Chapter 1.

introduction
1.1. Definition
A. Biochemistry: Biological Chemistry, Physiological Chemistry
Chemistry
General Chemistry
Organic ChemistryLast parts
Inorganic Chemistry
Physical Chemistry
Quantum Chemistry
B. Biochemistry
Structures of Biomolecules
Bioenergetics
Functions of Biomolecutes
Biomolecules: Large and small molecules
Large ones: Macromolecules like DNA, RNA , proteins and polysaccharides
Bioenergetics: Energy flow in the living cells
C. Conformation: 2 conformations of ethane
Eclipsed
Staggered
1.2. Road to modern biochemistry: Page 8 Fig 1.2
1.3. Biological Macromolecules: Page 12 Fig. 1.6
A. Starch and Cellulose: Homopolymers of Glucose
B. Proteins: Heteropolymers of Amino Acids :
Acids containing amine groups
C. Nucleic Acids: Heteropolymers of Nucleotides( dAMP AMP, dGMP GMP, dTMP
UMP, dCMP, CMP)
1.4. Organelles, Cells and Organisms
A. Archaebacteria: Methane bacteria
B. Prokaryotes: Pro-Before, Karyon- nuts or kernel
Page 16 Table 1.1
C. Eukaryotes: Eu- Good or well
Human body digestive system Liver Hepatocytes Nucleus Chromatin
DNA Nucleotides Base, sugar and phosphate C, H, O, N Page 19 Fig. 1.11
Page 21 Table 1.2
1.5 Life at the Extremes: Page 16 Window on Biochemistry
1.6 Handling cell components: Page 24 Window
 Chapter 2. The flow of biological
information: Cell communication
2.1. Brief Image of information flow: Page 30 Fig. 2.1

Transcription
Translation
 2.2. Storage of Biological information in DNA
Genome: The total genetic informational content for each
cell
Exact duplication
Expression of stored information
DNA molecules
Watson and Crick in 1952: Double helix structure
Complementary base pairs by specific hydrogen bondings: C-G and A-T
C-G: triple hydrogen bonds A-T: double hydrogen bonds
Bases: inside the helix , the backbone : sugar and phosphate
Human Genome Project
To map and sequence the estimated 3 billion nucleotide base pairs
Other living organisams: Bacillus subtilis, Caenorhabditis elegans, Yeast,
Arabdopsis thaliana, Rice
30,000-40,000 genes in the human genome
Proteomics: The name given to the broad field investigating the thousands
of protein products from the genome
Bioinformatics: Computer applications to organize the mass of nucleic
acid sequence data and studying relationships between protein sequence and
structure.
 2.3 Replication
5 to 3, Semi conservative replication
DNA polymerases
Polymerase Chain Reaction (PCR)
2.4 Transcription
Double helix DNA, RNA polymerase
rRNA, mRNA, tRNA: Page 35 Table 2.1
 2.5 Translation
Genetic code: triplet code Page 38 Fig. 2.7
Exons and introns
Introns are absent in prokaryotes
RNA processing: Page 38 Fig. 2.8
Catalytic RNA
2.6 Errors in DNA Processing
DNA mutations: sickle cell anemia and other inborn metabolic errors
2.7 Information flow through cell membranes
A. Signal transduction:
B. Second Messengers: cAMP, cGMP, Ca2+
2.8 Drug design:
Page 44 Fig 2.11
A. Interference of Protein synthesis including transcription and translation
B. Receptor binding to block the initiation
C. Disruption of Signal pathway
 Chapter 3 Biomolecules in Water
Water content: Page 48 Table 3.1, 71-83%
3.1 Water the Biological Solvent
Weaker interactions: noncovalent bonds- 1-30kj/mole (cf.
350kj/mole for C-C bond) Page 50 Table 3.2

Reversible and specific

Van der Waals forces
Ionic bonds
Hydrogen bonds
Hydrophobic interactions
B. The structure of water
Page 51 Fig. 3.1, sp3 orbitals
 3.2 Hydrogen bonding and Solubility
Physical properties of water: Page 53 Table 3.3 , Fig. 3.5

Solvation: Page 54 Fig. 3.6

Amphiphilic
Hydrophobic interaction
Micelles
3.3. Cellular Reactions of Water
A. Ionization of water
B. pH and pK
pH = -log [H+] , pKa = -log Ka
pH values of some natural fluids: Page 58 Fig 3.10
HA H+ A- Ka = [H+][A-]/[HA] :
Acid Conjugate Base
pH = pKa log [A-]/[HA]: Handerson-Haselbalch Equation
H3PO4 H+ H2PO4-1 pKa1=2.14
H2PO4-1 H+ HPO4-2 pKa2 = 7.20
HPO4-2 H+ HPO4-3 pKa3 = 12,4
Titration curve
CH3COOH + NaOH = CH3COONa + H2O
Acid Conjugate base
pH = pKa log [A-]/[HA]
If [A-]/[HA]= 1 , log [A-]/[HA] = 0. So pH = pKa

3.4 Buffer system

Acid base conjugate pairs
Buffering blood and other cellular fluids: Page 62, Window, Table 3.5
Buffer exercises : Acetate buffer, Phosphate buffer
 Chapter 4. Amino acids, Peptides and Proteins:
Proteins architecture and Biological Functions
4.1. The amino acids in proteins
A.D- and L-form: Mirror image ( Enantiomers)
B.Classification and Properties

Carboxyl Net Charge Migration A cation

Amine group exchanger
group
pH 7 pH 1 pH =7 pH=1 Binding Elution

Neutral 1 1 0 +1 0 + + Second

Basic 2 1 +1 +2 Cathode ++ ++ Last

(positively
charged)
Acidic 1 2 -1 Less Anode Less Less First
(negatively than than + than +
charged) +1
C. Modified amino acids: 4-hydroxy proline, 5-hydroxy lysine
D. Reactivity of amino acids
Reagents reacting with amine group: Page 77 Fig 4.9
 4.2. Polypeptides and Proteins
Peptide bonds: Page 101 Fig 5.4
Average molecular weight of all amino acids in the polypeptides:
110
B. Amino terminus ( N-terminus), Carboxyl terminus( C-terminus)
C. Peptidases, or Proteases
D. Oligopeptides: Glutathione(3AA), Enkephalin (5AA), oxytocin( 9AA),
vasopressin (9AA), insulin (51 AA)
E. Classification
Shape- globulins, fibrous proteins
Function- Page 79-82
Components- Simple proteins, Complex( Conjugated) proteins ( glyco-, lipo- , metalo-
chromo-, phospho-, nucleo-)

4.3 Four levels of protein structure

A. Primary structure: Amino acid sequence and disulfide bonds
B. Secondary Structure: Conformation of neighboring amino acids:
-helix,: Right handed or left handed coil: One turn of the helix: 0.54 nm and 3.6
residues: Page 102 Fig. 5.5
-pleated sheet: parallel, antiparallel: Silk Fibroin or proteins of spider webs
Bends and loops:
proline and glycin at the bend:
Extended bends: loops
Super secondary structure or Motifs ( Domains)
The individual elements of secondary structures are often combined into stable,
geometrical arrangements.
, ,,
C. Tertiary structure: Conformation of distant amino acids
Page 100 Fig. 5.3
Primary structure determines the tertiary structure.
Denaturing, Renaturing, Native proteins Page 109 Fig 5.14

