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BIOLOGY 22 MODULE 1 – Chemical Basis of Life


Levels of Organization – biological functions are ultimately based on the properties of atoms and molecules


Subatomic particles – neutrons, electrons, protons






Complexes of compounds


Organelles – bodies within cells that perform specific functions



Specific combination of organelles

Can metabolize and reproduce

Least elaborate living structure

Significance of Chemistry/Physics in Biology


Biology based on chemistry


Chemistry based on physics

Important Concept in Chemistry


Matter, Atoms, Atomic Structure Matter – anything that has mass and occupies space (e.g. solid, liquid, gas, plasma)

Atomic Theory – Dalton


All matter is made of atoms

All atoms are made of subatomic particles

Atoms – units of matter

Bohr – proposed structure of atom (similar to solar system)

Parts of atoms





Electron – in an electron cloud

Important concepts

Electrons are arranged in shells according to energy

levels Filled innermost shell – 2 electrons Filled outermost shell – 8 electrons

Same number of valence = similar chemical behaviors



Compounds / Molecules

Pure substances made of one kind of atom

Cannot be decomposed


Chemical reaction – processes where atoms combine/break with

other atoms Molecule – two or more atoms, may be same atoms (e.g. H2)

Compound – molecule containing at least 2 kinds of atoms (e.g.



Chemical Bonds

Ionic Bond


One atom gains electrons, one atom loses electrons

Bond strength = 5-10 kcal/mol

Cations – atom that loses electrons (+) Anions – atom that gains electrons (-)

Covalent Bond


Two or more atoms share electrons

Electrons behave as if they belong to each atom

Bond strength = 50-100 kcal/mol



Nonpolar covalent – e.g. H2


Atoms of the same element

Equal sharing

No charge

Does not mix with polar covalent bonded molecules


Polar covalent – e.g. H2O


Atoms of different elements

Unequal sharing

One of the shared electrons tends to get

pulled towards one element Resulting molecule has a positive and negative

end Greater pull = more electronegative atom

Hydrogen Bond


Formed between water molecules

Slightly positive end of one molecule is attracted to slightly

negative end of another molecule Bond strength = 3-5 kcal/mol

Stabilize DNA

Represented by dotted line

Van der Waal’s Forces – e.g. antigen-antibody, insect on ceiling

Occur where electron clouds overlap, creating weak

attraction Bond strength = 1-2 kcal/mol



Free Radicals Molecules containing atom with a single unpaired electron in outer shell Steals electrons from other atoms, creating more free radicals from donor molecules Can do harm by disrupting biomolecule structure Represented by a dot next to atomic symbol

Chemical Reactions Synthesis reaction – e.g. glucose glycogen; amino acids proteins


A + B AB


Decomposition reaction – e.g. fats glycerol + fatty acids


AB A + B


Exchange reaction


Double displacement


Reversible reaction

End product can revert to the original combining reactants

Inorganic Compounds – ionically bonded molecules required for biological functions; NO CARBON

o Water



Most abundant in biosphere

75% of earth’s surface

60% of RBC

75% of muscle 92% of blood plasma 65-75% in living organisms (average) 58% in humans



Polar covalent bond of H and O

Hydrogen bond between H2O molecules

Ice = crystalline structure



Water molecules are highly dipolar


Excellent solvent + suspending medium

Participant in many chemical reactions



Water molecules are cohesive


Molecules tend to stick together

Highest surface tension due to H bonds


Water molecules are adhesive


Molecules tend to stick to surfaces

Capillary action drawn into small channels


Water expands when it crystallizes

Water reaches highest density at 4C


Ice is less dense than water floats

Allows for organisms to live in ponds/lakes during


winter Water has a high specific heat


Absorbs and releases heat very slowly

Maintains temperature in oceans


Water has a high heat of vaporization


Needing a lot of heat to convert from liquid to gas


Water has neutral pH



Needed for life to exist

Raw material in photosynthesis basis of life

Major component in hydrological cycle cycling of matter

and nutrients, dissipates energy

o Acids and Bases


Substances that give off H+ in solutions

Proton donors

pH < 7


Substances that give off OH- in solutions

Proton acceptors

pH > 7


Degree of acidity or alkalinity based on concentration of H+

in solution pH = -log [H+]


