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INTRODUCTION TO BIOCHEMISTRY

MUHAMMAD SHARIR BIN ABDUL RAHMAN

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1.1 The Chemical Elements of Life1.2 Important Biomolecules1.3 The Cell as Basic Unit of Life1.4 Water Molecule1.5 Ionic and Polar Substances

Dissolve in Water1.6 pH Scale1.7 Buffered Solutions Resist Change

in pH

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1.1 Chemical elements of life Organic chemistry = study of carbon,

hydrogen and their derivatives.

We concentrate on aspect of organic chemistry that we need to understand what happen in living cells.

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Organic chemists study reactions that take place in laboratory. Biochemists study how reactions occur in living cells.

Biochemical reactions involve specific chemical bonds or functional groups (parts of molecules).

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General formulas of organic compounds

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General formulas of functional groups

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General formulas of linkages in biochemical compounds

Ester & ether linkages are common in fatty acids and lipids.

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Can chemist make the molecules of life in the lab?

In 1828, Friedrich Wohler a German scientist performed a miracle experiment.

He synthesized urea, waste product of animal from ammonium cyanate, a compound from mineral.

NH4OCN H2NCONH2

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Chemical reactions that occur inside cells are the same kind of reactions that occur in a chemistry lab.

The biggest difference is that almost all reactions inside cells are catalyzed by enzymes, thus proceed at very high rates.

It is very useful to distinguish between biochemical reactions that take place in an organism (in vivo) and those that occur under laboratory conditions (in vitro).

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1.2 Important biomolecules

Most biomolecules contains O2 and N2. These are among the most

electronegative elements. Others are C, H2, P. Many of these functional groups are polar. Their polarity nature plays crucial role in

their reactivity.

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Biochemistry deals with large molecules referred to as macromolecules.

Biological macromolecules are usually polymers created by joining many smaller organic molecules (monomers) via condensation (removal of the elements of water).

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MACROMOLECUL

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MONOMERS

Protein Amino acid

Lipid Fatty acid

Polysaccharides Monosaccharide

Nucleic acid (DNA &

RNA)

Nucleotide

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Each monomer joined into a macromolecular chain is termed as residue.

Certain carbohydrates consist of repetition of a single residue.

Proteins and nucleic acids consist of different types of residues which are connected in specific order.

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Proteins 20 common amino acids incorporated into

proteins in all cells. Each contain an amino group, a carboxylate

group and side chain group (R). R is unique to each amino acids. Peptide bond = bond between carbon atom of

1 amino acid residue and the nitrogen atom in the next residue.

This amid linkage condense 1 water molecule

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Many proteins works as enzymes and structural components of cells.

Sequence of amino acid residues determines the three-dimensional structure (conformational structure) of proteins.

Β-sheet α-helix

Adapted from Weis WI and Drickamer K (1994) Structure, 2:1227-40

Structure of mannose-binding lectin

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Polysaccharides

Carbohydrates (saccharides) primarily composed of carbon, oxygen and hydrogen.

Simple sugars = Monosaccharides. Sugar polymers = Polysaccharides. Structures drawn in:

Fisher projection (open chain and ring form) Haworth projection (ring form, most common) Envelop conformation

Example: ribose (C5H10O5)

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Example: Glucose and cellulose C-1 of glucose binds to C-4 of another glucose

(glycosidic bond) = cellulose Monomer = glucose Polymer = Cellulose, glycogen and starch

Cellulose is the major component of flowering plant stems &tree trunks.

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Nucleic Acids

Nucleic acids (polynucleotides) = composed of many nucleotides.

Plentiful in eukaryotes and prokaryotes. Nucleotides consists of five-carbon sugar (ribose

or deoxyribose), a heterocyclic nitrogenous base and at least one phosphate group.

Nitrogenous base of nucleotides = purines and pyrimidines.

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Purines = adenine (A) and Guanine (G) Pyrimidines = Cytosine (C), Thymine (T),

Uracil (U) In nucleotide the base is joined to C-1 of sugar

and phosphate group is attached to other sugar carbons (usually C-5)

Example: Adenosine Triphosphate (ATP) Glycosidic bond (Adenine to ribose) Phosphoester linkage (C-5 to α phosphoryl) Phosphoanhydrides (β,ϒ,α phosphoryl group)

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Polynucleotides = C-3 oxygen atom of sugar covalently linked to phosphate group of one nucleotide (phosphoester linkage).

Nitrogenous base at C-1.

DNA and RNA (tRNA, mRNA, rRNA).

