biochem lecture

7/30/2019 Biochem Lecture

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1.1. Definition

A. Biochemistry: Biological Chemistry, Physiological Chemistry

Chemistry

General Chemistry

Organic ChemistryLast parts

Inorganic Chemistry

Physical ChemistryQuantum Chemistry

B. Biochemistry

Structures of Biomolecules

Bioenergetics

Functions of Biomolecutes

Biomolecules: Large and small moleculesLarge ones: Macromolecules like DNA, RNA , proteins and polysaccharides

Bioenergetics: Energy flow in the living cells

C. Conformation: 2 conformations of ethane

Eclipsed

Staggered

Chapter 1. introduction


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A. Starch and Cellulose: Homopolymers of Glucose

B. Proteins: Heteropolymers of Amino Acids :

Acids containing amine groupsC. 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


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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


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Page 21 Table 1.2


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1.5 Life at the Extremes: Page 16 Window on Biochemistry

1.6 Handling cell components: Page 24 Window


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Chapter 2. The flow of biological

information: Cell communication2.1. Brief Image of information flow: Page 30 Fig. 2.1

Transcription

Translation


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2.2. Storage of Biological information in DNA

Genome: The total genetic informational content for each

cell

Exact duplication

Expression of stored information

DNA moleculesWatson 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 pairsOther 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.


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2.3 Replication

5 to 3, Semi conservative replication

DNA polymerases

Polymerase Chain Reaction (PCR)

2.4 TranscriptionDouble helix DNA, RNA polymerase

rRNA, mRNA, tRNA: Page 35 Table 2.1


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2.5 Translation

Genetic code: triplet code Page 38 Fig. 2.7


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Exons and introns

Introns are absent in prokaryotes

RNA processing: Page 38 Fig. 2.8

Catalytic RNA


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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


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Chapter 3 Biomolecules in Water

Water content: Page 48 Table 3.1, 71-83%


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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


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B. The structure of water

Page 51 Fig. 3.1, sp3 orbitals


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3.2 Hydrogen bonding and Solubility

Physical properties of water: Page 53 Table 3.3 , Fig. 3.5

Solvation: Page 54 Fig. 3.6

AmphiphilicHydrophobic interaction

Micelles


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3.3. Cellular Reactions of Water

A. Ionization of water

B H d K


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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 EquationH3PO4 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 basepH = pKa log [A-]/[HA]

If [A-]/[HA]= 1 , log [A-]/[HA] = 0. So pH = pKa

3.4 Buffer system

Acidbase conjugate pairs

Buffering blood and other cellular fluids: Page 62, Window, Table 3.5

Buffer exercises : Acetate buffer, Phosphate buffer


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Chapter 4. Amino acids, Peptides and Proteins:

Proteins architecture and Biological Functions


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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


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4.2. Polypeptides and Proteins

Peptide bonds: Page 101 Fig 5.4

Average molecular weight of all amino acids in the polypeptides: 110

A i i ( i ) C i ( C i )


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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 proteinsFunction- 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 bondsB. 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.

, , ,


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C. Tertiary structure: Conformation of distant amino acids

Page 100 Fig. 5.3


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Primary structure determines the tertiary structure.

Denaturing, Renaturing, Native proteins Page 109 Fig 5.14

D. Quaternary structure

Monomeric, oligomeric

Subunits


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4.4. Hemoglobin

A. Hemeglobin

B. Heme binding to globin

C. Oxygen binding: Page 115, Fig. 5.19

Sigmoidal curvePositive cooperation( Myoglobin: Hyperbolic)

D. Bohr effect: Page 115 Fig. 5.20H+ and CO2 decrease the affinity of hemoglobin for oxygen molecule

4.5. Fashionable hair: Page 114, Windo


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Chapter 5. 6. Enzymes 1

6.1 Biological catalysts

A. Catalysts: Page 127 Fig 6.2


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6 2 E Ki ti


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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 K If V 1/2 V K [S]


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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. 6.5E. Characteristics of enzyme reactions

Enzyme concentration, pH, Temperature

6 3 S b t t bi di d ti


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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


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B General Acid Base catalysis: An Enzyme donates a proton and accept it in the


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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 electrontransfer between metal ions and substrate. Fig. 6.14 a

D Covalent catalysis


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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


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6.4 Enzyme inhibition

A. Reversible and irreversible inhibitors

DIFP, Pesticides

B. Reversible inhibitors: Page 145 Fig 6.19


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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


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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


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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 PFinal 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


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C. Models to describe allosteric regulation


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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