Buffer systems – e.g. carbonate-bicarbonate system in blood


Mechanisms that maintain homeostatic pH values

React with strong acids/bases, replace them with weak acids/bases



Yield neither H+ nor OH-

Do not affect pH

Formed by reaction of acid and base


Trace Elements – elements occurring in nature and needed in smaller amounts in biological systems

Magnesium – chlorophyll, enzymes

Iodine – thyroxin

Iron – hemoglobin

Calcium – bone

Sodium – nerve impulse

Chlorine – digestive chemicals, photosynthesis

Potassium – nerve impulse

Organic Compounds / Biomolecules – very complex molecules responsible for “living” properties exclusive distribution in living/previously living matter


Chemical composition principal bonds = C-C and C-H


Unique/Exclusive Properties of Carbon

Carbon is versatile


Can form as many as 4 covalent bonds with other atoms


Carbon can be joined into various structures


Rings – e.g. benzene

Linear chains that vary in length and location of double

bonds – e.g. butane Branches – e.g. isobutane

2D structures

3D structures


Properties of Organic Compounds

Can react with various other compounds to form different

molecules Large size, do not dissolve easily (nonpolar)

Useful materials for body structure

Carbon + covalent bonds = good source of energy

C-C bonds are shorter and more stable at different temperature

C-C = shortest bond known Stability of life exists in extreme environments


Functional Groups – groups to atoms attached to C backbone; where most chemical reactions happen (break C-C, transfer groups)






= insoluble in H2O


= nonpolar

does not form H bonds


= shared electrons




= soluble in H2O


= forms H bonds

= in alcohols, sugars


-C= O


= forms H bonds


= in sugars

= C=O + H = aldehyde

= C=O w/o H = ketone




= forms H bonds


= acid

= ionized to COO-

= in lipids




= forms H bonds


= base

= ionized to NH3+




= very soluble


= forms H bonds

= always ionized




= forms weak H bonds


= HS + HS S-S

= in polypeptides




Molecules with same elemental ratios occur in different

spatial arrangements/structures Biological molecules = amazing variety of forms


Structural isomers – e.g. nitrogenous bases (A T C G)


Differ in arrangement of covalent bonds


Geometric isomers


Always involve arrangement around a double bond

Trans – different sides of double bond

Cis – same side of double bond Important in enzymes




Isomeric forms that form when carbon is bonded to 4

different functional groups Form a 3D tetrahedron





Consists of C, H, O O, H in a 2:1 ratio

Formula = Cx(H2O)y

Functional groups – hydroxyl, carbonyl

Bonds – glycosidic


Monosaccharides – simple sugars


Monomers building blocks of carbohydrates

3 carbons = triose


4 carbons = tetrose

5 carbons = pentose ribose, deoxyribose

6 carbons = hexose most abundant glucose,

fructose, galactose, etc. Disaccharides – from dehydrations synthesis of 2 monosaccharides


Maltose (malt sugar) = glucose + fructose

Sucrose (cane sugar) = glucose + fructose

Lactose (milk sugar) = glucose + galactose

Oligosaccharides – 8-12 monomer units cell membrane

Polysaccharides – more than 20 monomer units (e.g. dextrines)


100s or 1000s of glucose units

Animal starch

Highly branched

Unstable, metabolizable, decomposable


Principal storage product in plant

Moderately branched

Unstable, decomposable


2000 glucose units

Plant cell wall


Very stable

Digested by cellulose


Tough structural nitrogenous polysaccharide

Exoskeleton of insects, cell wall of fungi




Structural polysaccharide

Major C H O in connective tissue matrix


Fibers – e.g. hemicelluloses, pectins, gums, mucilages


Stable, unbranched

Dietary fiber vehicle for toxin elimination

Gives feeling of fullness

Lowers risk of cancer / cardiovascular disease, obesity, etc.



