the pathway reactions involve
dehydrogenation and decarboxylation to yield a pentose (ribulose 5 phosphate and
ribose 5 phosphate)
The 2nd phase (non-oxidative reversible phase) involves two enzymes, transketolase and
transaldolase that convert ribulose 5-phosphate back to glucose 6-phosphate by series
of reactions
III.
Lipid Metabolism
A. Fatty Acid Oxidation
-
Each step in the oxidation process involves an acyl CoA derivative, a separate
enzyme, coenzymes NAD & FAD
Increased fatty acid oxidation leading to ketone body formation by the liver is a
characteristic of starvation and Diabetes mellitus
Free fatty acids are transported in the blood (long fatty acids bind with albumin and
short fatty acids are more water-soluble and exist in the unionized form or as an
anion
Oxidation of fatty acids require initially ATP and Coenzyme A for the activation of
the fatty acid catalyzed by Acyl-CoA synthetase (thiokinase)
Free Fatty Acids (FFA) cannot penetrate the inner mitochondrial membrane so it has
to undergo the following transformations;
o
Acyl CoA is oxidized producing acetyl CoA (2 carbons is cleaved from the acyl CoA at
a time). The chain is broken between the alpha and the beta bond (beta oxidation).
Fatty acids with an even number of carbon atoms produce acetyl CoA. Those with
odd number carbon atoms produce acetyl CoA and Propionyl CoA. Propionyl CoA is
the glucogenic substrate derived from oxidation of odd numbered carbon fatty
acids.
-
Enzymes that catalyze the reactions and their coenzymes in Beta oxidation
1. Acyl Co A Synthetase CoA, ATP, Mg
2. Acyl CoA dehydrogenase FAD
3. delta2 -enoyl-CoA hydratase
4. L-(+)-3-hydroxyacyl-CoA dehydrogenase NAD
5. Thiolase CoA
Reactions 2-5 are repeated until completion of the oxidation process
Palmitate with 16 carbons will yield 8 acetyl CoA requiring 7 rounds of the Beta
oxidation cycle
o
28 + 80 = 108 2 ATP (ATP used in the activation of the fatty acid in the first
reaction) = 106 mol of net ATP produced by 1 mol of palmitate.
NADH + H = 2.5 ATP; FADH2 = 1.5 ATP
Peroxisomes oxidize very long chain fatty acids and produce acetyl CoA and
Hydrogen peroxide (broken down by catalase). Dehydrogenation (NADH, FADH
produced) is not linked directly to phosphorylation (ATP production).
B. Ketogenesis
-
Occurs in conditions causing high rate oxidation of fatty acids (ex. Uncontrolled
diabetes mellitus, starvation. Ketone bodies in normal well-fed mammals do not
exceed 0.2 mmol/L.
Two (2) acetyl CoA condenses (catalyzed by thiolase) to form acetoacetyl CoA.
The reaction is reversible.
Acetoacetyl CoA condenses with acetyl CoA (by HMG CoA synthase) to form
HMG CoA
HMG CoA is split into Acetyl CoA and acetoacetate by HMG CoA lyase
Acetoacetate is reduced (utilizing NADH) to 3-hydroxybutyrate: 3hydroxybutyrate is oxidized (using NAD) to acetoacetate. Both reactions are
catalyzed by 3-hydroxybutyrate dehydrogenase
Regulation of ketogenesis
1. Factors that regulate mobilization of fatty acids from adipose tissue (Fatty
acids are precursors of ketone bodies in the liver. The liver extracts 30% of
the fatty acids that pass through it).
2. CPT I activity (found in the outer mitochondrial membrane) catalyze the
condensation of Acyl CoA and carnitine
a. in the fed state, CPT I activity is low thus reducing -oxidation
(Malonyl-CoA, the initial intermediate in fatty acid biosynthesis
formed by acetyl-CoA carboxylase in the fed state, is a potent
inhibitor of CPT-I)
b. during starvation, the CPT I activity is increased (when
concentration of free fatty acids increases with the onset of
starvation, acetyl-CoA carboxylase is inhibited directly by acyl-CoA,
and [malonyl-CoA] decreases, releasing the inhibition of CPT-I and
allowing more acyl-CoA to be -oxidized
3. Acetyl CoA produced by -oxidation may either be oxidized in the TCA or is
utilized to form ketone bodies. The partition of acetyl-CoA between the
ketogenic pathway and the pathway of oxidation to CO2 is regulated so that
the total free energy captured in ATP which results from the oxidation of
free fatty acids remains constant as their concentration in the serum
changes. This may be appreciated when it is realized that complete
oxidation of 1 mol of Palmitate involves a net production of 106 mol of ATP
via -oxidation and CO2 production in the citric acid cycle (see above),
whereas only 26 mol of ATP are produced when acetoacetate is the end
product and only 21 mol when 3-hydroxybutyrate is the end product. Thus,
ketogenesis may be regarded as a mechanism that allows the liver to oxidize
increasing quantities of fatty acids within the constraints of a tightly coupled
system of oxidative phosphorylation.
