Organic Chemistry study of compounds of carbon and hydrogen and other derivatives

Friedrich Whler synthesized urea (waste product of animal metabolism), from

ammonium cyanate
Reactions of molecules are based on the reactions of their respective functional groups
Functional groups
o Contain oxygen and nitrogen (electronegative elements)
o Polar nature crucial in reactivity
o Not important: alkyl halides and acyl chlorides
o Important: esters and anhydrides of phosphoric acids
ATP
Origin of chemical elements
o Thermonuclear reactions in stars
o Explosions of stars
o Action of cosmic rays outside the stars since the formation of the galaxy
Isotopes biologically important elements
o Carbon, oxygen, nitrogen, phosphorus and sulfur stable nucleus
Monomer smaller molecules
o Amino acids, nucleotides and monosaccharides
Polymer macromolecules
Proteins combined amino acids
Nucleic acids combined nucleic acids
Polysaccharides polymerization of sugar monomers
Polymerization of proteins
o Spontaneous reaction with the loss of water
o Sequence of amino acids determine the properties if the protein formed
Genetic code in the sequence of monomeric nucleotides that polymerize to form nucleic
acids
All building blocks have a head and a tail (sense of direction at monomer level)
Enzymes
o Catalytic activity they increase the rates of chemical reactions compared with
uncatalyzed reactions
Calatysis and catalytic effectiveness of a given enzyme depends on its amino acid
sequence
Sequence of amino acids in proteins sequence of nucleotides in nucleic acids
DNA coding material
Genetic code relationship between the nucleotiode sequence in nucleic acids and the
amino acid sequence in proteins
RNA (ribonucleic acid)
o Nucleic acid
o Capable of catalyzing its own processing
o Original coding material (exemplified in viruses)
RNA world theory
o RNA is the origin of life
o Polynucleotides can direct the formation of molecules whose sequence is an exact
copy of the original
Depends on the template mechanism highly effective in producing exact
copies but is a slow process
o Polypeptides more effective catalysts than polynucleotides
o Genetic code nucleic acids; catalysis proteins
o RNA (originally) can catalyze and encode its replication
DNA became the primary genetic material

RNA intermediary role in directing the synthesis of proteins under the direction of the
genetic code in the DNA
Development of catalysis and a coding system came about separately
Theory: Life began on clay
o Coding arose first; coding material was in the surface of naturally occurring clay
o Code patterns on the surface of the clay
o Process of crystal growth responsible for replication
o Nucleotides then RNA molecules (released from the clay surface enclosed in lipid
sacs forming protocells
o Protocells
Cold side double stranded polynucleotides
Warm side single stranded template
Moves to the warm side where strands separate RNA in each
daughter cell
o Ribozymes develop and direct the duplication of RNA
Catalyze metabolic reactions
o Proteins (rather than ribozymes) catalyze the reactions in a cell
o Enzymes catalyze the production of DNA
o RNA intermediary between DNA and proteins
o PNA combined (best) properties of proteins and nucleic acids
All cells contain DNA
Genome total DNA of a cell
Genes individual units of heredity, controlling traits by coding for a functional proteins or
RNA
Types of Cells
Prokaryotes
Karyon kernel, nut
Single celled
Bacteria and cyanobacteria
1 3 micrometers
Lacking membrane-enclosed organelles
Has plasma membrane
Lipid bilayer

Eukaryotes
True nucleus
Multi-cellular or single celled
Single celled yeasts and Paramecium
Well defined nucleus
More complex than eukaryotes
10 100 micrometers
Existence of organelles has distinct
function and is surrounded by its own
membrane
Has a cell membrane or plasma
membrane
Lipid bilayer

Organelles

Nucleus with nuclear membrane

Mitochondria energy-yielding oxidation reactions
o plasma membrane of prokaryotes
Endoplasmic reticulum internal membrane system
Ribosomes sites of RNA synthesis; bound to ER
o Prokaryotes free in cytosol
Cytoplasm portion of the cell outside the nucleus
Cytosol aqueous portion of the cell outside the membrane bound organelles