D. Quaternary structure
Monomeric, oligomeric
Subunits
4.4. Hemoglobin
A. Heme globin
B. Heme binding to globin
C. Oxygen binding: Page 115, Fig. 5.19
Sigmoidal curvePositive cooperation( Myoglobin: Hyperbolic)
D. Bohr effect: Page 115 Fig. 5.20
H+ and CO2 decrease the affinity of hemoglobin for oxygen molecule
4.5. Fashionable hair: Page 114, Windo
 Chapter 5. 6. Enzymes 1
6.1 Biological catalysts
A. Catalysts: Page 127 Fig
6.2
B. Cofactor- in addition to the protein component, another
chemical entity , in order to function properly.
Metal ions- Zn+2, Mg+2
Coenzymes: Orgnometallic molecules
C. Prosthetic groups: cofactor covalently bonded to the proteins
Holoenzyme: protein + cofactor
Apoenzyme: without cofactor
E. Classification : Page 129 Table 6.2
6.2 Enzyme Kinetics
A. Michaelis Menten equation derivatisation
k2 k4
E + S ES E + P
k1 k3
ES formation rate: k1[E][S] + k4[E][P], often k4 is very small to be neglected.
ES degradation rate: k3[ES] + k2[ES]
At Steady state: Rate of formation = rate of degradation
k1[E][S] = k3[ES] + k2[ES]
[E]total = [E] + [ES]
k1([E]total-[ES]) [S] = [ES](k3 + k2)
k1[E]total[S]-k1[ES][S] = [ES](k3 + k2)
k1[E]total[S]= [ES](k3 + k2) + k1[ES][S]
[ES]( k3 + k2 + k1[S]) = k1[E]total[S]
[ES] = k1[E]total[S] / ( k3 + k2 + k1[S])
[ES] =[E]total[S] / ( k3 + k2)/k1 +[S])
(k3 + k2)/k1 = Km
[ES] =[E]total [S] / ( Km +[S])
dP/dt = Vo = k3[ES] =k3[E]total[S] / ( Km +[S])
k2[E]total = Vmax
Vo= Vmax [S]/(Km + [S])
 B. Km: If V = 1/2 Vmax, Km =[S]
C. Turnover number = Vmax/[E]total
D. Lineweaver-Burk Equation
From Vo= Vmax [S]/(Km + [S])
1/Vo = (Km + [S])/Vmax[S]
1/Vo = Km/Vmax 1/Vmax + 1/Vmax Page 134 Fig. 6.5
E. Characteristics of enzyme reactions
Enzyme concentration, pH, Temperature
6.3 Substrate binding and enzyme action
A. Active site
Lock and Key model; Page 137 Fig 6.10
Induced fit model: page 138Fig. 6.11
Transition state analog model: Page 138 Fig. 6.12
B. General Acid-Base catalysis: An Enzyme donates a proton and accept it in the
final step
Proton transfer to the carbonyl group
Water attack to from a tetrahedral intermediate
Acceptance of the proton from the intermediate
C. Metal ion catalysis:
Alkali metal ( Na+, K+) and transition metals ( Mg+2, Mn+2, Cu+2 Zn+2 Fe+2
Fe+3 Ni+2)
Hold a substrate properly oriented by coordinate covalent bonds ,
Page 140 Fig. 6.14 a
Polarize the scissile bond or stabilize a negatively charge intermediate. Fig. 6.14 a
Participate in biological oxidation-reduction reactions by reversible electron
transfer between metal ions and substrate. Fig. 6.14 a
D. Covalent catalysis
A nucleophilic functional group on an enzyme reacts to form a covalent bond with
the substrate. Page 140, Step 1 and 2
 6.4 Enzyme inhibition
A. Reversible and irreversible inhibitors
DIFP, Pesticides
B. Reversible inhibitors: Page 145 Fig 6.19
 Competitive inhibitors: Resemble the structure of normal substrate and
binds
to the active site of the enzyme
E+S ES E+P
+
I

EI

Noncompetitive inhibitors: Both inhibitor and substrate can bind

simultaneously to the enzyme molecule.
E + S ES E+P
+ +
I I

EI + S ESI

Uncompetitive inhibitors: The inhibitor binds only to the ES complex

E + S ES E+P
+
I

ESI
 C. Protease inhibitor: page 146 Window
Alzheimers disease (AD)
-secretase
Amyloid precursor protein ( APP) A-40 + A-42
AIDS
HIV protease- Viral growth and development: Phe-Pro, Tyr-Pro
 Chapter 7: Enzymes II: Coenzymes,
Regulation, Abzymes, and Ribozymes
7.1. Enzyme: Coenzyme partners :
Vitamins and Coenzymes: Page 157 Table 7.1
Metals as nutrients: Page 161 Table 7.2
7.2. Allosteric enzymes
A. Regulatory enzyme
E1 E2 E3 E4 E5
A B C D E P
Final product inhibition
The beginning substrate in the sequence
An intermediate formed in the pathway
Some external factor such as a hormone
All of the above
B. Positive and negative Effectors
Effectors: Bomolecules influencing the action of an allosteric enzyme.
Allosteric enzymes
much larger and more complex than nonallosteric enzymes
regulatory sties for binding specific efectors
Page 165 Fig. 7.2
C. Models to describe allosteric regulation
MWC concerted model: TT RR Reaction products Page 165 Fig. 7.5
Sequential model: TT TR RR Reaction products
7.3. Cellular regulation of enzymes
A. Covalent modification of regulatory enzymes
Phosphorylation of OH group in serine, threonine or tyrosine:
Example: Page 168 Fig. 7.7
Attacheeent of an adenosyl monophosphate to a similar OH group
Reduction of cystein disulfide bonds
B. Activation by proteolytic cleavage
Zymogen active enzyme + peptide: Page 169 Table 7.3 and Fig 7.8
C. Regulation by isoenzymes
Enzymes existing in different molecular forms( Multiple forms)
Lactate Dehydrogenase (LDH): M4 in muscle H4 in heart
7.4 Site directed mutagenesis and Abzymes and Ribozymes

A. amino acid sequence of known enzymes

B. Abzymes or Catalytic antibody: Protein antibodies by using transition state analogs
as antigens
C. Ribozyme: Catalytic RNA : The catalytically active region 19 -30 nucleotides
 Chapter 8 Carbohydrates: Structure
and Biological function
8.1. Monosaccharides
A. Carbo + Hydrate
B. Aldose and Ketose
C. Triose, Tetrose, Pentose, Hexose
D. Diastereoisomers: D-Threose and D-Erythrose
E. Epimers: Mannose and Galactose are epimers of glucose
F. Structure: Page 182 Fig. 8.5 and 8.6
8.2. Carbohydrates in cyclic structures
A. Difficult to be oxidized to the acid, compared with other aldehydes.
B. Hemi acetal and Hemi ketal
C. Anomers ( , form) : ( = 113.4o = 19o)
D. Mutarotation:52.2o