a. Fall in Oxaloacetate can be caused by increased NADH/NAD ratio
due to -oxidation of fatty acids
b. Decreased NAD will reduce the activity of Malate dehydrogenase
(NAD is a coenzyme) thus lowering Oxaloacetate.
c. Oxaloacetate is needed in the oxidation of acetyl CoA oxidation of
acetyl CoA in the TCA will decrease with low Oxaloacetate
d. Pyruvate carboxylase is activated by increased levels of acetyl CoA
which in turn increases Oxaloacetate for gluconeogenesis (a
condition that occurs in starvation and uncontrolled Diabetes
mellitus).
o
impaired fatty acid oxidation and lipid accumulation with muscular weakness.
Treatment is by oral supplementation with carnitine.
1. Inherited CPT-I deficiency - affects only the liver; cause reduced fatty acid
oxidation and ketogenesis (because fatty acid will not be available in the
mitochondria for -oxidation), with hypoglycemia.
2. CPT-II deficiency acylcarnitine that was transported by the carnitine
acylcarnitine translocase to the mitochondrial matrix will not be converted
back to carnitine and acyl- CoA (precursor of -oxidation). It affects
primarily skeletal muscle and in severe cases the liver.
Treatment is by using sulfonylurea drugs (glyburide [glibenclamide] and
tolbutamide) which will reduce fatty acid oxidation and, therefore,
hyperglycemia by inhibiting CPT-I.
3. Inherited defects in the enzymes of -oxidation and ketogenesis also lead to
nonketotic hypoglycemia, coma, and fatty liver. Defects are known in longand short-chain 3-hydroxyacyl-CoA dehydrogenase (deficiency of the longchain en-zyme may be a cause of acute fatty liver of pregnancy). 3Ketoacyl-CoA thiolase and HMG-CoA lyase deficiency also affect the
degradation of leucine, a ketogenic amino acid
4. Jamaican vomiting sickness is caused by ingesting the toxin hypoglycin
(from the unripe fruit of the akee tree) toxin. This inactivates medium- and
short-chain acyl-CoA dehydrogenase, inhibiting -oxidation and causing
hypoglycemia.
5. Dicarboxylic aciduria is characterized by the excretion of C6C10 dicarboxylic acids and by nonketotic hypoglycemia, and is caused by a lack
of mitochondrial medium-chain acyl-CoA dehydrogenase.
6. Refsum's disease is a rare neurologic disorder due to a metabolic defect
that results in the accumulation of phytanic acid, which is found in dairy
products and ruminant fat and meat. Phytanic acid is thought to have
pathological effects on membrane function, protein prenylation, and gene
expres-sion.
7. Zellweger's (cerebrohepatorenal) syndrome occurs in individuals with a
rare inherited absence of per-oxisomes in all tissues. They accumulate C26
C38 polyenoic acids in brain tissue and also exhibit a generalized loss of
Glucose which is the main fuel in the diet is the primary substrate for lipogenesis
14. In state of starvation (caloric deficiency), fatty acids are utilized to supply
acetyl CoA for energy (ATP) production. The rate of synthesis is low in
restricted caloric intake, high-fat diet, or a deficiency of insulin (in DM).
15. Short term regulation of long-chain fatty acid synthesis is due to allosteric
and covalent modification
16. Long term regulation is due to changes in gene expression of enzymes
involved
17. Regulation of Acetyl CoA carboxylase
a. allosterically activated by Citrate and by long chain acyl
molecules (negative feedback);
Long chain acyl molecules may accumulate due to
1) Increased lipogenesis will cause accumulation of long acyl
molecules due to decrease in the esterification of fatty acid
synthesized.