Chloroplasts where photosynthesis takes place

Chromatophores capable of photosynthesis

Prokaryotic cells

DNA concentrated in the nuclear region

Single, closed, circular molecule of DNA
Genome attached to the cell membrane
DNA circles bound to the plasma membrane
Cytosol granular in appearance because of the presence of ribosomes (RNA and protein
ribonucleoprotein particles)
Ribosomes sites of protein synthesis
Cell membrane or plasma membrane an assemblage of lipid molecules and proteins
Cell wall made up of polysaccharide material (polymerization of sugars); for protection

Eukaryotic cells

Presence of subcellular organelles

Nucleus, mitochondrion and chloroplast separated by a double membrane
Nucleus houses the DNA; RNA synthesis
o Surrounded by a nuclear double
membrane
Mitochondria enzymes that catalyze
important energy yielding reactions
o Carry DNA independent from the one
in the nucleus
o Double membrane
Outer membrane smooth
Inner membrane many folds
(cristae)
o Space within the inner membrane
matrix
o Contain ribosomes similar to those in
bacteria
o 1 micrometer in diameter and 2 8
micrometers in length
Chloroplasts sites of photosynthesis
o Carry DNA independent from the one in the nucleus
Plant cell wall polysaccharide cellulose; shape and mechanical stability
Nucleolus rich in RNA
o RNA is synthesized in a DNA template for export to the cytoplasm through nuclear
pores
Chromatin aggregate of DNA and protein
Chromosomes tightly coiled
Endoplasmic reticulum continous single membrane system
o Attached to the cell membrane and to the nuclear membrane
o Occurs in 2 forms:
Rough ER studded with ribosomes bound to the membrane
Smooth ER do not have ribosomes
Ribosomes site of protein synthesis
Chloroplast green plants and green algae

o 2 micrometers in diameter and 5 10 micrometers in length

o Grana photosynthetic apparatus
o Contain an independent DNA and ribosomes similar to those of bacterias
Golgi apparatus close to smooth ER
o Involved in the secretion of proteins from cells
o Sugars are linked to other cellular components such as proteins
Lysosomes membrane enclosed sacs containing hydrolytic enzymes
Peroxisomes contain enzymes involved in the metabolism of hydrogen peroxide
o Catalase catalyzes the conversion of H2O2 H2O + O2
Glyoxysomes found in plant cells only
o Catalyze glyoxylate cycle
o Lipids carbohydrates with glyoxylic acids as intermediate
Cytosol viscous liquid
o Has some internal organization
Cytoskeleton or microtrabecular lattice lattice of fine strands that seem to consist
mostly of protein that is connected to all organelles
Cell membrane separates the cell from the outside world
o Lipid bilayer with several types of proteins embedded in the lipid matrix
o Some proteins transport specific substances across the membrane barrier in both
directions
Vacuoles sacs in the cytoplasm surrounded by a single membrane
o Isolate wastes substances that are toxic to the plant and is produced in greater
amounts than the plant can secrete in the environment
o Can be poisonous enough to discourage herbivores from ingesting them

Classification of living things

Kingdom Monera
o Prokaryotic organisms
o Bacteria and cyanobacteria
o Eubacteria (true bacteria) and archaebacteria (extremophiles) can be classified
under Monera since it lacks a well define nucleus
Kingdom Protista
o Unicellular organisms Euglena, Volvox, Amoeba, Paramecium
o Multicellular organisms algae
Kingdom Fungi
o Yeasts, molds and mushrooms
Kingdom Plantae
Kingdom Animalia

Endosymbiosis a symbiotic relationship in which a smaller organism is completely contained

within a larger organism
Source of energy in life processes

Sun ultimate source of energy

Photosynthetic organisms trap light energy and use it to drive the enrgy-requiring
reactions that convert CO2 and water to carbohydrates and oxygen
o Reduction gain of electrons
Non-photosynthetic organisms (animals that consume carbs) use them as energy sources
o Oxidation loss of electrons

Measurement of energy changes

Thermodynamics
o Processes that release
energy is favoured
o Change in energy depends
only on the state of the
molecules present at the
start and at the end of the process
o Hydrolysis of ATP 30.5 kJ/mol-1 ATP = 7.3 kcal/mol ATP
o Spontaneous reactions characteristic of a reaction or process that takes place
without outside intervention
o Free energy (G)
G < 0 exergonic energy is released; spontaneous
G > 0 endergonic energy is absorbed; non spontaneous
G = 0 equilibrium no net charge at both directions
o Enthalpy (H) heat of reaction at constant pressure
o Entropy (S) important in determining the enrgetics of protein folding