8.3. Reactions of monosaccharides

A. Reducing sugars: Reduction of Cu+2 to Cu +1
B. Lactone formation: intermolecular ester
C. Deoxy sugars: Another form of reduced sugars
D. Esterification with phosphoric group ( ATP)
F. Amino derivatives: Glucosamine, Galactosmine, N-acetylglucosamine
E. Glycoside: ROH + Anomeric OH group of sugar a glycoside ( Page 189 Fig. 8.14)
8.4. Disaccharides : Page 191 Fig. 8.16
A. Maltose
B. Cellobiose
C. Lactose
D. Sucrose
8.5. Polysaccharides
A. Starch: : Glucose ( 14) linkage : Page 194 Fig 8.19
Amylose and Amylopectin( branches with (1 6) linkage)
B. Glycogen
C. Cellulose: Glucose ( 14) linkage:
D. Chitin: N-acetylglucosamine ( 14) linkage: Page 197 Fig. 8.24
E. Peptidoglycans: The rigid cell walls of bacteria: N-acetylglucosamine
( 14) + Glucuronic acid ( 13)
8.6. Glycoproteins
A. Functions: Immunological protection, Cell-cell recognition, Blood clotting and Host-
pathogen interaction
B. Structure: Page 200 Fig. 8.29
O-glycosidic bonds: OH groups of serine threonine residues in the protein
N-glycosides bonds: the side chain amide nitrogen of the amino acid residue
asparagines.
C. Lectins: Proteins specifically recognizing sugar moiety of a protein.
Concanvalin A: Mannose
Wheat germ agglutinin: N-acetylglucosamine
Peanut lectin: N-acetylgalactosamine
 Chapter 9. Lipids, Biological
membranes and cellular transport
9.1. Fatty acids
A. Nomenclature: Page 209, Table 9.1
B. General characteristics: Page 209 Table 9.2
C. Soap: Na or K salt of fatty acids,
D. Essential fatty acids: Linoleic and Linolenic acids
E. -3 tatty acids: Eicosa pentaenoic acid EPA (20:5 Delta 5, 8, 11, 14, 17)
Docosahexaenoic acid( DHA)( 22:6 Delta 4, 7, 10, 13, 16, 19)
9.2. Triacylglycerols and Wax
A. Structures: Page 211 Fig. 9.2
B. Saponification: hydrolysis by NaOH: Glycerol + Soap
C. Hydrolysis by Lipases: Glycerol + Fatty acids
D. Wax: Fatty acid ester of an alcohol having a higher carbon number
9.3. Polar lipids
A. Phosphatidic acid : Page 217 Fig. 9.7
B. Glycerophospholipids: Page 216 Fig. 9.6
C. Spingolipids:
D. Spinosine structure Page 218 Fig. 9.8
E. Lipid bilayer: Instead of micelle formation, polar lipids form lipid bilayers
9.4 Steroids and terpenes
A. Cholesterol and its derivatives: Page 219 Fig. 9.10, Page 222 Fig. 9.11
B. Plant sterol: Stigmasterol, Campesterol and -Sitosterol Page 221 Window
C. Terpenes: Page 223 Fig 9.12
 D. Eicosanoids: Arachidonate derivatives (20:4 Delta 5,8.11,14)
Prostaglandins: PGD2: physiological sleep PGE2: Wakefulness
Thromboxanes: Blood clotting formation
Leukotrienes: Contraction of smooth muscle , especially in the lungs
Lipid soluble Vitamins Page 224 Table 9.4
F. Electron carriers: Ubiquinone ( Coenzyme Q) Page 225 Fig. 9.14
 9.5 Biological Membranes
A. Biological roles
Physical barriers as protective shields to isolate the cells and organelles
sensitive interiors fro their exterior environments
Organization and compartmentation of biochemical activities within tissues
and cells
Selective filter to allow the entry of nutrients necessary for the cells growth
and development and the exit of metabolic waste products
Communication ith its surroundings through protein receptors
Energy transduction-Mitochondria and photosynthetic organisams
 B. Membrane components and structure
Lipids, Protein and carbohydrates
Carbohydrates: covalently bound to lipid and proteins
Less than 5% Outside the membrane
Lipids: Bilayer
No simple diffusion of amino acids, ugars, proteins and nucleic acids
Free diffusion of water and small nonpolar molecules such CO2 and
hydrocarbons
Fluidity of vegetable oil
Free lateral movement but no flip-flop movement
Cholesterol not found in plants. 3% in mitochondrial membrane 38% in
plasma membrane
Proteins: The dynamic activities of the cell membrane
Peripheral proteins : Receptor sites or enzymes
Integral proteins ( 1,0M NaCl solution): channel or gate : Large portion of
hydrophobic amino acid residues ( Transmembrane segment)
Fluid mosaic model:Page 229 Fig 9.18
9.6 Membrane transport
A. Passive transport and Active transport
Passive transport: Along with the concentration gradient
Simple diffusion
Facilitated diffusion: permeases Page 234 Fig. 9.24
Active transport: Against the concentration gradient using ATP: Na-K pump
Page 237 Fig. 9.26
B. Uniport and Cotransport: Page 231 Fig. 9.20
Uniport
Cotransport: Symport and Antiport
 Chapter 10. DNA and RNA:
Structure and Function
10.1. RNA and DNA chemical structures
A. Components of nucleotides
Nitrogenous bases: Purine and Pyrimidine Page 245 Fig. 10.2
A five- carbon carbohydrate Ribose or Deoxyribose
One, two or three phosphate groups
B. Nucleoside: a nitrogenous base linked to ribose or deoxyribose through N-
glycosidic bond
C. Nucleotide: nucleoside- phosphate ester
D. Nomenclature of nucleosides and nucleotides: Page 247 Table 10.1
E. Other nucleotides: Coenzyme A, FAD NAD and NADP
F. Nucleic acids: 3,5 phosphodiester bonds : Page 249 Fig 10.
10.2. DNA
A. Comparison of DNA from different species: Page 250 Table 10.2
 B. Features of DNA
Two right handed helical polynucleotide chains to form a helix
Antiparellel
Outside of the helix: the alternating deoxyribose and phosphate groups
Inside: Purine and pyrimidine bases
Two weak forces
Hydrogen bonds; A- T and C-G
Wan der Waals and hydrophobic interaction between stacked bases

C. Conformational varieties of DNA Page 254 Fig. 10.10

B-DNA; Crystallized in water and retains water molecules withing the crystal
structure
Most common under physiological conditions
10.5 bases per turn a diameter of 20A
A-DNA: Dehydrated form of B-DNA
11 bases per turn 26A
Z-DNA: Observed in short strands of synthetic DNA
Left handed helix, 12 bases per turn 18A
Also found in short stretches of native DNA-Gene regula
D. Melting of DNA
De and Re naturation
Hyperchromic effect