2) Increased lipolysis (breakdown of esterified FA) results to
increase in the production of fatty acids or its influx into the cell
b. covalently activated by dephosphorylation and inactivated by
phosphorylation
1) insulin triggers dephosphorylation acetyl carboxylase
is active in the dephosphorylated form. Also Inhibits
lipolysis and is important in gene expression and is
antagonized by glucacon.
a) Insulin also increases glucose uptake thus increasing
glycolysis. Glycolysis produces Glycerol-3-phosphate
and Pyruvate.
b) Glycerol-3-phosphate used substrate for esterification
of fatty acids
c) Pyruvate is the precursor for acetyl CoA
2) glucagon triggers phosphorylation acetyl carboxylase
is inactive in the phosphorylated form
2015 REVIEWER
1. Lysosomes - Referred to as suicide bags of the cell, containing a variety of hydrolytic and
degradative enzyme
2. High specific heat - The ability of water to absorb and store a large amount of heat
3. Nucleus - The most prominent feature of the eukaryotic cell, serving as its
information center
4. Water as hydrophilic colloid system maintains body temperature for its main function
5. Iron in the body is absorbed in the ileum.
6. Transferrin is the glycoprotein involved in the transport or iron.
7. Ferritin is the major protein involved n the storage or iron.
8. Lactoferrin is the Iron that has anti-microbial effects thus can protect the newborn
9. Low ph is necessary in the absorption of iron
10. Protein digestion starts in the stomach where the acidic environment favors denaturation.
11. Excess NH4 from the breakdown of amino acids are converted into urea and excreted
12. Five carbon amino acids enter the citric acid cycle as Ketoglutarate
13. Example of a non-competitive inhibition - lead combines with the sulfhydryl group of enzymes.
14. Apoprotein is the protein, heat labile, non dialyzable portion a complex enzyme system.
15. Activity of enzymes is expressed in terms of velocity.
16. In an enzyme-substrate reaction, a large Km means a low affinity of enzyme for the substrate
17. Vitamin C as co-enzyme can act alternately as an oxidizing and reducing agent
18. The enzyme Lyase can bring about the cleavage of C-C, C-O, and C-N bonds in a substrate.
19. Km and Vmax are the two constants that are always measured whenever enzymes are
characterized.
20. Lyases are enzymes that catalyze the addition or removal of water, ammonia or carbon dioxide to
double bonds.
21. Alkaline phosphatase is the nonfunctional serum enzyme that is diagnostic of obstructive liver
diseases
22. Carbonic anhydrase requires zinc as cofactor.
23. ALA dehydratase is a zinc containing enzyme that is sensitive to the inhibition of lead.
24. Cyclooxygenase (COX1 and COX2) or Prostaglandin H synthase is inhibited by NSAIDS (ex.
Aspirin). COX2 is selectively inhibited by coxibs (ex. Celecoxib).
25. Anti-inflammatory corticosteroids inhibit transcription of COX2 but not COX1.
26. The quantitative value of the Michaelis constant or Km, is a measure of the relative affinity between
the substrate and enzyme
27. Acid phosphatase is valuable in the diagnosis of metastatic carcinoma of the prostate gland.
28. Ligases join two molecules along with breakdown of a pyrophosphate (P-P) bond
29. Oxygen is the H+ acceptor of oxidases
30. Acetylcholine stimulates the secretion of the following saliva, pancreatic enzymes, and gastric juices
1. Primary structure of proteins determined by the sequence of amino acids in the polypeptide chain
and sulhydril bridges
2. Secondary - the folding of short (3- to 30-residue), contiguous segments of polypeptide into
geometrically ordered units. Ex. Helix structure
3. Tertiary - the assembly of secondary structural units into larger functional units such as the mature
polypeptide and its component domains
4. Quaternary - the number and types of polypeptide units of oligomeric proteins and their spatial
arrangement
5. Glutamine is the amino acid that serves as the major mode for disposing ammonia from the brain
6. Transamination of pyruvate will produce alanine
7. Tyrosine is the amino acid precursor of catecholamines.
6. Degeneracy of the genetic code is an important feature of the genetic code that may protect the
codon in the event of a single base substitution:
7. Single base insertion or deletion on the genetic code changes the reading frame and result to a
frameshift mutation.
8. Tumor p53 suppresor protein plays a key role in both the G1 and G2 chekpoint control.
9. Southern blot is the technique involved in the analysis of DNA.
10. Cosmids are used for cloning DNA fragment with a length of 400,000 bp
11. The enzymes required for the synthesis of cDNA are, reverse transcriptase, DNA ligase,
andRnase H
12. DNA chips(microarray) is the method based on the preparation of large arrays of oligonucleotides
on miniaturized solid supports for analysis of DNA sequence.