Amino Acids

20 are found in proteins

General structure:
o -carboxyl group is attached to
Hydrogen
Amino group
Carboxyl group
Side chain group (R)
Determines the identity of the particular amino acid
Chiral
o Nonsuperimposable mirror image
o Exhibited in many biomolecules
o Carbon with 4 different groups bonded to it
o Occurs in all amino acids except Glycine
Glycine is achiral
o 2 nonsuperimposable mirror image
o Stereoisomers
Optically active compounds that rotate due to polarized light
Standard molecule - Glyceraldehyde
2 possibilities based on the position of the -amino group
Laevus (L) left proteins
Dexter (D) right nature, bacterial cell walls and antibodies
o Classification:
Polar / Non-polar
Acidic / Basic
Functional groups

Amino Acid Classification

Nonpolar side chain (Net charge = 0; Zwitterions)

Glycine (G)
Alanine (A)

Valine (V)
Leucine (L)
Isoleucine (I)
o Has 2 chiral alpha carbon
Proline (P)
o Aliphatic cyclic structure
o CNC
o Secondary amine = imine
Phenylalanine (F)
o Aromatic
Tryptophan (W)
o Side chain contains an indole
o Aromatic
Methionine (M)
o S + aliphatic HC groupings

acid

Polar side chains (net charge = 0)

electrically neutral at neutral pH,

Serine (S)
o Polar group - OH
o Aliphatic HC
Threonine (T)
o Polar group - OH
o Aliphatic HC
o Has 2 chiral alpha carbon
Tyrosine (Y)
o Polar group OH
o Aromatic HC
Phenol stronger acid than alcohol
Cysteine (C)
o Polar group SH (thiol)
o Forms disulfide bonds
Oxidation ()
Reduction ()
Glutamine (Q)
o Amide groups derived from carboxyl
group derivative of
glutamic acid
Asparagine (N)
o Amide groups derived from carboxyl group derivative of aspartic acid

Acidic negatively charged at neutral pH

Glutamic Acid (E)

Aspartic Acid (D)

Basic

Histidine (H)
o Imidazole side chain + amino group
o Net charge = 2
o Nitrogen containing groups

ring

Arginine (R)
o Nitrogen containing groups
Lysine (K)
o Nitrogen containing groups

Uncommon Amino Acids

Derived from the common amino acid

Produced by modification after the protein is synthesized (post translational modification)
Modication not common
o Hydroxylation
Found in collagen
4 Hydroxyproline
5 Hydrolysine
o Tyroxine
Extra iodine containing aromatic group in the side chain
Produced in the thyroid gland
Posttranslational modification of the tyrosine residues in thyroglobulin
Released as a hormone

Free Amino Acid

Neutral pH
Carboxyl group carboxylate (-)
Amino group (+)
Zwitterion
o Amino acids without charged portions
o +=o Electrically neutral
Amphoteric
o Can act as acids and bases
Dipolar
o + alpha amino group
o - alpha carboxyl group
Optically active consequence of a chiral alpha carbon (except glycine)

Titration of Amino Acids

Titration curve reaction of each functional group with H ion

Titratable groups - carboxyl and amino group
Alanine
o Low pH
Net charge = 1
o High pH
Net charge = -1
Alpha carbon
o pKa = 2
Amino groups
o pKa = 9 10.5
Electrophoresis method for separating molecules in an electric field
Isoelectric pH pH at which a molecule has no net charge

The Peptide Bond

Amino acids can be linked by forming covalent bonds

o Water is eliminated and amino acid residues remain
Peptides compounds formed by linking small numbers of amino acids ranging from 2
several dozens
Amino acid Peptide Bonds Polypeptide Chains Proteins
Amino Acid + carboxyl group = amide
Resonance structure structures that differ from one another only in the positioning of the
electrons
Peptide group that forms the link between the 2 amino acids is planar
o Stronger because of resonance stabilization
If you change the pH of the amino acid, the net charge will also change
o Net charge
+1 cationic form
0 neutral (isoelectric zwitterion)
-1 anionic