Condensation reaction


Formation of carbohydrates by removal of H2O

Dehydration synthesis




Breaking of carbohydrates by addition of H2O




Series of dehydration synthesis of simple sugars

resulting in polysaccharides


Structural building blocks of DNA and RNA deoxyribose

and ribose Energy rich molecules glycogen

Major component in connective tissue matrix glycosaminoglycans



Definition and structure

Large organic compounds that are insoluble in water but

soluble in organic solvents (e.g. ether, chloroform, alcohol) Glycerol


3C alcohol with 3OH

Backbone of lipid

Fatty acids


Building blocks C H O in chains

Have a terminal carboxylic group confers acidity

Formic acid – formalin

Acetic acid Propionic acid Butyric acid – butanol Functional groups – carboxyl

Bonds – ester bonds



Simple lipids – triglyceride (fats)


3 fatty acids + glycerol bonded with ester bond

Saturated fats no double bond (linear)


Animal origin except for coconut oil

Solid at room temperature

Raise cholesterol level


Unsaturated fats w/ double bond (bent)


Plant origin

Liquid at room temperature

MUFA – monosaturated fatty acid single

double bond PUFA – polysaturated fatty acid more than 1

double bond (healthier) Lower cholesterol level


Trans fatty acids – e.g. margarine, spreads, dairy, etc.


MUFA/PUFA undergo partial hydrogenation

removal of double bonds Product = similar to saturated acid


Complex lipids – fatty acids + glycerol + additional group


Phospholipids – e.g. lecithin


Glycerol + 2 fatty acids + phosphate

Cell membrane

Also in brain cells and nerves




Myelin sheath




Alcohol + 1 fatty acid

H2O repellent, cell wall protection


Steroids – lipids without fatty acid tail


Skeleton of 4 interlocking C rings

e.g. vitamin D, cholesterol, sex hormones, ecdysone



Esterification – removal of H2O formation of fats

Ester bond holds fats together

Glyoxidic cycle – conversion of fatty acids to glucose



Energy storage 2x more than glycogen

Cushioning and protection of organs

Insulation adipose tissue


Diffusion through cell membrane


Impulse conduction


Water repellent

Cell wall protection in mycobacteria


Message transmission

Membrane fluidity


Proteins Definition and Structure

Biomolecules made out of amino acids

Amino acids


C center + H + COOH + NH2 + R group

Unique properties from R group

21 known amino acids

Essential amino acids – cannot be easily produced by

body acquired through diet Nonessential amino acids can be produced by

body glycine – simplest amino acid

cysteine – gives toughness to proteins (S) Diversity of proteins from various combinations of amino

acids Functional groups – carbonyl, amino, sulfhydryl, others

Bonds – peptide bonds

Structural Organization

Primary structure – e.g. ribonuclease (124 amino acids)

In ribosomes

Linear sequence of 40-1000 amino acids

Joined by peptide bonds

Not functional

Secondary structure


Binding of primary structures

Hydrophilic end attracted to aqueous surface of

molecule Hydrophobic end attracted to non-aqueous center of molecule Joined by H bonds

Helical structure – alpha helix

Sheet structure – beta pleated sheet Not functional

Tertiary structure


Globular (3D) structure

Joined by numerous bonds


Hydrophobic – Van der Waal’s forces

H bonds

Ionic bonds – C+ attracts electrons

Covalent bonds – between HS



Most proteins are tertiary

Quaternary structure


Two or more polypeptide chains join into one

molecule Numerous bonds (same as tertiary)

hemoglobin 2 alpha helix + 2 beta pleated sheet collagen 3 chains of fibrous protein



Protein synthesis/translation


Creation of protein in ribosomes from mRNA

Involves removal of H2O

Molecular Techniques


Immunoprecipitation – determine structure of protein

constituents Gel electrophoresis – differentiation of complex proteins



Proteins sensitive to heat, pH, electricity, pressure, etc.

