BIOCHEMISTRY

Biochemistry- structures and functions of the different classes of biomolecules and

macromolecules ( proteins, nucleic acids, carbohydrates, lipids
-bio: Life---> chemistry of life
 

The Cell
- basic unit of life
PROKARYOTE EUKARYOTE
No nucleus nucleus
Membrane-bound organelles Membrane bound organelles
Monera [bacteria Protista
1. Eubacteria Fungi
2. Archaebacteria  
-circular DNA Plantae
-plasmids-> vectors in DNA cloning Animalia
-ribosomes: protein synthesis  
 
Parts of a Plant/Animal Cell
1. Plasma/Membrane
1. Protection/ barrier
2. Fluid mosaic model
o Lipid bilayer
 Polar head
 Non polar tails
 

 
1. Proteins
o Peripheral: can act as receptors; cell to cell signalling and attachment
o Integral: embedded within the cell membrane; ion channels; enzymes
 Cholesterol:
o controls both fluidity and rigidity of cell membrane
 Glycolipids
 Semi-permeable/ semi-selective
o Non-polar molecules [Co2, H20]
 Passive diffusion: concentrated gradient> high to low
o Polar molecule [ glucose]
-Facilitated diffusion: carrier molecule/ protein
o Ions
o Active transport: Low to high concentration
o Ion channels
 Plant vs. Animals
o Plant cell membrane
o Cytoplasm/ cytosol
 Cytoplasm: everything inside the cell
 Cytosol: liquid
o Organelles: organ-like structures
 Nucleus
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 Stores the cell's genetic information as DNA in chromosomes
o Trancription: DNA to RNA
 Mitochondrion
 Powerhouse of the cell : ATP synthesis (oxidative phosphorylation)
 Organ for respiration
 Endoplasmic Reticulum
 Smooth ER: no ribosomes
o Lipid synthesis
 Rough ER: ribosomes present
-Protein synthesis
 Golgi Apparatus
 Storage sites for proteins
o Protein processing/ modification ( post-translational modification0
 Ex: Glycosylation: attachment of carbohydrates to proteins
o Ribosomes
o Actual site of protein synthesis
o Complexes of rRNA and proteins
Eukaryotic ribosomal sub-unit: 70s
o 30s: 16s rRNA and 20 proteins
o 50s: 5srRNA and 23srRNA and 30 proteins
Bacterial ribosomal sub-unit: 80s
o 40s:
o 60s
o Lysosomes
o Suicide sacs
o Examples of cells that has a lot of lysosomes
o Macrophages/ phagocytes: eats foreign microorganisms
 Phagocytosis: cell-eating
o Contains hydrolytic enzyme mixture
o Peroxisomes:
o Chloroplast
o Contains the green pigment chlorophyll-> photosynthesis
o Cytoskeleton
o Elaborate network of large filamentous rod-like proteins
o Structural support and..
o Microtubules
o Composed of tubulin
-Colchicine: inhibit formation of spindle fibers
o Inclusions
o …
 
Cell Cycles
MITOSIS MEIOSIS
Cell multiplication Cell division
Cytoplasmic division Both cytoplasmic and nuclear divisions
Somatic/ body cells Sex cells/ gametes
Daughter cells are diploids-> full Daughter cells are haploids-> half
   
o Human chromosomes:
o 46 chromosomes, 23 pairs
 22 pairs: somatic
 1 pair: sex chromosomes (female-XX; Male-XY)
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o Aneuploidy: any abnormality in the number of chromosomes
 

 
o Gap Phase: G1 and G2
o Cells starts to grow
 S-phase
o DNA synthesis and replication
Stages in Mitosis
 
 Prophase
 Replicated chromosomes condense each With 2 sister chromatids.
 The nuclear envelope
o breaks down allowing the chromosomes
o to attach to the spindle microtubules.
o Metaphase
o Chromosomes are firmly attached to the mitotic spindle and align at
the cell’s equator but have not yet split.
o Anaphase
o Paired chromatids separate to form pairs of 2 daughter chromosomes
& each is pulled slowly toward the spindle pole ¡t is attached to
o Telophase
o Final stage where the 2 sets of separated chromosomes arrive at the
spindles.
o Chromosomes decondense and become enclosed by new nuclear
envelopes.
 