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g f zy

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


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y p y g

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


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7.4 Site directed mutagenesis and Abzymes and Ribozymes


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g y y

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 region19 -30 nucleotides


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8.2. Carbohydrates in cyclic structures


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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-acetylglucosamineE. Glycoside: ROH + Anomeric OH group of sugar a glycoside ( Page 189 Fig. 8.14)

8.4. Disaccharides : Page 191 Fig. 8.16


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A. Maltose

B. Cellobiose

C. Lactose

D. Sucrose

8.5. Polysaccharides


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A. Starch: : Glucose ( 1 4) linkage : Page 194 Fig 8.19

Amylose and Amylopectin( branches with (1 6) linkage)

B. Glycogen


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C. Cellulose: Glucose ( 1 4) linkage:

D. Chitin: N-acetylglucosamine ( 1 4) linkage: Page 197 Fig. 8.24

E. Peptidoglycans: The rigid cell walls of bacteria: N-acetylglucosamine

( 1 4) + Glucuronic acid ( 1 3)

8.6. Glycoproteins


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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 residueasparagines.

C. Lectins: Proteins specifically recognizing sugar moiety of a protein.

Concanvalin A: Mannose

Wheat germ agglutinin: N-acetylglucosamine

Peanut lectin: N-acetylgalactosamine

Ch t 9 Li id Bi l i l


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Chapter 9. Lipids, Biological

membranes and cellular transport9.1. Fatty acidsA. Nomenclature: Page 209, Table 9.1

B. General characteristics: Page 209 Table 9.2


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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 St t P 211 Fi 9 2


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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 Ph h idi id P 217 Fi 9 7


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A. Phosphatidic acid : Page 217 Fig. 9.7

B. Glycerophospholipids: Page 216 Fig. 9.6


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C. Spingolipids:

D S i i t t P 218 Fi 9 8


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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 Ch l t l d it d i ti P 219 Fi 9 10 P 222 Fi 9 11


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A. Cholesterol and its derivatives: Page 219 Fig. 9.10, Page 222 Fig. 9.11


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B. Plant sterol: Stigmasterol, Campesterol and -Sitosterol Page 221 Window


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C. Terpenes: Page 223 Fig 9.12


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D. Eicosanoids: Arachidonate derivatives (20:4 Delta 5,8.11,14)

Prostaglandins: PGD2: physiological sleep PGE2: Wakefulness


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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


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9.5 Biological Membranes

A Biological roles


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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 cellsSelective 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


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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 acidsFree 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 membraneProteins: 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


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9.6 Membrane transport

A Passive transport and Active transport


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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 pumpPage 237 Fig. 9.26

B. Uniport and Cotransport: Page 231 Fig. 9.20

Uniport


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Uniport

Cotransport: Symport and Antiport

Chapter 10 DNA and RNA:


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Chapter 10. DNA and RNA:

Structure and Function

10.1. RNA and DNA chemical structuresA. 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


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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.


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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


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C pa N p ag a

B. Features of DNA

Two right handed helical polynucleotide chains to form a helix


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wo g t a ded e ca po y uc eot de c a s to o a e

Antiparellel

Outside of the helix: the alternating deoxyribose and phosphate groups

Inside: Purine and pyrimidine bases

Two weak forcesHydrogen 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 conditions10.5 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


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D. Melting of DNA

De and Re naturation


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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


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; g

B. General features Page 258 Fig. 10.15

Ribose rather than 2-deoxyribose


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y

Uracil instead of Thymine

More susceptible to hydrolysis than DNA due to an extra OH group

Hair- pin turns

Right- handed double helixes in RNAInternal loops and bulges

C. tRNA: The smallest types of RNA

Carriers of specific amino acids used for protein synthesis


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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


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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 lengthDNA 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


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B. Chromosomes: Page 267 Fig. 10.23

Functional units of packed genomic DNA in the


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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-astring form of

nucleosomes

Chromatin fiber: Nucleosomes winding tightly in

a structure reminiscent of a filament or fiberChromatids: 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


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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


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B. 2 Replication Forks:

C. The Origin: a discrete starting point in both directions


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D. Theta model: Page 276 Fig. 11.4

E. In eukaryotes: several initiation sites

f l


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11.2. Action of DNA polymerases

A. DNA polymerase 1

Isolated from E coli

Template and Primer, Mg+25 3 direction

B. DNA polymerases II and III: Page 278 Table 11.1

C. Okazki fragments: Page 279 Fig. 11.8

Continuous leading strand

L i S d ( Ok ki f )


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Lagging Strand ( Okazki fragments)