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Lipids and Membranes

Lipid = diverse class of molecules that are rich in C and H2 but contains only few O2

Simplest lipid = fatty acids = long chain hydrocarbons with a caboxylate group at one end.

Fatty acids commonly found as part of larger molecules called glycerophospholipids. Glycerophospholipid contains glycerol 3-phosphate

and two fatty acyl group Other kinds of lipids = steroids and waxes

Steroid:ex. Cholestrol Wax: Beeswax and earwax

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Lipids have a polar, hydrophilic head that can interact with aqueous environment and non-polar, hydrophobic tail.

Aqueous environment = hydrophobic tails of such lipids associate and produce a sheet called lipid bilayer.

Lipid bilayers forms the structural basis of all biological membranes.

Acts as barriers that impermeable to most water soluble components.

Flexible because lipid bilayers are stabilized by noncovalent forces.

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1.3 Cell basic of life

Every organism is either single or composed of many cells, except for virus.

A cell can be classified as prokaryotic or eukaryotic.

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Prokaryotic Cell

Prokaryotic cells contain genetic information that is not enclosed in a nucleus membrane (nucleoid region).

Cytosol has granular appearance because of ribosome.

They also lack membrane enclosed organelles.

Procakaryotes consist of the Kingdom Monera (bacteria).

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27 Bacterium, a prokaryote.

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Eukaryotic Cell

Genetic information of eukaryotes is enclosed in a nucleus membrane.

They also have membrane enclosed organelles.

Eukaryotes consist of the kingdom Animalia, Plantae, Fungi, and Protists (single cell eukaryotes).

29 Eukaryotic cell – animal cell

30 Eukaryotic cell – plant cell

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Eukaryotic Cell (cont’d)

Three most important organelles Nucleus: DNA and RNA synthesis. Chloroplast: Site of photosynthesis (plant cell only). Mitochondrion: contains enzymes that catalyze

important energy-yielding reactions (in animal cell only)

Nucleus Surrounded by nuclear envelope. Has nucleolus, and rich in RNA. RNA synthesized on a DNA template in nucleolus and

transport to cytoplasm. Near nuclear membrane has chromatin, aggregate of

DNA and proteins.

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Mitochondrion Double membrane with inner membrane has many

folds called cristae. In matrix, oxidation process occur to yield energy

for the cell Mitochondrial DNA located in internal matrix, also

has ribosome in matrix A theory suggested it comes from absorption of

aerobic bacteria by larger host cells

Endoplasmic Reticulum (ER) Rough and smooth RE, ribosomes bound on

membrane

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Chloroplast Photosynthetic apparatus found in grana, membranous

body stacked Also has DNA that differ from nucleus and has

ribosomes

Golgi apparatus Membranous sacs, involves in secretion of proteins Proteins are linked to sugar in Golgi apparatus.

Plasma membrane: Outer boundary of the cell. A continuous sheet of

bilayer lipid molecule. Contain proteins that function as enzymes, receptor for

hormones, molecular pumps and selective channels that allow entry of certain molecules in and out of cell.

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Cytosol Liquid interface of cells Organelles held in places by fine strands

(microtubules) of proteins

Cell wall External cell wall other than plasma membrane

Vacuoles Sacs that isolate waste that is toxic to plant,

occurs as poison for plant-eaters

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Lysosomes Membrane-bound vesicles that contain hydrolases

(catalyze hydrolytic reactions) & function optimally at pH ~5.

These enzymes (hydrolases) can catalyze the breakdown of nucleic acids, proteins, cell wall carbohydrates, and phospholipids.

Involve in intracellular digestion (autophagy) & digestion of material from outside the cell (heterophagy).

Heterophagy begins with invagination of the plasma membrane, a process called endocytosis. Example of heterophagy is to remove bacteria from the body.

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Peroxisomes or microbodies

Unlike lysosomes, they do not contain hydrolases.

An organelle responsible to protect cell from its own production of toxic hydrogen peroxide.

Most of catalase in the cell is contained in peroxisomes. This enzyme catalyzes the conversion of hydrogen peroxide to water and oxygen.

Example: white blood cells produce hydrogen peroxide to kill bacteria. The oxidative enzymes in peroxisomes break down the hydrogen peroxide into water and oxygen.

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VIRUS

Viruses consist of nucleic acid molecule (DNA or RNA) surrounded by a protein coat.

Viruses are not truly cells because they are unable to carry out independent metabolic reactions.

They can only propagate after infecting a host cell.

Viruses that infect prokaryotes are usually called bacteriophage or phage.