Chromosome Abnormalities
 
Down's syndrome/ Mongolism Trisomy 21 47 chromosomes
Turner's Syndrome   X
Edward's Syndrome Trisomy 18 E-syndrome
 
Klinefelter's Syndrome Trisomy 23 XXY
-gynecomastia
-hypogonadism
Triple X Syndrome Trisomy 23 XXX
Super-female
Warkany Syndrome 2 Trisomy 8 Genomic examination
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Patau Syndrome Trisomy 13 D-syndrome
 

Proteins
o Polymers of amino acids that are joined together by peptide bonds
 
Dynamic Functions
 
o Transport and Storage
o examples:
o Myoglobin, hemoglobin: 02 carriers
o Tranferrin: transport form of Fe
o Ferritin: storage form of Fe
o Muscle Contraction
o Actin and myosin: Calcium dependent
o Biological catalysts
o Enzymes
o Metabolic control
o hormones
o Examples of polypeptide hormones:
o insulin, glucagon-> carbohydrate metabolism
o Oxytocin-> "love hormone"; induce uterine muscular contraction
o Vasopressin-> anti-diuretic hormone
o Somatotropins/ growth hormones
o Thyroid hormones-> T3 and T4
o FSH
o Immune system
o Immunoglobulin
o IgA
o IgD
o IgE
o IgG: monomeric
o IgM
o Tissue Differentiation
o Tumour Necrosis Factor-alpha
 
Structural Functions
o Examples:
o Collagen, elastin-> muscles
o Keratin-> hair and nails
o Fibroin-> silk, spider web
 
Protein Classification
o Simple proteins- made up of amino acids only
o Collagen, elastin, keratin, fibroin
o Albumin, ovalbumin
o Prolamins-> rich in proline
o Glutein
o Conjugated Proteins- made up of amino acids and other organic/
inorganic components
o Nucleoproteins: with nucleic acids
o Lipoproteins: with lipids
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o Glycoproteins: with carbohydrates; more proteins than carbohydrates
o Mucoproteins: with carbohydrates; more carbohydrates than proteins
 mucus
o Chromoproteins: with metals; colored
 hemoglobin: iron, red
o Metalloproteins: with metals; not colored
 mettalothioneins: rich in cysteine (Zn,Hg, Cd
o Phorphoprotein: with phosphorus (phosphate
 casein-> milk protein
 
Amino Acids
o Building blocks of proteins
 
o Standard/ common amino acids
o Amino acids with at least one specific codon existing in the DNA genetic
code
o Ex: AUG-> methionine
 
o Derived amino acids
 Came from the standard amino acids usually derived by enzyme catalysed
reactions after the standard amino acid is incorporated in the protein structure
 Example: Gamma Carboxyglutamate, selenocysteine
 
Structure of the Standard Amino Acid
 They exist as alpha amino acids
 Carboxyl
 Hydrogen
 Amino
 Variable side chain
 19 exist as alpha amino acids
 Proline: not exist as alpha amino acid--> imino acid
 
Classification of the Standard Amino Acids based on nature of R-
group

Glycine      
Alanine      
Proline      
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Valine      
Leucine      
Isoleucine      
Methionine      

Serine      
Threonine      
Cysteine      
Asparagine      
Glutamine      
 

 
Aspartate      
Glutamate      
 
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Lysine      
Arginine      
Histidine      
 
 

 
 
 
 
 
 
 
 
 
 
 
Phenylalanine      
Tyrosine      
Tryptophan      
 
Properties of Amino Acids
 They are amphoteric substances
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 Both acid and basic
 They can exist as zwitterions/ dipolar ions
 pH at which an amino acid exists in its zwitter ionic form
 pH at which an amino acid is electrically neutral
 Isoelectric Point (pI)

 They are optically active or chiral(chirality)

 Ability of a compound to rotate a plane-polarized light either to the
right or to the left
 Dextro: d or
 Levo: l of -
 Chiral Center: C atom with 4 different groups
 Capable of UV absorption (Aromatic Amino Acids)
 
Tests and Results
Sagakuchi Test    
Ninhydrin Tes    
     
     
     