Denaturation – environmental factors disruption of bonds unfolding of protein loss of 3D conformation loss of function

Types and Functions Protein Type



Catalytic – speed up chem rxn

= enzymes


= ovalbumin


= casein

= seed protein



= hemoglobin


= myoglobin hemoglobin in

muscle tissue (enhanced)

albumin transport fatty acids



Contractile – muscle function

= actin


= myosin


Protective – immune function

= antibodies


= fibrinogen in blood clotting

= thrombin in blood clotting



= hemotoxin


= neurotoxin


Hormones – regulation

= insulin



= GH


Structural – support/strength

= collagen most abundant


= elastin

= glycoproteins

= keratin hair, nails




Biological catalysts that speed up chemical reactions

Lower activation energy

Activation energy – energy needed to start a reaction


Low activation energy – reaction starts easily

Methods to lower activation energy


Increasing temperature increased collision

of molecules DISADVANTAGE: denaturation Use of a catalyst

Nature of enzymes

Enzyme – protein with active sites produces

enzyme-substrate complex Enzyme action VERY SPECIFIC


Lock and key model

Simple binding of substrate to enzymecomplex Enzyme action VERY SPECIFIC Models Lock and key model Abandoned implication that enzyme never changes

Abandoned implication that enzyme never changes implication that enzyme never changes

Induced fit model Enzyme alters shape to better accommodate substrate Enzyme dynamic More acceped

better accommodate substrate Enzyme dynamic More acceped Enzymes function with:   Cofactors - minerals
better accommodate substrate Enzyme dynamic More acceped Enzymes function with:   Cofactors - minerals
better accommodate substrate Enzyme dynamic More acceped Enzymes function with:   Cofactors - minerals

Enzymes function with:


Cofactors - minerals

Coenzymes – vitamins + nucleic acid

Important factors in enzyme function


Temperature – 38C peak function

pH peak depending on enzyme

R groups

Charge of substrate


Enzymes form complexes with substrate but retain

their identity after the reaction Enzymes may detach from substrate

o Nucleic Acids



First isolated by Meischer from pus cell nuclei

Secret to life (NOT PROTEIN)

Polymer of nucleotides

Functional groups – hydroxyl, carbonyl, phosphate

Bonds – phosphodiester bonds



Pentose sugar component deoxyribose / ribose

Phosphate group

Nitrogenous bases


Purines – adenine, guanine

Pyrimidines – cytosine, thymine, uracil




Nucleoside structure = nitrogenous base + sugar

Nucleotide structure = nitrogenous base + sugar + phosphate group

Derivatives of Nucleotides

Energy carrier molecules ADP, ATP

High energy phosphate bonds + pentose sugar +

nitrogenous base Adenine in adenosine

Cofactors and coenzymes NAD, FAD

Signaling molecules endocrine function

Nucleic acids

Polymer of nucleotides

Storage of biological information


Outside – sugar + phosphate backbone bonded by phosphodiester bond

Inside – specific nitrogen base pairs stablized by hydrogen bond

Chargaff’s Rule

Adenine to thymine

Guanine to cytosine


DNA – deoxyribonucleic acid

DNA – deoxyribonucleic acid
DNA – deoxyribonucleic acid
DNA – deoxyribonucleic acid
DNA – deoxyribonucleic acid
DNA – deoxyribonucleic acid
DNA – deoxyribonucleic acid

Deoxyribose sugar

Adenine, thymine, guanine, cytosine

Double alpha-helix


RNA – ribonucleic acid


Ribose sugar

Adenine, uracil, guanine, cytosine

Single strand

Central Dogma of Biology

DNA transcribed to mRNA in nucleus

mRNA translated to protein in rough endoplasmic reticulum

DNA replicated to DNA in nucleus