Biological functions of small peptides

Hormones
Steroids
Peptide hormones
o Oxytocin and vasopressin
9 amino acid residue + amide group (C terminal end) and disulfide bond
between cystein residues at positions 1 and 6
o Oxytocin
Isoleucine residue at position 3
Leucine residue at position 8
o Vasopressin
Phenylalanine residue at position 3
Arginine residue at position 8

Hydrophobicity Index

Kyle and Doolittle

Hydrophobic Hydrophilic
Arginine most hydrophilic / most basic
Isoleucine most hydrophilic

Level of Protein Structure

1. Primary Structure
- Order or sequence of amino acids in the polypeptide chain
- Peptide bonds (covalent bond)
- Only L amino acids compose proteins
- Stabilizing force: peptide bonds
o Including disulfide bonds
- Determines the 3D structure
- Determines the properties
2. Secondary Structure

Arrangement in space of the atoms in the peptide backbone

Conformation of the polypeptide back bone
Have repetitive interactions resulting from H-bonding between the amide and the
carbonyl groups of the peptide backbone
- Stabilizing force: hydrogen bonding
o Linked in nitrogen (high electronegativity)
- Polypeptide backbone can fold into periodic structure -helix and -pleated sheet
- Sequence dependent
- Random coil if -helix and -pleated sheet cannot be
- Backbone can change directions by making reverse turns and loops
- Two bonds with reasonably free rotation (Ramachandran angles)
o Bond between alpha amino nitrogen of that residue and
o Bond between the alpha carboxyl group of that residue
3. Tertiary Structure
- 3D arrangement of all the atoms in the protein, including those in the side chains and
in any prosthetic groups
- Arrangement in space of all atoms in the polypeptide chain
- Stabilizing force: covalent and non covalent interactions
- Native conformation requirement for proteins to have a biological activity and
function
- Multipeptide - subunits
4. Quaternary Structrue
- Describes the interactions and arrangements of the subunits is an oligomeric protein
(more polypeptide)
- Stabilizing force: covalent and non covalent interactions
o Hydrogen bonds
o Electrostatic attractions
o Hydrophobic interactions
Nomenclature

C terminus retains its name

- ine - iyl except for arginine and glutamine
Tryptophan + yl
One word name

The Peptide Bond

Trans configuration
Planar (sp2)
o Structure is a hybrid of the resonance
Partial double bond character (approximately 40%) due to resonance
Peptide bonds
o Rigid (restricted rotation)
o Free rotation only occurs in single bonds
Peptide Bond shorter and stronger than N-C bond
Hydrolysis breaks peptide bonds
Ramachandran angles and are free rotating

-helix

Backbone coils into a compact rigid structure

Right handed DNA

Complete helical turn

o 3.6 amino acid residues
o 0.54 nm distance
Stabilizing force: H-bonds
o Pitch of the helix is = 0.54 nm
o Form between carbonyl O and NH which are 3.6 amino acids apart
o Parallel to the helical axis
Non formation
o Proline is a helix breaker rigidity
Rotation around the bond between the nitrogen and the alpha-carbon is
severely restricted
Prolines alpha-amino group cannot participate in intrachain hydrogen
bonding
o Series of Glycine single bonds become flexible
o Series of big / bulky side chain crowding (steric effect / steric hindrance)
o Series of side chains having same charges tendency of repulsion; electrostatic
repulsion

pleated sheets

Polypeptide back bone almost fully extended

o Zigzag formation
Backbone are aligned side by side so that H bonds are formed between carbonyl O of
one chain and NH group of the adjacent chain
o Parallel (H bonds alternating diagonal) run in the same direction
o Antiparallel (H bonds parallel) alternating chains that run in the opposite
direction
H bonds
o Can be formed between different parts of a single chain that is doubled back on
itself
o H bonding between peptide chains gives rise to a repeated zigzag structure
o Perpendicular to the direction of protein chain

Irregularities in Regular Structure

Beta bulge
o Non-repetitive irregularity found in antiparallel beta-sheets
o Occur between 2 normal beta - structure h bonds
2 residues in one strand
Protein folding requires that the peptide backbones and the secondary structures be able
to change directions
o Reverse turn
Transition between one secondary structure and another
Glycine is frequently encountered
Proline has the right geometry for a reverse turn

Supersecondary Structure

Independently folded portions of proteins

Energetically favorable contacts exist between the side chains in the 2 stretches of the
helix
Beta meander