     
Lead Sulfide Test Cysteine  
Methionine: negative result
     
 
Levels of protein Organization
 
 Primary Level/ Structure
 Refers to the amino acid sequence
 Peptide bond
 Dipeptide: 2 aa residues
 Oligopeptide: 3-10 aa residues
 Polypeptide :> 10 aa residues
 Protein:>30 aa residues
 

*always start at n terminus to c terminus

 
Amino Acid Sequencing
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 Sanger Method
 for determination of N-terminal amino acid
 reagent: 2,4-Dinitrofluorobenzene - reacts with N-terminal amino
acid
 Reaction Involves hydrolysis of protein/peptide
 Other: dansyl chloride and
 Edman Degradation
 involves treating a protein at pH 9.0 with (phenylisothiocyanate)
PITC
 PITC also reacts with N-terminal amino acid
 Does not involve hydrolysis of the proteinlpeptide
 
 Secondary Structure/Level
 refers to particularly stable arrangements of amino acid residues
giving rise
 to recurring structural patterns
 Stabilized by H-bonding
 Example:
 Beta pleated sheets
 Collagen helix
 b-turns/ loops
 alpha helix
o Random coil- no pattern in H-bond
 
Alpha Helix
o H bonding occurs for every 3.6 or 4 a.a residues
o Examples:
 Keratin
 Myoglobin
 Haemoglobin
Beta Sheet
 Beta strands- portions of the polypeptide chain that are almost fully
extended
-Multiple beta strands arranged side by side
 Fibroin protein
 Found in silk and spiderweb; purely beta sheet
 Rich in Ala and Gly
Loops/Beta turns
 Connect secondary structures
 Type I : proline- adopting a cis conformation to tighten turn
 Type II: glycine- flexibility

 
Collagen helix
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 Triple helix
 Amino acid sequence in collagen is generally a repeating tripeptide
unit, Gly-X-Y, where X is often Pro, and Y is often 4-hydroxyproline
 Steric effect: 'crowding effect'; bulky groups
 
 Tertiary Level/ structure
 describes all aspects of the three-dimensional folding a polypeptide
 Stabilize by the interactions of the R groups of the amino acids
 Non-polar amino acids- hydrophobic interactions
 Polar amino acids- Ser, Thr, asparagine, glutamine- h bonding
 Acidic amino acid-Asp, Glu- ionic interaction
 Basic amino acid- His, Lys,..- ionic interaction
 Rich in cysteine- disulfide bond/ linkage: covalent bond
 
o Quaternary Level/ Structure
o occurs only if protein has two or more domains or subunits
(multimeric proteins)
o Domain/subunit - polypeptide that folds independently
Myoglobin Hemoglobin
   
o Sickle Cell Anemia
 Molecular disease of hemoglobin
 Point mutation of beta domain gene
 
Protein Denaturation and Folding
Denaturation- a loss of three dimensional structure sufficient to cause loss of function
o Quaternary, tertiary, secondary with loss of fxn
o Primary- hydrolysis of peptide bond
Thermal Denaturation
o Increase temperature- irrevesible denaturation
o Extremes of ph- interferes with ionic interactions
o Organic solvents
- alcohols: interferes with H bonding interactions
--S-S-: beta-mercaptoethanol
o Salts- high salts concentration: interferes with ionic interactions
 Salting out
Native Conformation- when protein is folded normally
 Misfolding of proteins---> disease
Example:
Alzheimer's disease  
 
 
 
 
Bovine spongiform  Mad cow disease
encephalopathy  First thought as viral
disease
 Cause:
abnormal/misfolded prion--> proteinaceous
infection only
 Manifestations on cows/
cattles: restlessness--> paralysis
 
 
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Greutzfeldt-jakob  Caused by prion
disease  Rare; kuru like disease
causing dementia
Variant creutzfeldt  Tansmission of BSE from
jakob cattle to human
 Abnormal prion is heat-
and protease resistant and it can make
normal prion misfold
Kuru disease Cannibalism; started from a tribe
 
Enzymes
 catalysts of biological systems
 most striking characteristics of enzymes are their catalytic power
and specificity
 