D. Details of DNA replication: Page 281 Fig. 11.9 and

Page 282 Table 11.2


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E. Eukaryotic chromosomes and Telomeres

Telomeres:

Th f i li d d i k ti DNA H d d d f t f


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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 isinhibited

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


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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


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11.4. Synthesis of RNA:

The molecular vehicle carrying the genetic information from

DNA to protein synthesis


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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 synthesisDNA-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. 11.19Initiation: 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 triphosphatesTermination: 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)


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11.5. Post-transcriptional modification of RNA

A. tRNA

Trimming of the ends by phosphoester bond cleavage


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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

residuesSplicing of coding sequences

Exons: Coding regions on the gene

Introns: noncoding regions

SnRNP and catalytic RNA participate in the splicing


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Chapter 12. Translation of RNA : Thegenetic code and protein metabolism


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genetic code and protein metabolism12.1. Process of protein synthesis

A. Characteristics of protein synthesis

Location: Ribosomal particlesRibosomes :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


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12.3. Post-translational processing of proteins

A. Protein folding

Chaperones: Catalysts to guide and facilitate folding


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p y g g

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 asparaginesAddition 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


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D. Proteasome and protein degradation

Proteins are continuously being degraded and replaced by newly synthesized protein

molecules


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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 associatedwith large protein complexes

-26S complex (20S + 19S )

-Ubiquitin pathway: 76 Amino acids, covalent attachment by an ATP-dependent process


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12.4. Regulation of protein synthesis and gene expressionA. E. coli: 4000 genes, Humans: 30,000-40,000 genes.

B. A fraction of genes is expressed at any given time.


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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


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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


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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 proteins20-100 AA, Hydrogen bonds between

Lys, Arg, Glu, Asn,Gln and the bases in Major

groove in DNA

Three classes of regulatory proteins

HelixTurnHelix motif: Most

common in prokaryotes Page 329 Fig. 12.19

Zinc finger motif: found only in eukaryotes, Page 330 Fig.12.20


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Leucine Zipper motif: Page 331 Fig. 12.22


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Chapter 13: Recombinant DNA and

th t i i Bi t h l


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other topics in BiotechnologyBiotechnology:

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

diseaseUsing 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 metalsGene therapy: Gene replacement in individuals with genetic disorders

Forensic medicine

13.1. Recombinant DNA TechnologyA. Molecular cloning

The covalent insertion of a DNA fragment


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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


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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 cellEfficient 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 DNAA. Design of recombinant DNA Page 343 Fig. 13.4

Formation of poly T tail in Foreign DNA to be inserted

Li i i f l id d P l A il i


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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


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C. Isolation and cloning of a single geneIdentify, 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

d l d l ti f l i DNA f t


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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


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E. Biochips: Page 348 WindowMicroarray analysis

An orderly arrangement of experimental samples

D t i t t ti


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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


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13.3 DNA amplification by Polymerase chain reactionRequirements

2 synthetic oligonucleotide primers about 20 bases, which are complementary to the flanking

sequences II and IV


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q

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-53--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


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C. Applications of PCRForensics: 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


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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 technologyA. Recombinant protein products

Human insulin expressedE. coli

Growth hormone Page 355 Table 13 1


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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


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Thiobacillus ferrooxidans: Desulfurization of coal

Plants: Using Ti plasmid ofAgrobacterium

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.


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Chapter 14. Basic concepts of cellular

metabolism and bioenergetics


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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 metabolismA. Two paths of metabolism

Catabolism: the degradative path, Releasing the potential energy from food into ATP

Page 369 Table 14.1


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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 pathwaysPage 368 Fig. 14.3.


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D. ATP cycle Page 370 Fig. 14.4


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D. Stages of metabolismCatabolism

Stage 1: Breakdown of macromolecules into their respective building blocks

Stage 2: Building blocks are oxidized to a common metabolite Acetyl CoA


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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:


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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


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Chapter 15: Metabolism of

carbohydrates


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carbohydratesGlycolysis

Phsophogluconate Pathway ( Pentose phosphate pathway)

Gluconeogenesis

Glycogen synthesis Page 394 Fig. 15.1

15.1. The energy metabolism of glucoseA. First five reactions of glycolysis

Page 396 Fig. 15.2: Energy Input

B.Sceond five reactions of glycolysis:

Page 396 Fig. 15.2: Energy Out put


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CATP and NADH balance: Page 399 Table 15.2


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15.2. Entry of other carbohydrates into glycolysisPage 400 Fig. 15.3

Glycogen in animal cells: phosphorlytic cleavage by glycogen phosphorylase

Fructose


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Glycerol

Galactose: UDP-derivatives are involved.