E. Tertiary structure of DNA

Supercoiled DNA and Relaxed DNA : Page 257 Page 10.14
10.3. RNA structural Elements
A. Classification; Page 251 Table 10.3
B. General features Page 258 Fig. 10.15
Ribose rather than 2-deoxyribose
Uracil instead of Thymine
More susceptible to hydrolysis than DNA due to an extra OH group
Hair- pin turns
Right- handed double helixes in RNA
Internal loops and bulges
C. tRNA: The smallest types of RNA
Carriers of specific amino acids used for protein synthesis
74-93 nucleotides in a single chain
Cloverleaf structure for tRNA Page 260 Fig. 10.17

D. rRNA
Much larger than tRNA but shares many of the same elements as tRNA
 10.4. Cleavage of DNA and RNA by nucleases
A. DNases, Rnases
B. Exonucleases, Endonucleases
C. DNA restriction enzymes
Recognize specific base sequences in double-stranded DNA : Palindrome
sequences
Eco R1, Hpa1 Bam H1

10.5. Nuclei acid-protein complexes

A. Viruses
The protein molecules form a protective shell around the nucleic acid core.
Usually not considered as forms of life
Average about 100nm in length
DNA viruses, RNA viruses
Bacteriophages(Phages) : Viruses that are specific for bacteria:
The majority of pahges are DNA viruses.
RNA viruses: TMV, HIV Page 266 Fig.10.22
B. Chromosomes: Page 267 Fig. 10.23
Functional units of packed genomic DNA in the
nucleus of eukaryotic cells
The packaging must be highly ordered and
compact in order to fit the huge DNA molecules
(1-2m) into the cells nucleus( 5 um in diameter).
Nucleosomes: DNA-histone complexes:
One chromosome- 1 million nucleosomes
Chromatin: Beads-on-a string form of
nucleosomes
Chromatin fiber: Nucleosomes winding tightly in
a structure reminiscent of a filament or fiber
Chromatids: Each chromosome of the duplicated
pair
Sister chromatids: The two chromatids of
a given pair
C. Small nuclear
riboncleoprotein particles ( snRNPs):
RNA processing
D. Ribosomes: Supramolecular
assemblies of RNA and
protein
 Chapter 11: DNA replication and
Transcription: Biosynthesis of DNA and RNA.
11.1. Replication of DNA
A. Semi-conservative replication: Page 272 Fig. 11.1 and Page 273 Fig. 11.2
B. 2 Replication Forks:
C. The Origin: a discrete starting point in both directions
D. Theta model: Page 276 Fig. 11.4
 E. In eukaryotes: several initiation sites

11.2. Action of DNA polymerases

A. DNA polymerase 1
Isolated from E coli
Template and Primer, Mg+2
5 3 direction
B. DNA polymerases II and III: Page 278 Table 11.1
C. Okazki fragments: Page 279 Fig. 11.8
Continuous leading strand
Lagging Strand ( Okazki fragments)
D. Details of DNA replication: Page 281 Fig. 11.9 and
Page 282 Table 11.2
E. Eukaryotic chromosomes and Telomeres
Telomeres:
The presence of specialized ends in eukaryotic DNA: Hudndreads of repeats of a
hexanucleotide sequence ( Human AGGGTT)
Shorten during the normal cell cycle
If telomeres become too short, chromosomes become unstable and cell division is
inhibited
Telomerase:
The synthesis of telomeres.
Ribozyme containing an RNA molecule that serves as a template to guide the addition
of the right nucleotides.
Becomes activated in human cancer cells
 11.3. DNA damage and repair
Mutation: Changes in the base sequence of DNA

A. Spontaneous Mutations:
Mismatching of base pairs: 1/1010
The actual error rate of base incorporation during replication: 1/104-105
( Repair systems correct most mismatched base)
Base modifications caused by hydrolytic reactions
Nucleotieds containing purine bases can undergo spontaneous hydrolysis at the N-
glycosidc bond to remove the purine ring.
Deamination reaction: The conversion of cytosine to uracil