Parts of an enzyme
 Substrate: molecules that enters into an enzymatic reaction
 Cofactor: substances that enzymes require for their activities
 Co-enzymes: Organic compounds derived from vitamins

Co-enzyme A Vit.B5 Transfer of acetyl group

NAD/NADH Vit.B3 Transfer of electron- redox
FAD/FADH2 Vit. B2 Transfer of electron- redox
Pyridoxal phosphate Vit. B6 Transaminase -NH4
Thiamine pyrophosphate Vit. B1 Transfer of aldehyde group
o Prosthetic Group: tightly bound co-factor
 Examples: Essential trace minerals
 
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 Apoenzyme: protein function of enzyme; without a bound to co-factor
 Holoenzyme/ holoprotein: apoenzyme plus cofactor/prosthetic group;
ACTIVE FORM
 Zymogen/ Proenzyme: INACTIVE FORM
 Pepsinogen activator
 Trypsinogen activator
 Fibrinogen
 
Classification of Enzymes
• Based on the International Union of Biochemistry
 
 Oxidoreductases
 Catalyze redox reactions
 Example:
 lactate dehydrogenase
 Transferases
 Catalyze transfer of functional group from one molecule to another
 Examples:
 transaminase- transfer of -NH2 group
 Phase II enzymes: UDP-glucoronyl-transferase :glucoronidation
 Acetyltranferase: acetylation
 Sulfotransferase: sulfonation
o Kinases: transfer of PO3 from ATP
o Hyrolases
o Catalyze hydrolytic cleavage reactions - breaking a bond by
introducing water
o Examples:
 Nucleases- nucleic acids
 Lipases- lipids
 Amylases- carbohydrates
 Proteases/ peptidases- proteins/ peptide bonds
 Acetylcholinesterases- breakdown of Ach --> acetate, choline
o Lyases
o Catalyses addition of groups to double bonds or removal of groups to
form double bonds
o Examples:
 carbonic anhydrase
 Decarboxylases
o Isomerases
o Catalyze rearrangements or interconversion of isomers
o Example:
 glyceraldehyde to dihydroacetate phosphate by triphosphate
isomerase
 mutases: position isomers
o Ligases
o Catalyze condensation reactions - joining of two molecules together
o Synthases/ synthetases
o Examples:
 DNA ligase: okazaki fragments
 glycogen synthase: synthesis of glycogen
 Cheletases- metal chelates
 
Properties of Enzymes
o Catalytic Activity- increase rate of biological reactions
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o Specificity
 Active site: a specialized region of the enzyme where the subtrate
interacts
Group Absolute
Class or a group of structurally One specific molecule
related compounds
Examples: Proteases- proteins Example: Acetylcholinesterase- only acts at
acetylcholine receptors
Models for enzyme- substrate binding
1. Lock and Key Model
a. Lock: enzyme
b. Model: substrate
1. Induced Fit Model- as the substrate binds to the enzymes, the enzyme
undergo conformational change
2. Transition State analogue Model- reactants are first converted to transition
state before forming a product; enzyme stabilizes the TS
a. Rate of reaction dependent on the energy of TS
b. Inc. energy TS-> slow rate
c. Dec.energy TS-> fast rate
 
Enzyme Kinetics
1. Michaelis-Menten Equation
 

 
 
1. Lineweaver- Burk Equation-double reciprocal
1 km 1 1
= + m
v vmax [ S ] v ax
 
 
 
 
 
 
 
Enzyme Inhibition
A. Irreversible enzyme inhibition- the inhibitor forms a covalent cond with
active site of enzyme--> permanently inactive
 Example: acetylcholinesterase --> organophosphates [malathion,
parathion, tabun, sarin, soman]
B. Reversible enzyme inhibition- inhibitor forms a weak interaction, usually non
covalent with the enzyme
 Competitive Inhibition: Inhibitor is a structural analogue of the
subtrate; binds to active site
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 Non-competitive Inhibition: inhibitor is not a structural analogue of
the subtrate
 Does not bind to active site
 Binds to an allosteric site
 Uncompetitive Inhibition: the inhibitor preferentially binds to E.S
complex, not to the free enzyme and forms an E.S.I complex
 Mixed Inhibition: the inhibitor can form a complex both with free
enzyme E and with the enzyme substrate complex E.S