Antiparallel sheet is formed by a series of tight reverse turns connecting stretches

of the polypeptide chain
Greek key peptide chain that doubles back on itself in a pattern
Motif
o Repetitive supersecondary structure
o Allows beta meander and greek key to be arranged into a beta barrel in the
tertiary structure of the protein
o Tell us much about protein folding
o Found in proteins and enzymes with very dissimilar functions
Domains
o Domains with similar conformation = same function
o Short polypeptide sequences within a protein direct the post translational
modification and sub-cellular localization
o Specific sequences
Bound to a membrane or secreted from the cell
Mark a protein for phosphorylation by a specific enzyme
o

Collagen Triple helix

Collagen

Component of bone and connective tissues

Most abundant proteins in vertebrates
Water insoluble fibers
3 polypeptide chains wrapped around each other in a rope like twist or triple helix
o repeating sequence on 3 amino acid residues
Hydroxylysine, hydroxyproline, glycine
o Every 3rd position is glycine
Tropocollagen
o Triple helical molecule
o 300 nm long; 1.5 nm in diameter
Requires ascorbic acid to remain active

Tertiary

Involve side chain interactions

o Covalent and noncovalent
Polypeptide falls into its 3D structure
o Native conformation
o Biological function / activity
Covalent bond
o Disulfide bond
o Metal ion coordination system
Non covalent
o Hydrophobic interactions
o Ionic bond
o Salt bridge
o Electrostatic
o Hydrogen bonding
3D shapes
o Globular
Almost spherical

Transport, regulatory, catalytic

Fibrous
Rod like
Insoluble in water
Structural movement
Defense

Quaternary Structure

Oligometric protein
Alcohol dehydrogenase tetramer
Glutamine synthase decamer

Protein Denaturation

Loss of the higher levels of structure leads to unfolding of protein and subsequent loss of
biological function

Physical and Chemical Agents

Physical
o Heat or temperature
Non covalent interaction easily broken
KE
o Mechanical agitation / stress
Chemical
o Strong acids and Bases
o Organic solvents non polar
o Detergents
o Reducing agents (disulfide bonds)
-mercaptoethanol HSCH2CH2OH
DTT
o Heavy metal ions (toxic)
Hg, Pb, Fe

Peptide sequencing
Steps:
1. Check for purity
- Column chromatography
- Purity can be validated by
o Electrophoresis
o Isoelectric focusing, based on pI
2. Amino Acid composition is determined
- Hydrolyze peptide to constituent amino acids
o 6M HCl in an evacuated ampoule (to avoid reversion of reaction) and then
heated at 105 110 oC for 24 48 hours
- Separate amino acids in the mixture
o Cation exchange column
- Detect and quantitate the individual amino acids
o Ninhydrin Reaction (violet; proline yellow)

o Use of fluorescent reagent

Anakysis of amino acids
o Composition
o Identity
o Quantity
3. Terminal residue Analysis
- N terminal residue analysis
a. Sangers Method
a. Reagent 2,4 DNFB (2,4 dinitrofluorobenzene)
b. Product 2,4 DNP AA (2,4 dinitrophenyl derivative
c. Amino groups reacts
b. Edman Reaction
a. Reagent PITC (Phenylisothiohydantoin)
b. Product PTH AA (Phenylthiohydantoin)
c. Amino acid reacts
- C terminal residue analysis
a. Hydrazynolysis
i.
Most reliable technique
ii.
Hydrazine cleaves all peptide bonds yielding amino- acyl hydrazidases of all
amio acids except the C terminal residue
b. Carboxypeptidase Treatment (CP)
i.
Peptidase (enzyme)
ii.
Carboxypeptidase requires the presence of carboxyl group
iii.
Will only react to the carboxyl group
iv.
CP A and CP B will not cleave if P is next to the C terminal residue
v.
CP C and CP Y: all free C-terminal residues are cleaved
4. Fragment Analysis
- Cutting the peptide produces a new N and C terminus
- Chemical method
a. Cyanogen Method
i.
Reagent Cyanogen Bromide
ii.
Cleaves the peptide after internal M residues
- Enzymatic Method
a. Trypsin
i.
Protease that cleaves peptide bonds of basic amino acid residues R and K except
when P follows R and K in the primary structure
b. Chymotrypsin
i.
Protease that cleaves peptide bonds of aromatic amino acid residues F, W and Y
except when P follows these amino acids in the primary structure
5. Solving the sequence
- Put together all information from amino acid composition, N terminus and C
terminus identification and fragment analysis to solve the sequence of the unknown
peptide
-