15.3. Pyruvate metabolismA. Lactate fermentation:Page 404 Fig. 15.6

B. Ethanol fermentation: Page 405


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15.4. Biosynthesis of carbohydratesA. 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


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Pyruvate carboxylase

Phosphoenolpyruvate carboxykinase

Fructose 1,6 bisphosphataseSummary of gluconeogenesis: Page 410


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B. Activation of glucose and galactose for biosynthesisFormation of NDP-glucose Page 411 Fig. 15.10


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C. Synthesis of polysaccharidesGlycogen: Glycogen synthase UDP-glucose and (glucose)n

Starch:Starch synthase, UDP-glucose and (glucose)n

Cellulose: Cellulose synthase , UDP (GDP)-glucose and (glucose)n


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D. Synthesis of disaccharides

Lactose: Lactose synthase ( Galactosyl transferase + -lactalbumin)

UDP-galactose + glucose UDP + lactoseWithout -lactalbumin: UDP-galactose + N-acetylglucosamine UDP + N-

acetyllactosamine

Sucrose: Sucrose 6-phosphate snthase

UDP glucose + fructose 6-phosphate sucrose6 phosphate + UDP

15.5. Regulation of carbohydrate metabolism

A. Glycogen phosphorylase and Glycogen synthase

Page 417 Fig. 15.13.


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B. Phosphofructokinase+ effectors: AMP and Fructose-2,6-bisphosphate

effectors: ATP and citrate

C. Hexokinase

F d b k i hibi i b l 6 h h


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Feed back inhibition by glucose 6 phosphate

D. Pyruvate kinase and pyruvate carboxylase

ATP inhibits pyruvate kinaseAcetyl CoA stimulates pyruvate carboylase

Chapter 16. Production of NADH and NADPH:

Citric acid cycle, the glyoxylate cycle and the

phosphogluconate pathway


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phosphogluconate pathway

16.1. The pyruvate dehydrogenase complexOxidation of Pyruvate

Pyruvate dehydrogenase complex

Composition: Page 427 Table 16.1

St i th id ti P 427 Fi 16 3


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Steps in the oxidation Page 427 Fig. 16.3


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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 l f NADH d 1 l f FADH2


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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 biosynthesisA. Regulation aerobic pyruvate metabolism: Page 439 Table 16.4

Pyruvate dehydrogen complex

Citrate synthase

Isocitrate deh drogen


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Isocitrate dehydrogen

-ketoglutarate dehydrogen comples

B. Anabolic roles of the citric acid cycle: Page 440 Fig. 16.11


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C. Anaplerotic reaction to replenish the citric acid cycle intermediates: Page 440 Table16.5

Oxaloacetate

Malate


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16.4. The Glyoxylate cycleIn 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+


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16.5 The phosphogluconate pathway Page 444 Fig. 16.14


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Chapter 17. ATP formation by

electron-transport chains


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p

17.1. Mitochondrial electron transportA. Reactions catalyzed by NAD-and FAD-linked dehydrogenases: Page 452 Table 17.1

B. The electron transport chain: Page 453 Fig. 17.2Go = -nF Eo

n: number of electrons

F: 96.5kj/volt.mole

Page 454 Table 17 2


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Page 454 Table 17.2

17.2. Components of the electron transport chainA. Complex 1. NADH-CoQ reductase:

FMN Semiquinone FMNH2: Page 455 Fig. 17.4


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Fe-S cluster: Page 456 Fig. 17.5


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B. Complex II: Page 457 Fig. 17.7Succinate dehydrogenase

Acyl-CoA dehydrogenase


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C. Complex III: Q cycle: Page 458 Fig. 17.102 CoQH2 + 2 Cyt C (oxid) + CoQ 2 CoQ + 2 Cyt (red) + CoQH2 + 2H+


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D. Complex IV: Cytochrome C oxidase

O2 + 4e- + 4H+ 2H2O

Two hemes ( a and a3 )

Cu++

17.3. Oxidative phosphorylationA. Coupling of Electron transport with ATP synthesis: Page 460 Fig. 17.12


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B. Chemiosmotic couplingElectron 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


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C. Components of ATP synthase: Page 462 Fig. 17.14

Fo: Proton channel

F1: subunits, :ATP synthesis

D. Regulation of oxidative phosphorylationATP/ADP ration

Uncoupling of electron transport and ADP phosphorylation

New born animals

Hibernating bears


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g

Brown fat: a specialized type of adipose tissue having high concentrations of mitochon