B. Induced mutations
Ionizing radiation
Chemicals: Heterocyclic base analogs : Page 286 Fig. 11.14
Alkylating agents: Page 286 Fig. 11.15
Intercalating agents: Flat, hydrophobic molecules that insert between stacked base
pairs in DNA: Page 287 Fig. 11.17
11.4. Synthesis of RNA:
The molecular vehicle carrying the genetic information from
DNA to protein synthesis.
A. Template strand: Sense strand: The strand of duplex DNA used as a template for
RNA synthesis
B. DNA-directed RNA synthesis
DNA-directed RNA polymerase: RNA polymerase
In Eukaryotic cells: RNA polymerase 1. II and III
large ribosomal RNA genes,
II. Protein-encoding genes,
III. Small RNAs including tRNA and 5S rRNA
Three steps: Page 291 Fig. 11.19
Initiation: subunit binds to RNA polymerase
subunit recognizes promotor
RNA polymerase binds to DNA
subunit dissociates from RNA polymerase
RNA polymerase begins to movealong the template strand
Elongation: Ribonucleoside triphosphates
Termination: factor interacts with RNA polymerase. Transcriptiion is terminated.
protein independent-GC-rich region, followed by an AT-rich region and a poly
A region
RNA, DNA, RNA polymerase and factor are released.
C. RNA-directed RNA synthesis: in RNA viruses( Q, MS2, TMV and R17)
 11.5. Post-transcriptional modification of RNA
A. tRNA
Trimming of the ends by phosphoester bond cleavage
Ribonuclease P near the 5end of pre-tRNA,
An endonuclease remove a small section from the 3end of the tRNA
Splicing to remove an intron
Addition of terminal sequences: CCA
Heterocyclic base modification, usually methylation
B. mRNA
Capping: Page 295 Fig. 11.24
Almost immediately after synthesis, the 5 end of the mRNA is modified by hydrolytic
removal of a phosphate from the triphosphate functional group.
GMP addition via GTP to the 5end resulting in an unusual 5-5triphosphae covalent
linkage.
Methylation
Poly A addition
Addition of a poly A tail to the 3end of mRNA after removal of a few 3 base
residues
Splicing of coding sequences
Exons: Coding regions on the gene
Introns: noncoding regions
SnRNP and catalytic RNA participate in the splicing
 11.6. Base sequences in DNA
A. Maxam-Gilbert chemical cleavage method
B. Sanger chain-termination sequencing method-
Dideoxy method Page 299 Fig. 11.27
Strands to be sequenced + short primer strand
DNA polymerase
dATP + dd ATP , dGTP + ddGTP, dCTP + ddCTP, dTTP + ddTTP Page 298
Fig. 11.26
Electorphoresis separating the reaction mixture according to the base size
 Chapter 12. Translation of RNA : The
genetic code and protein metabolism
12.1. Process of protein synthesis
A. Characteristics of protein synthesis
Location: Ribosomal particles
Ribosomes :25nm, 2500 kDaltons, around 15,000 ribosomes in E coli cell
70S ( 30S + 50S) { Eukaryotes: 80S ( 60S +
40S)]
66% RNA and 34% protein Page 307 Fig. 12.1
Move along mRNA templates deciphering the code for conversion from
nucleotide to amino acid sequence
Bring to the template the tRNA charged with the properamino acid
Catalyze the formation of peptide bonds between amino acids using
ATP or GTP.
Protein synthesis begins at the N-terminus.
Aminoacyl-tRNA synthetases: an amino acid is covalently linked by an eser
bond to the 2 or 3OH end of a specific tRNA.
20 aminoacyl-tRNA synthetases, one for each amino acid.
Genetic codes: Page 311 Table 12.2
Triplets
Degenerative
Universal
12.2. Three stages of protein synthesis
A. Initiation:
Ribosomal recognition of the starting point on the mRNA and entry of tRNA-activated N-
formylmethionine(fMet)
mRNA + IF + 30S subunit GTP-IF + fMet on AUG of mRNA: 30S initiation complex
50S subunit attachment with hydrolysis of GTP and IF detachment.: 70S initiation
complex
B. Elongation
70S initiation complex, the next amminoacyl tRNA in the A ribosomal bind site and EF
Formation of the first peptide bond: Peptidyl transferase a ribozyme associated with the 50S
ribosome
Translocation using GTP hydrolysis and removal of deacylated tRNA from the codon region
The 3rd charged tRNA + GTP hydrolysis on the new formed A site
C. Termination
RF on stop codon and activation of peptidyl tranferase
Hydrolysis of the ester bond liknking the carboxyl group the newly synthesized protein to the
tRNA in the P site
70S ribosome dissociated into its subunits
D. Polysomes: Clusters of ribosomes on a mRNA molecule Making many identical proteins
molecules from a single copy of mRNA
E. Protein synthesis and Energy
Two anhydride bonds in ATP for aminoacyl-tRNA formation
One GTP for entry of each amino acid into the A site
One GTP during each translocation step
12.3. Post-translational processing of proteins
A. Protein folding
Chaperones: Catalysts to guide and facilitate folding
Some chaperones are enzymes that couple ATP hydrolysis to the protein
folding process.
B. Biochemical modifications
Proteolytic cleavage: N-formylmethionine removal
Zymogens
Amino acid modification: Phosphorylation and hydroxylation
Attachment of carbohydrates: Glycoproteins
-Serine or threonine
-amide nitrogen of asparagines
Addition of prosthetic groups: Heme, FAD, biotin and pantothenic acids
C. Protein targeting: How are proteins sorted and transported to their final
destination?
Signal sequence: -14-26 amino acids at the amino terminus
usually removed when the protein reaches its final destination
Basic region + Hydrophobic region + Nonhelical region Page 324 Fig. 12.12
D. Proteasome and protein degradation
Proteins are continuously being degraded and replaced by newly synthesized protein
molecules
Biological meanings:
-removal of damaged or misfolded proteins.
-Destruction of regulatory proteins not needed at the time
-Adaptation to changing conditions
Half life
-RNA polymerase: 1.3 minutes
-Hemoglobin: 100 days
Proteasome: Page 325 Fig. 12.14
-Degradation of unwanted intracellular proteins by ATP-dependent proteases associated
with large protein complexes
-26S complex (20S + 19S )
-Ubiquitin pathway: 76 Amino acids, covalent attachment by an ATP-dependent process
12.4. Regulation of protein synthesis and gene expression
A. E. coli: 4000 genes, Humans: 30,000-40,000 genes.
B. A fraction of genes is expressed at any given time.
C. Regulation steps of protein synthesis: page 326 Fig.12.15
But most gene expression is controlled a the level of transcription initiation-The number
of mRNA molecules
D. 2 types of gene expression
-Constitutive expression: continuous transcription, resulting in a constant level of certain
protein products- House keeping genes for general cell maintenance and central
metabolism
-Inducible or repressible expression: Activation and deactivation, resulting in an increase
or a decrease in mRNA and protein levels.
E. Principles of regulating gene expression
Operon model in prokaryotes: Page 326 Fig. 12.16
Operons: Genes for proteins that are related in
function are clustered into units on the
chromosome
Components of an operon
Structural genes: Genes to be transcribed
and translated
Promoter region: RNA polymerase binding
site
Regulatory protein binding sites
Activator binding site
Repressor binding site( Operator)
Binding domain of regulatory proteins
20-100 AA, Hydrogen bonds between
Lys, Arg, Glu, Asn,Gln and the bases in Major
groove in DNA
Three classes of regulatory proteins
Helix Turn Helix motif: Most
common in prokaryotes Page 329 Fig. 12.19
Zinc finger motif: found only in eukaryotes, Page 330 Fig.12.20
Leucine Zipper motif: Page 331 Fig. 12.22
 Chapter 13: Recombinant DNA and
other topics in Biotechnology
Biotechnology:
Application of our understanding of the intricate workings of the cell to the solution of
practical problems
Examples:
Making of cheese, wine and other food commodities
Use of bacterial cells to produce large quantities of scarce proteins needed to treat
disease
Using enzymes to catalyze reaction steps in the industrial production of speciality
chemicals or biochemicals
Plant gene modification
Production of fuel alcohol from plant material
Using bacteria and plants for cleanup of chemical waste site: remediation
Mining of metals
Gene therapy: Gene replacement in individuals with genetic disorders
Forensic medicine
 13.1. Recombinant DNA Technology
A. Molecular cloning
The covalent insertion of a DNA fragment
fro one type of cell or organism into the
replicating DNA of another type of cell
If the inserted fragment is a functional
gene carrying the code for a specific protein
and an upstream promoter region is present
in the DNA, Many copies of that gene and
translated protein are produced in the host
cell
Page 340 Fig. 13.1
B. Cloning Vectors
Vector: Carrier for the foreign DNA
Plasmid: Self-replicating , extrachromosomal DNA molecules
Circular, double stranded, 3000-30,000 base pairs
Contains genetic information for the translation of
proteins that confer a specialized and sometimes protective characteristic on the
organism
Under antibiotics, many copiesmay accumulate 30-
40% of the total cellular DNA
The typical plasmid will accept foreign DNA inserts
up to 15,000 base pairs.
PBR 322: 4363 base pairs are sequenced.
1 EcoR1 site, different restriction sites
Bacterophage DNA
Lamda phage
50,000 base pairs, double stranded
Many copies of recombinant phage DNA can be
replicated in the host cell
Efficient package of recombinant phage DNA into
virus particle
Lamda phage can accepts DNA fragments up to 23,000
base pairs
Yeast artificial chromosome (YAC), Bacterial Artificial
chromosomes (BAC)
13.2 Preparing recombinant DNA
A. Design of recombinant DNA Page 343 Fig. 13.4
Formation of poly T tail in Foreign DNA to be inserted
Linearization of plasmid and Poly A tails on it
Mixing the two and ligation with DNA ligases
 B. Transformation and Selection
Incorporation of recombinant DNA into the host cell: 1/10,000 molecules is successful.
Selection markers: Drug resistances Page 345 Fig. 13.5 and 13.6
 C. Isolation and cloning of a single gene
Identify, locate and sequence a specific gene that occurs only once in a chromosome.
-Genomic DNA is cut into many thousands of large fragments using restriction
endonucleases- a random population of overlapping DNA fragments
-Isolation of similar size fragments by EP or ultracentrifugation
- Formation of poly T tail in Foreign DNA to be inserted
Linearization of plasmid and Poly A tails on it
Mixing the two and ligation with DNA ligases
D. Transformation and Selection
Incorporation of recombinant DNA into the host cell: 1/10,000 molecules is successful.
Selection markers: Drug resistances Page 345 Fig. 13.8
 E. Biochips: Page 348 Window
Microarray analysis
An orderly arrangement of experimental samples
Data interpretation
Nucleic acids:
Ordered sets of DNA( 1,000 samples) with fluorescent tag fixed at discrete locations
on the solid surface of a glass (silicon) chip by robotical deposition
Formation of a hybrid generates a fluorescent spot at a definite site on the chip
Identification of paired sequences in cDNA and mRNA
Proteins: Protein microarray
Specific protein protein interactions ( Antibodies)
Protein Drug interactions
Determination of expressed level of the genes
 13.3 DNA amplification by Polymerase chain reaction
Requirements
2 synthetic oligonucleotide primers about 20 bases, which are complementary to the flanking
sequences II and IV
A heat stable DNA Polymerase: Taq (Thermus aquaticus) DNA polymerase
dATP. dGTP, dCTP, dTTP
DNA template
Protocol Page 350 Fig. 13.10
5---CCCGGG------------TTTAAA---3
AAATTT:
3---GGGCCC------------AAATTT---5 CCCGGG