Classification of Proteins
Based on Composition
1. Simple amino acids only; simple proteins
2. Conjugated has prosthetic groups (non-protein part)
Based on Shape
Globular
Spherical

Fibrous
Elongated; rods

Soluble
Non - structural

Insoluble
Structural

Denaturation of Proteins

Extremes of temperature and pH have a drastic effect on protein conformation

Loss of organized structure of a globular protein
Does not alter primary structures
Denaturation
Breaking up the 3D
shape
Temperatures
Heavy metals (Hg
and Pb)
Detergents
Mechanical stress

Hydrolysis
Breaking down to
smaller peptides or
amino acids
Changes in pH
Enzymes
Temperature

Effect of Temperature

As T, in rate of molecular movement of the individual molecules within the solution

As T further, the bonds within the proteins vibrate more violently
Weaker hydrogen bonds and hydrophobic interactions are disrupted and the characteristic
3-Dal conformation of the protein is disorganized

Effect of pH

When the pH is changed dramatically, the acid or base will change the charge of the
proteins
Interferes with salt bridges and H bonds that stabilize the tertiary structures

Heat

Disrupts H bonds
Vibrate too violently coagulation / precipitation

Microwave radiation

Violent vibrations that disrupts H - bonds

UV radiation

Same effect as heat

Violent whipping or shaking

Globular extend to longer lengths

Detergent

Affects R group interactions

Disrupts hydrophobic interactions

Organic solvents

R group interactions also form H bonds

Quickly denature proteins

Salts of heavy metals

Metal ions combine with thiol and forms poisonous salts

Reducing agents

Reduce disulfide linkages

Globular and Fibrous proteins

Globular

Approximately spherical in shape / consists of many lobes (Domains)

Hydrophobic core surrounded by a hydrophilic external surface which interacts with water
Soluble and form compact spheroidal molecules
Have tertiary and quaternary structure in addition to the primary and secondary structures
Myoglobin
Haemoglobin
Enzymes
Receptor proteins

Heme

Ferrous ion group + porphyrin / tetrapyrrole

Essential component of the proteins haemoglobin and myoglobin
6 metal ion coordination bond
Non covalent on tertiary structures
o H bond
o Ionic bonds
o Salt bridge
o Iron coordination bonds
4 nitrogen
5 imidazole nitrogen
Protein part globin, distal H forms the 5th coordination complex
Molecular oxygen
o Haemoglobin 4, tetramer
o Myglobin 1, monomer
6th coordination
Graphs
o Hb
Sigmoidal, releases O2 easily after a lag phase
+ cooperativity
o Mb
Hyperbolic
Higher affinity

Myoglobin and Hemoglobin

Hemoproteins
Conjugated
Prosthetic groups

Hemoglobin

Transport protein
Oxygen blood and tisse
Tetramer

Myoglobin

Storage protein
Monomer tertiary level

Fibrous

Collagen
Fibroin
Keratin

Collagen

Most abundant protein (skin and bones)

Insoluble
Utilized outside the cell
Connective tissue (cartilage, bones, tendons)
Triple helical structure (tropocollagen) stabilized by aldol crosslinks covalent bond
Not alpha helical
Structure is 33% G and 33% P

Diseases of the Collagen

Fibrosis excessive collagen synthesis

- Pulmonary fibrosis - lungs
- Hepatic fibrosis liver
o Liver detoxifies everything
o Overconsumption of alcohol
Ehlers Danlos (rubber man)
o Skin
o Caused by insufficient collagen production
Osteogenesis imperfect (brittle bone syndrome)
o Fragile bone

Elastin

Gives elasticity to the tissues and organs without breaking

Single polypeptide chain
Have crosslinks

Expand without breaking

o Have homophobic amino acids (A, V, L, G)

Keratin

Tough, fibrous, insoluble protein that makes up the skin, hair, nails, claws, hooves, feather
and horns
Contains high percentage of sulfur containing amino acid
o Largely cysteine disulfide bridges (oxidation readucion reaction) resulting in a
fairly rigid structure
o Human hair 14% C
Types:
o -keratin
-helical coiled coil structure
Humans and other mammals
o -keratin
twisted sheet structure
birds and reptiles