13. Antibiotic resistance gene is an important feature of a cloning vector because it will allow
screening of the host (successfully transfected host)
14. Dnase 1 an enzyme that does not form phosphodiester bonds.
15. DNA amplification is the diagnostic technique to use in patients at with sickle cell anemia or at
risk of this disease.
16. DNA methylation is the process that occurs at the 5-position of Cytidine and is often correlated
with gene inactivation
17. A specific nuclease detects damaged areas following ultraviolet damage to DNA in the skin.
18. Northern Blot Analysis Detects RNA molecules
19. RNA polymerase synthesizes RNA primer to initiate DNA synthesis
20. The function of a promoter site on DNA is to Initiate transcription
6. chylomicrons the fraction of the plasma lipoproteins that is located closest to the
negative pole when separated by electrophoresis on agarose gel
(Harpers
Ch 27 p 268-271)
17. Citrate the compound that is transported out of the mitochondria that contains the
acetate group needed for fatty acid biosynthesis in the cytosol
18. Carnitine ferries the fatty acids (acyl CoA) through the inner mitochondrial
membrane for beta-oxidation in the matrix
19. Mitochondrial matrix where the activation of medium chain and short fatty acids
occurs in the for beta-oxidation
(Harpers pp 238-239)
20. Malonyl coenzyme A is the product formed in the committed (rate limiting) step of
fatty acid synthesis
( Harpers Ch 23 pp 230)
22. Cholesterol - is the precursor for the synthesis of bile acids (metabolic product),
Vitamin D, and Steroid hormones
23. Cardiolipin Structure is composed of three glycerol, two phosphoric acid and 4 fatty
acids
24. Thromboxane - the eicosanoids that can promote platelet aggregation
25. Lecithin lipid that acts as surfactant and deficient in cases of Respiratory Distress
syndrome
26. Palmitic acid is the end-product of extra-mitochondrial lipogenesis
27. Acetyl CoA is the two carbon product released by the action of thiolase in the betaoxidation of fatty acids
28. Carnitine transport is the committed step in beta-oxidation
29. HMG-CoA reductase enzyme that catalyze the rate-limiting step in cholesterol
synthesis
30. Isopentenyl pyrophosphate the formation of which is the most expensive stage in
the biosynthesis of cholesterol
31. alpha lipoprotein functions in the reverse transport of cholesterol in the blood.
32. Insulin the hormone which is antilipolytic
33. Hormone-sensitive lipase the major regulatory enzyme in lipolysis
34. Dihydroxyacetone phosphate the source of glycerol 3-phosphate for triglyceride
synthesis in adipose tissue
35. acetoacetic acid is produced by the reaction that is catalyzed by HMG-CoA lyase
36. Phospholipase C hydrolyzes phospholipids specifically phosphatidylinositol-4,5bisphosphate (PIP2) and produces second messengers inositol triphosphate (IP3)
and diacylglycerol (DAG)
37. Ceramide precursor of sphingolipids
38. Clyclooxygenase catalyze the production of prostaglandins, thromboxanes, and
prostacyclins
39. Polyunsaturated fatty acids up-regulate LDL
40. HMP shunt main source of NADPH for lipogenesis
41. Substrate level phosphorylation direct phosphorylation of ADP to produce ATP (An
example of substrate level phosphorylation that occurs in glycolysis is the production of
ATP when 1,3 bisphophoglycerate is converted into 3-phosphoglycerate).
main source of ATP formation in brown adipose
tissue
45. Acetyl CoA carboxylase catalyzes the initial and controlling step in lipogenesis
46. Ascorbic acid - is needed in the rate limiting reaction of bile acid synthesis
47. [NADH]/NAD+] ratio increase levels is the biochemical explanation for fatty liver and
hyperuricemia in chronic alcoholics
48. Fatty acids the major source of energy for oxidative metabolism in the heart
49. Carnitine shuttle transport system that shuttles activated fatty acid molecule from the
cytoplasm to the inner mitochondrial membrane during -oxidation of fatty acids
50. Apo B-48 is the apoprotein found exclusively associated with chylomicrons
BIOCHEMISTRY
REFERENCES :
1. Biochemistry by Harper, 25th edition
2. Textbook of Biochemistry with Clinical Correlation by Thomas Devlin
3. Biochemistry Campbell 3rd edition
4. Biochemistry a Case Oriented Approach by Mosby
5. Biochemistry by Orten and Newhaus
6. Molecular Biology of the Cell by Alberts