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1.4 Water Molecule Principle component of most cells.

Electronegativity = the tendency / affinity of atom to attract electron (e-) to itself in chemical bond.

O and N are highly electronegative compared to C and H.

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Polarity

When 2 atoms of same electronegativity create a bond, e- will be shared equally between the 2 atoms.

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In O-H bonds in water, oxygen (O) is more electronegative than hydrogen (H) electronegativity difference is large.

So the probability that the bonding e- are closer to O is higher than to H.

The difference in electronegativity between O and H give rise to partial negative and positive charge.

δ+ = partial positive, δ- = partial negative This bond is called polar bond.

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In situation where electronegativity difference are small, sharing of e- in the bond is near to equal. Eg: C-H bond in CH4

This is called non-polar bond The bond in a molecule may be polar, but the

molecule itself can be non-polar because of its geometry. Eg: CO2

C=O is polar, but CO2 molecule is linear. A molecule where its atoms are positioned

linearly will become non-polar.

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In CO2 molecule, the attraction of the O for e- in one bond is cancelled out by the equal and opposite attraction for the e- by the O on the other side of molecule.

O = C = Oδ - δ -2δ +

δ = délta

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Water (H2O) is a bent molecule with a bond angle of 104.3 UC.

Unlike CO2 ,the e- sharing in H2O is uneven and are not cancelled out.

Therefore in H2O molecule, the e- are found at O end rather than the H end.

Bond with positive and negative ends are called dipoles.

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The radius called Van der Waal radius

Dipole moment

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1.5 Ionic and polar substance dissolve in water Ionic compounds (full charges)(KCl K+ and

Cl- in water) and polar compounds (partial charges) like dipoles such as ethanol, C2H5OH and acetone, (CH3)2C=O are tend to dissolve in water.

This is caused by electrostatic attraction between unlike charges.

Negative end of water dipole attracts positive ions, or positive end of other dipole.

Positive end of water dipole attracts negative ion (end) of other dipole.

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If aggregation of substance in water happens, its electrostatic force between unlike charge has lower energy, so the system is more stable and likely to exist.

Ion dipole interaction with water

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Polar compounds that easily dissolve in water includes alcohols, amines, carboxylic acids

Dipole-dipole of polar interaction in water (dipole-dipole interaction)

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Attraction between dipoles of these molecules and water molecules makes them dissolve.

Ionic and polar substance are called hydrophilic = water loving.

Hydrocarbons (C-H) are non-polar. No dipole-dipole and ion-dipole interaction in

hydrocarbons. Less energy between non-polar molecule and

water molecule Water molecule tends to associate with

themselves This is called hydrophobic = water hating

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Non-polar interactions called hydrophobic interaction

E.g. fatty acids and cholesterol

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Hydrogen bonding Hydrogen bonding = non-covalent interaction

of molecules, and special case of dipole-dipole interaction.

When hydrogen is covalently bonded with (very) electronegative atom (N or O), it has partial positive charge.

Partial positive charge can interact with unshared pair of e- (source of negative charge) on another negative atom.

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All 3 atoms aligned in straight line, forming hydrogen bond

Non-covalently bond One type of electro-static bond Weaker than covalentbond (20kJ mol-1)

Linear and non-linear hydrogen bond in water (draw non-linear hydrogen bond)

Hydrogen bon donor

Hydrogen bon acceptor

linear

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~20 kJ mol-1 of heat is released when hydrogen bonded water molecules form in water under standard conditions.

Standard conditions: 1 atm pressure, a temperature of 25C, and a concentration of 1M of reactants and products.

In other words, +20 kJ of heat energy is required to disrupt hydrogen bonds between water molecules.

FYI, energy required to break a covalent O-H bond is ~460 kJ mol-1, while energy to break a covalent C-H bond is ~410 mol-1 .

The strength of hydrogen bond is weak, only less than 5% of the strength of normal covalent bonds.

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In H 2 O hydrogen bonding forms tetrahedral structure of molecule, where

one H 2 O is hydrogen bonded to 4 other H 2 O molecules.

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Why can this happen? Explain.

Molecular weight

Melting point( $C)

Boiling point ( $C)

Water (H 2 O )18.02 0.0 100.0

Ammonia (NH3) 17.03 -77.7 -33.4

Methane (CH4)

16.04 -182.5 -161.5

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Hydrogen bonding also affects water as solvent.

Alcohols, amines, carboxylic acids, esters, aldehydes, ketones – all form hydrogen bond with water.

The polar solute serves as donor or acceptor of hydrogen bond.