Biological Catalysts Enzymes

Catalysts

Not altered or changed

Speeds up the rate of the reaction
Being used but regenerated in the end
Bring reactants together
Enzymes

Biological Catalysts

Increases reaction rates to a much greater extent

Enzymes
o Proteins (more complex)
o Substrate specific
o Reaction type specific
Trypsin (reaction type specific) peptide bond hydrolysis
o Speed up reaction rates
Catalysts
Product
o Single product
o Predictable
pH and temperature affect affinity

Inorganic Catalyst

Simple catalyst (atom)

Used in inorganic reactions
Uses metals

Two things catalysts cant do:

1. Cannot alter the reaction equilibria

K eq =

[Products ]
[Reactants ]

2. Cannot G

G=G productsG reactants

Classification of Enzymes

Enzyme manual
Based on the type of reaction
Id numbers EC Number

6 Types of Reactions (Main Classes)

1. Oxireductases
- Catalyze redox reactions
o Oxidation
Dehydrogenation
Loss of electrons
o Reduction
Rehydrogenation
Gains electrons
- In Organic chemistry: the reaction continues
a. 1 alcohol aldehyde carboxylic acids
b. 2 alcohol ketones
c. 3 alcohol no reaction
CH3CH2OH + NAD+ CH3CHO + NADH
- NAD+ NADH + H+
- FAD FADH2
o NADH and FADH2 Electron Transport Chain = ATP
2. Transferases
- Catalyze reactions that involve transfer of groups from one molecule to another

AB+C A+ BC

Glucose+ ATP Glucose6 phosphate+ ADP

-

Kinase transfers the phosphate group

Transaminase transfers amino group
o Alaninetransaminase - Indication of liver damage
3. Hydrolases
- Catalyzes reactions in which the cleavage bonds is accomplished by adding H 2O
- Carboxypeptidase, Trypsin, Amylase
- Phosphoanhydride bond that is broken in ATP

ester alcohol +carboxylic acids

amide carboxylic acid+amine

4. Lyases
- Catalyze reactions in which groups are removed to form a double bond and are added
to a double bond
- Lysis of substrates
o Decarboxylation
Removal of the carboxyl group
Catalyzed by lyases
o Carboxylation
Not catalyzed by lyases
o Dehydration
Removal of water
Catalyzed by lyases
o Hydration
Addition of water
Catalyzed by lyases
5. Isomerases
- Catalyze intramolecular rearrangements
o Same molecular composition
- Different arrangements
o Cis Trans Isomeration
o Enantiomerization
6. Ligases
- Catalyze bond formation between 2 substrate molecules
- Ligation bond formation
- Synthetases
- Reductive amination
o Incorporation or release of ammonium
- Carboxylation
o Incorporation or release of carboxyl group

How do enzymes work?

E+S
Enzyme +
Substrate
1

<

[ES]
Complex

Substrate (S) is in its most stable; lowest energy form

Within the complex, substrate (S) is forced into a high energy form in which certain
bonds have been weakened. Atoms that will form new bonds must connect with each
other
Once the chemical reaction is completed, enzyme (E) and products (P) separate from each
other. Enzyme (E) becomes available for another substrate (S)

Why are enzymes powerful catalysts?

E+P
Enzyme +
Product
3

Proximity Effect enzymes bring substrates at the active site

Orientation Effect enzymes bring substrates at the right distance and orientation for
reaction to occur
Energy effect enzymes lower the energy barrier inducing strain in the substrate
Catalytic effect ability of the enzyme to provide groups (acidic, basic, polar, non-polar)
required for the reaction

Features of the Active Site

Small portion of the entire volume of the enzyme. Only a few amino acid residues are in
contact with the substrate
3D entity. Amino acid residues in the active site come from different parts of the linear
amino acid sequence
Active site substrate binding involve non-covalent interactions only (weak forces)
Specificity of binding depends on precisely defined arrangement of atoms in the active site
(lock-and-key and induced-fit models)
Water is largely excluded from the active site (i.e. Hydrophobic)