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


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17.5. Photosynthetic Electron TransportA. Photosynthesis: Reductive carboxylation

( cf. Oxidative decarboylation = Citric acid cycle)

Two phases of photosynthesis: Page 467 Fig. 17.17


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B. Chloroplasts: Page 468 Fig. 17.18


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C. Comparison between Mitochondria and Chloroplasts

Mitochondria Chloroplasts

Electron flow NADH(FADH2) O2 H2O NADP+


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Proton flow during

elctron transport

Innermembrane

Intermembrane space

Inter membrane 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. PhotophosphorylationProton movement from stroma to lumen ( from outside to inside


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17.6 Synthesis of carbohydrates by the Calvin cycleA. Stage 1: Addition of CO2 to an acceptor molecule ( Ribulose 1,5-bis phosphate) Page

479 Fig. 17.29


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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


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Chapter 18. Metabolism of fatty acids

and lipids


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18.1. Metabolism of dietary triacylglycerolsA. 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 fatsDigestion, mobilization and transport of dietary triacylglycerols: Page 489 Fig. 18.1


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C. Schematic diagram of a chylomicron Page 490 Fig. 18.2


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E. Fatty acids in muscle cells: Activation of fatty acids in muscle cytoplasmAcyl CoA synthetase Page 493 Top Formula


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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


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B. Steps of beta oxidation

Entry into the mitochondrial matrix. Page 495 Fig. 18.6

Individual reactions. Page 496 Fig. 18.8


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In summary,

Palmitoyl ScoA + 7 FAD + 7 NAD + 7CoASH + 7 H2O

8acetyl ScoA + 7FADH2 + 7NADH + 7H+

C. ATP balance Page 499 Table 18.2


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D. Beta oxidation of unsaturated fatty acidsDouble bonds in the intermediate enoyl CoA: Trans

Double bonds in naturally occurring fatty acids: Cis

Metabolism of 16:2 9,12: Page 500 Fig. 18.10


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E. Beta oxidation of fatty acids with odd numbers of carbons: End product isPropionyl CoA

Degradation of Propionyl CoA: Page 501 Fig. 18.12


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18.3 Biosynthesis of fatty acidsA. Comparison of both processes ( Cata- and Anabolism). Page 503 Table 18.3


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B. Transport of citrate from mitochondria to cytoplasm : Page 503 Fig. 18.14


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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.


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Step 2: Activated isoprenes : Page 509 Fig. 18.21


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Step 3: Formation of squalene

Step 4: Formation of Cholesterol

C. Cholesterol as a precursor for other steroids: Page 513 Fig. 18.25


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18.5 Transport of lipids in bloodA. Lipoproteins: Page 515 Table 18.5


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Chapt 19 Metabolism of amino acids

and other nitrogenous compounds


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19.2. Biosynthesis of amino acidsUse 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


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anaplerotic reaction to replenish -ketoglutarate

Glutamine synthetaseGlutamate +NH4+ + ATP Glutamine + ADP +Pi

B. Essential and non essential amino acids: Page 529 Table 19.2

19.3. Catabolism of amino acidsA. Transamination by aminotransferase

The amino group is transferred to an -keto acid, usually -ketoglutarate.

B. Catabolism of carbon skeletons: Page 536 Fig. 19.13


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19.5 Amino acids as precursors of other biomoleculesA. Porphyrins: From succinl CoA

B. Biogenic amines and other products: Page 544 Fig. 19.20


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C. Melanins: From tyrosineD. 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-methylenetretra hydrofolate(FH4)


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p , y y ( )

dTMP + FH4

Chapter 20 Integration , Coordination,

and specialization in metabolism20.1. Overall strategies of metabolism


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g f

Review of metabolism. Page 559 Fig. 20.1

20.2. Metabolic specialization and integrationA. Metabolic profiles of organs Page 561 Table 20.1


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C. Production and Distribution of ketone bodies Page 565 Fig. 20.5


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20.3. Metabolic control by hormones. Page 567 Table 20.2


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20.4. Metabolic responses to stressful conditionsA. Conventional lifestyle

After meal, blood glucose level - Up

Stimulation of insulin secretion

Suppression of glucagons secretion


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Promotion of glucose uptake into the liver, where glycogen synthesis is enhanced andglycogen 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 metabolismStarvation/ Fasting Page 569 Table 20.3 and Fig. 20.7


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C. Biochemistry of exercise

Sprinting: Page 570 Table 20.4


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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

biochem lecture

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