5--CCCGGG-------------TTTAAA---3
3---GGGCCC------------AAATTT-5
3--GGGCCC-------------AAATTT--- 5 5CCCGGG------------TTTAAA---3-

5--CCCGGG-------------TTTAAA---3
3---GGGCCC------------AAATTT-5
CCCGGG
3--GGGCCC-------------AAATTT--- 5 5CCCGGG------------TTTAAA---3-
AAATTT

3---GGGCCC------------AAATTT-5
CCCGGG------------TTTAAA
5CCCGGG------------TTTAAA---3-
GGGCCC------------AAATTT
Results: 2n
 C. Applications of PCR
Forensics: DNA finger printing
Restriction Fragment Length Polymorphisms ( RFLPs); Each personss DNA has
a unique sequence pattern, the restriction enzymes cut differently and lead to different
sized fragments
PCR-based Analysis: Faster, simpler and no requirement fro radioactive probes
 13.4. Applications of recombinant DNA technology
A. Recombinant protein products
Human insulin expressed E. coli
Growth hormone Page 355 Table 13.1
Bacterial Host:
Lack in posttranslational modifications
Unable to carry out important exon splicing reactions
Animal cell as host
Endocytotic up take of clacim phosphate precipitated DNA
Electroporation: a brief high voltage pulse
Microinjection
 B. Genetically altered(Modified) organism (GMO)
Bacteria:
Pseudomonas: complex chlorinated hydrocarbons for bioremediation
Thiobacillus ferrooxidans: Desulfurization of coal
Plants: Using Ti plasmid of Agrobacterium
Tumefaciens
Tomato, Soybean, Corn
Plants in high salinity, drought and extreme cold
Animals: Transfer into germ cells
Ethnic problems
Dolly, Giant mouse
C. Human gene therapy
The attempt to correct a genetic defect by inserting the normal gene into the cells
of an organism
AIDS, Brain cancer, obesity, multiple sclerosis,
Page 358, Table 13.2.
 Chapter 14. Basic concepts of cellular
metabolism and bioenergetics
Metabolism: Sum total of all chemical reactions in an organism
Autotrophs: Energy from sun and CO2 in most cases
Heterotrophs: Obtain energy by ingesting complex carbon containg compounds
14.1. Intermediary metabolism
A. Two paths of metabolism
Catabolism: the degradative path, Releasing the potential energy from food into ATP
Page 369 Table 14.1
Anabolism: Biosynthesis, Using the free energy stored in ATP
Page 369 Table 14.1
B. Possible sequential arrangements for metabolic pathways
Page 368 Fig. 14.3.
D. ATP cycle Page 370 Fig. 14.4
 D. Stages of metabolism
Catabolism
Stage 1: Breakdown of macromolecules into their respective building blocks
Stage 2: Building blocks are oxidized to a common metabolite Acetyl CoA
Stage 3: Acetyl CoA enters into Citric Acid Cycle , Respiratory assembly, Oxidative
phsphorylation
Anabolism:
Three stages like catabolism, but divergent.
Requires energy in the form of ATP and NADPH
The two processes are similar in terms of intermediates and enzymes but they are not
identical.
14.2. The chemistry of metabolism: Page 372 Table 14.2
 14.3. Concepts of bioenergetics