Models of Enzyme-Substrate Binding

Lock
o
o
o

and key
Lock enzyme
Key substrate
Enzyme is assumed to be a rigid molecule; the active site and the substrate have
complementary shapes to allow for a perfect fit
Induced fit / hand and glove
o Glove enzyme
o Hand substrate
o Enzyme is assumed to be a flexible molecule; binding of the substrate induces a
conformational change in the enzymes active site to have an induced fit

Coenzymes
Vitamin

Coenzyme form

Thiamine (B1)

Thiamine
pyrophosphate

Riboflavin (B2)
Pyridoxine (B6)
Niacin
Panthotenate

FAD and FMN

Pyridoxal
phosphate
NAD and NADP
Coenzyme A

Biotin
Folic Acid

Biocytin
Tetrahydrofolic acid

Vitamin B12

Deoxyadenosylcoba
lamin and
methylcobalamin

Reaction or
Process Activated
Decarboxylation
Aldehyde group
transfer
Redox
Amino acid
transfer
Redox
Acyl group
transfer
Carboxylation
One carbon group
transfer
Intramolecular
rearrangement

Apoenzymes + Coenzyme Holoenzymes

Enzyme type
Decarboxylation;
Transferase
Oxidoreductases
Transferase
Oxidoreductases
Transferase
Ligases
Transferase
Isomerases

Apoenzymes inactive
Coenzyme
o Ions
o Derived from water soluble vitamins
Vitamin C
B complex
Holoenzyme active
Vitamins
o Cannot be synthesized by the body
o Tablets inactive form
o Activates when induced
o Should be achieved in the diet

Isozymes or Isoenzymes

Multiple forms of enzymes

Enzymes with different primary structures but catalyzing essentially the same reaction
o Different amino acid sequence
Gathered from different samples
Different locations
Creatine phosphokinase (CPK)
o Dimer
o M and B
o Exists in 3 forms
CPK - 1 / CPK BB
Brain
Homodimers
CPK - 2 / CPK MB
Heart
Heterodimers
CPK - 3 / CPK MM
Skeletal muscles
Homodimers

Enzyme kinetics
Enzymes

Study of reaction rates of chemical reactions

Concentration of reactants and products in molarity
o Molarity = mole of solute / liter of solution
Can be determined either by: (which is easier to use)
1. Rate of disappearance of a reactant
2. Rate of appearance of a product

Typical kinetic experiment

Measures the effect of substrate

Enzyme [E] = k
o Constant
o Low concentration
Substrate varies [S]
o Measure the volume (V) for every dilution

Simple enzymes
Hyperbolic graph
Monomeric enzymes
Simple kinetics:
Michaelis Menten kinetics

Allosteric enzymes
Sigmoidal graph
Oligomeric enzymes
Complex kinetics:
Kinetic constants

Michaelis Menten Equation

Km = affinity of the substrate to the enzyme

Low value; high affinity

o High affinity
High value; low affinity
o Loose affinity
Approximate values

Factors affecting enzyme affinity

1. Temperature
a. Low temperature; low activity
b. Raises for every 10 degrees rise
c. Optimum temperature peak
d. Lowered activity for every increase of temperature thereafter
i. Exemptions to extremophiles
2. pH changes
a. Optimum pH = 6.7 to 7
i. Pepsin = 2 (acidic)
ii. Arginase = 10 (basic)
3. Activators
a. Increase enzymatic activities
4. Inhibitors
a. Decrease enzymatic activities
b. Reversible enzymes
i. Bind non covalently to the enzyme
ii. E + I < E-I
iii. Types:
1. Competitive inhibitors
a. Bind to the same site where the substrate is binding to
i. Inhibitor is similar to the substrate
b. Substrate analogs
c. There should be a high probability of the substrate than
inhibitors to ensure the binding of the substrate
d. Vmax = same; Km = increase; slope of the plot = increased
i. Intersect at the y - axis
2. Noncompetitive inhibitors
a. Substrate and enzyme does not compete because the inhibitors
bind at another site
i. Causes conformational change (affects the affinity of the
enzyme)
b. More difficult to overcome
c. Vmax = decreased; Km = same; slope of the plot = increased
i. Intersect at the x - axis
3. Uncompetitive inhibitors
a. Same slope

b. Parallel lines
c. Vmax = decrease; Km = decrease; slope of the plot = same
c. Irreversible inhibitor
i. Bind covalently to the enzymes
ii. E + I E-I
iii. Suicide inhibitor