A. Standard free energy change

Go: The energy change under standard conditions:
1 atm of pressure, 25oC, 1.0M at the initial conc.
Go: at pH 7.0 instead of pH 0
A + B C + D
At equilibrium
Keq = [C][D]/[A][B]
G = Go + RT ln [C][D]/[A][B]
R: the gas constant: 8.13j/mole
T: the absolute temperature 273 + 25= 298K
At equilibrium, G = 0
Go = -2.303RT log Keq
Go 0 : Spontaneous, release of energy Go 0 : not spontaneous,
input of energy
B. Energy rich compounds
Acid anhydrides: Phosphanhydride bonds :
resonance stabilization,
charge repulsion
Phosphoenolpyruvate
Thioesters
Page 387 Table 14.6 and Fig. 14.14
 Chapter 15: Metabolism of
carbohydrates
Glycolysis
Phsophogluconate Pathway ( Pentose phosphate pathway)
Gluconeogenesis
Glycogen synthesis Page 394 Fig. 15.1
 15.1. The energy metabolism of B.Sceond five reactions of
glucose glycolysis:
A. First five reactions of Page 396 Fig. 15.2: Energy
glycolysis Out put
Page 396 Fig. 15.2: Energy
Input
CATP and NADH balance: Page 399 Table 15.2
 15.2. Entry of other carbohydrates into glycolysis
Page 400 Fig. 15.3
Glycogen in animal cells: phosphorlytic cleavage by glycogen
phosphorylase
Fructose
Glycerol
Galactose: UDP-derivatives are involved.
15.3. Pyruvate metabolism
A. Lactate fermentation:Page 404 Fig. 15.6
B. Ethanol fermentation: Page 405
15.4. Biosynthesis of carbohydrates
A. Gluconeogenesis: primarily in the liver Page 407 Fig 15.7
The irreversible reactions of glycolysis that are bypassed in gluconeogenesis Page 407
Table 15.3
Pyruvate carboxylase
Phosphoenolpyruvate carboxykinase
Fructose 1,6 bisphosphatase
Summary of gluconeogenesis: Page 410
B. Activation of glucose and galactose for biosynthesis
Formation of NDP-glucose Page 411 Fig. 15.10
C. Synthesis of polysaccharides
Glycogen: Glycogen synthase UDP-glucose and (glucose)n
Starch:Starch synthase, UDP-glucose and (glucose)n
Cellulose: Cellulose synthase , UDP (GDP)-glucose and (glucose)n
D. Synthesis of disaccharides
Lactose: Lactose synthase ( Galactosyl transferase + -lactalbumin)
UDP-galactose + glucose UDP + lactose
Without -lactalbumin: UDP-galactose + N-acetylglucosamine UDP + N-
acetyllactosamine
Sucrose: Sucrose 6-phosphate snthase
UDP glucose + fructose 6-phosphate sucrose 6 phosphate + UDP
15.5. Regulation of carbohydrate metabolism
A. Glycogen phosphorylase and Glycogen synthase
Page 417 Fig. 15.13.
B. Phosphofructokinase
+ effectors: AMP and Fructose-2,6-bisphosphate
effectors: ATP and citrate
C. Hexokinase
Feed back inhibition by glucose 6 phosphate
D. Pyruvate kinase and pyruvate carboxylase
ATP inhibits pyruvate kinase
Acetyl CoA stimulates pyruvate carboylase
Chapter 16. Production of NADH and NADPH:
Citric acid cycle, the glyoxylate cycle and the
phosphogluconate pathway
16.1. The pyruvate dehydrogenase complex
Oxidation of Pyruvate
Pyruvate dehydrogenase complex
Composition: Page 427 Table 16.1
Steps in the oxidation Page 427 Fig. 16.3
 16.2.The Citric acid cycle:
A. Reactions: Page 434 Fig. 16.8
B. Summary of the citric acid cycle
Acetate leave the cycle as 2CO2
3 moles of NADH and 1 mole of
FADH2
1 mole of ATP or GTP from CoA
thioester
16.3. The citric acid cycle in regulation and biosynthesis
A. Regulation aerobic pyruvate metabolism: Page 439 Table 16.4
Pyruvate dehydrogen complex
Citrate synthase
Isocitrate dehydrogen
-ketoglutarate dehydrogen comples
B. Anabolic roles of the citric acid cycle: Page 440 Fig. 16.11
C. Anaplerotic reaction to replenish the citric acid cycle intermediates: Page 440 Table
16.5
Oxaloacetate
Malate
16.4. The Glyoxylate cycle
In plant and some microorganisms Page 442 Fig. 16.12
Glyoxysomes: specialized cell organelle in plant seeds
2 acetyl CoA + NAD+ + 2 H2O Succinate + 2 CoA + NADH + H+
16.5 The phosphogluconate pathway Page 444 Fig. 16.14
 Chapter 17. ATP formation by
electron-transport chains
17.1. Mitochondrial electron transport
A. Reactions catalyzed by NAD-and FAD-linked dehydrogenases: Page 452 Table 17.1
B. The electron transport chain: Page 453 Fig. 17.2
Go = -nFEo
n: number of electrons
F: 96.5kj/volt.mole
Page 454 Table 17.2
17.2. Components of the electron transport chain
A. Complex 1. NADH-CoQ reductase:
FMN Semiquinone FMNH2: Page 455 Fig. 17.4

Fe-S cluster: Page 456 Fig. 17.5

CoQ: Page 456 Fig. 17.6
B. Complex II: Page 457 Fig. 17.7
Succinate dehydrogenase
Acyl-CoA dehydrogenase
C. Complex III: Q cycle: Page 458 Fig. 17.10
2 CoQH2 + 2 Cyt C (oxid) + CoQ 2 CoQ + 2 Cyt (red) + CoQH2 + 2H+

D. Complex IV: Cytochrome C

oxidase
O2 + 4e- + 4H+ 2H2O
Two hemes ( a and a3 )
Cu++
17.3. Oxidative phosphorylation
A. Coupling of Electron transport with ATP synthesis: Page 460 Fig. 17.12
 B. Chemiosmotic coupling
Electron transport through the carriers in the inner membrane causes the
unidirectional pumping of protons from the inner mitochondrial matrix to the other side
of the membrane( into the inter-membrane space)
C. Components of ATP synthase: Page 462 Fig. 17.14
Fo: Proton channel
F1: subunits, :ATP synthesis
 D. Regulation of oxidative phosphorylation
ATP/ADP ration
Uncoupling of electron transport and ADP phosphorylation
New born animals
Hibernating bears
Brown fat: a specialized type of adipose tissue having high concentrations of
mitochondria
17.4. Recycling of cytoplasmic NADH
Cytoplasmic NADH but be recycled by electron shuttle systems
A. Glycerol 3-phosphate shuttle: Page 464 Fig. 17.15
B. Malate-aspartate shuttle: Page 465 Fig. 17.16
17.5. Photosynthetic Electron Transport
A. Photosynthesis: Reductive carboxylation
( cf. Oxidative decarboylation = Citric acid cycle)
Two phases of photosynthesis: Page 467 Fig. 17.17
B. Chloroplasts: Page 468 Fig. 17.18
C. Comparison between Mitochondria and Chloroplasts

Mitochondria Chloroplasts
Electron flow NADH(FADH2) O2 H2O NADP+
Proton flow during Innermembrane Inter membrane space
elctron transport Intermembrane space Inner membrane
O2 Consumed Generated

D. Photosynthetic light reactions

2H2O + NADP+ 2NADPH + 2H+ +O2
Photosystems I and II:
Z scheme : Noncyclic electron flow Page 475 Fig. 17.25
ATP and NADPH formation
Cyclic electron flow: Page 477 Fig. 17.27
ATP formation only

E. Photophosphorylation
Proton movement from stroma to lumen ( from outside to inside
17.6 Synthesis of carbohydrates by the Calvin cycle
A. Stage 1: Addition of CO2 to an acceptor molecule ( Ribulose 1,5-bis phosphate) Page
479 Fig. 17.29

B. Stage II: Entry of 3-phosphoglycerate into main stream metabolism

3-phosphoglycerate + ATP 1,3 bisphosphoglycerate
1,3 bisphosphoglycerate + NADPH + H+ glyceraldehydes-3 phosphate
C. Stage III: Syntheis of carbohydrates from Glyceraldhyde 3 phosphate
D. Completion of the Calvin cycle by regeneration of Ribulose 1,5-bisphosphate
CO2 + C5 2C3
2C3 C6
C3 + C6 C4 + C5
C4 + C3 C7
C7 + C3 2C5
E. Hatch-Slack pathway: In C4 plants
Page 483 Fig. 17.31
 Chapter 18. Metabolism of fatty acids
and lipids
18.1. Metabolism of dietary triacylglycerols
A. Three primary sources of fatty acids for energy metabolism in humans and other
animals
Dietary triacylglycerols
Triacylglycerols synthesized in the liver
Triacylglycerols stored in adipocytes as lipid droplets
B. Initial digestion of fats
Digestion, mobilization and transport of dietary triacylglycerols: Page 489 Fig. 18.1
C. Schematic diagram of a chylomicron Page 490 Fig. 18.2
D. cAMP activation of triacylglycerol lipase Page 491 Fig. 18.3
E. Fatty acids in muscle cells: Activation of fatty acids in muscle cytoplasm
Acyl CoA synthetase Page 493 Top Formula
18.2. Catabolism of fatty acids
A. -Oxidation
Fatty acids are degraded in a stepwise fashion by removal of a C2 unit at each step
Initial oxidation process occurs on the carbon followed by cleavage of the bond
between carbons and
B. Steps of beta oxidation
Entry into the mitochondrial matrix. Page 495 Fig. 18.6
Individual reactions. Page 496 Fig. 18.8

In summary,
Palmitoyl ScoA + 7 FAD + 7 NAD + 7CoASH + 7 H2O
8acetyl ScoA + 7FADH2 + 7NADH + 7H+
C. ATP balance Page 499 Table 18.2
D. Beta oxidation of unsaturated fatty acids
Double bonds in the intermediate enoyl CoA: Trans
Double bonds in naturally occurring fatty acids: Cis
Metabolism of 16:29,12: Page 500 Fig. 18.10
E. Beta oxidation of fatty acids with odd numbers of carbons: End product is
Propionyl CoA
Degradation of Propionyl CoA: Page 501 Fig. 18.12
18.3 Biosynthesis of fatty acids
A. Comparison of both processes ( Cata- and Anabolism). Page 503 Table 18.3
B. Transport of citrate from mitochondria to cytoplasm : Page 503 Fig. 18.14
C. Fatty acid synthase: Multi enzyme complex in mammals:
Page 505 Table 18.4
Malonyl CoA formation is the rate limiting step in fatty acid synthesis.
 D. Biosynthesis of unsaturated fatty acids
In endoplasmic reticulum by faty acyl-CoA desaturases
E. Regulation of fatty acid metabolism
-oxidation and syntheis must be coordinated so they do not occur simultaneously.
The availability of carbohydrates and fatty acids.
Abundant glucose High production of citrate
Positive modulator for aceyl-CoA carboxylase Increase in
Malonyl CoA formation Blocking the action of carnitine acyltransferase I Turn off
of fatty acid degradation
The increase of fatty acid in the mitorchodria enhances -oxidation under conditions
of low blood glucose.

18.4 Cholesterol
A. Roles
Essential component of animal membrane
Precursor for steroid hormones, bile salts and vitamin
D
B. Cholesterol biosynthesis Page 508 Fig. 18.20
Step 1. Acetyl CoA mevalonate:
HMG CoA reductase :major regulatory step in cholesterol biosynthesis
Step 2: Activated isoprenes : Page 509 Fig. 18.21

Step 3: Formation of squalene

Step 4: Formation of Cholesterol
C. Cholesterol as a precursor for other steroids: Page 513 Fig. 18.25
18.5 Transport of lipids in blood
A. Lipoproteins: Page 515 Table 18.5
Chapt 19 Metabolism of amino acids
and other nitrogenous compounds
19.1. The nitrogen cycle
A. Nitrogen fixation by bacteria and legume root nodules
Nonsymbiotic microorganisms: Klebsiella, Azotbacter and Clostridia
Symbiotic microorganisms: Rhizobia genus: The bacteria and host plant
develop a cooperative association
Plant: carbohydrate for the bacteria
Bacteria: ammonia for the plant
B. The nitrogenase complex
NADPH: Oxidative or photosynthetic
An electron-transfer protein:
Ferredoxin-Closeridia and Rhizobia
Flavodoxin: Azotobacter
ATP
The enzyme complex
Iron-sulfur protein: ATP binding
Molybdenum-iron protein ( Mo-Fe proteins): N2 binding
 19.2. Biosynthesis of amino acids
Use of nitrogen
Glutamate dehydrogenase:
-ketoglutarate + NH4++ NADPH + H Glutamate + NADP + H2O
The reversal of this eaction is more important in amino acid catabolism and in
anaplerotic reaction to replenish -ketoglutarate
Glutamine synthetase
Glutamate +NH4+ + ATP Glutamine + ADP +Pi
B. Essential and non essential amino acids: Page 529 Table 19.2
19.3. Catabolism of amino acids
A. Transamination by aminotransferase
The amino group is transferred to an -keto acid, usually -ketoglutarate.
B. Catabolism of carbon skeletons: Page 536 Fig. 19.13
19.4. Elimination of NH4+
A. Glutamate dehydrogenase
Amino acid -ketoglutarate NADA + H +NH4+

aminotransferase Glutamate dehydrogenase

-keto acid Glutamate NAD + H2O

B. The Urea cycle: Page 539 Fig. 19.16

19.5 Amino acids as precursors of other biomolecules
A. Porphyrins: From succinl CoA
B. Biogenic amines and other products: Page 544 Fig. 19.20
C. Melanins: From tyrosine
D. Purine and pyrimidine nucleotides:Page 548 Fig. 19.24
Ribonucleotide reductase:
Ribonucleotide + NADPH + H+ Deoxyribonucleotide + NADP + H2O
Methotrexate and flurouracil: Inhibitor of thymidylate synthetase
Dump + N5, N10-methylene tretra hydrofolate(FH4)
dTMP + FH4
 Chapter 20 Integration , Coordination,
and specialization in metabolism
20.1. Overall strategies of metabolism
Review of metabolism. Page 559 Fig. 20.1
20.2. Metabolic specialization and integration
A. Metabolic profiles of organs Page 561 Table 20.1
B. Integrated metabolic pathways
Cori cycle: Page 563 Fig. 20.3
Glucose- alanine cycle Page 564 Fig. 20.4
C. Production and Distribution of ketone bodies Page 565 Fig. 20.5
20.3. Metabolic control by hormones. Page 567 Table 20.2
20.4. Metabolic responses to stressful conditions
A. Conventional lifestyle

After meal, blood glucose level - Up

Stimulation of insulin secretion
Suppression of glucagons secretion
Promotion of glucose uptake into the liver, where glycogen synthesis is enhanced and
glycogen breakdown is inhibited.
Fatty acid synthesis is stimulated in the liver. Triacylglycerols are distributed by VLDL
in the bloodstream for storage in adipose tissue.
Abundant glucose available in muscle is stored in glycogen.
A few hours after meal
Insulin secretion is decreased and glucagons secretion increases.
In order to maintain a constant level of blood glucose, glycogen is mobilized in the liver
Lipase action in adipocytes is activated by removal of insulin inhibition.
Decreasing levels of insulin slow glycolysis in muscle, liver and adipocytes by reducing
their permeability to glucose.
B. Disturbances that modify metabolism
Starvation/ Fasting Page 569 Table 20.3 and Fig. 20.7
C. Biochemistry of exercise
Sprinting: Page 570 Table 20.4

20.5. Biochemical factors in obesity

A.
Having a body weith more than 20% over an ideal standard weight.
Major risk factor diatetes hear disease, high blood pressure and stroke as well
as some cancers.
B. Leptin
A product of ob gene
Appears to act as a hormone to regulate body weight by monitoring the
amount of fat stored in the body of the mouse