Sei sulla pagina 1di 14

BIOLOGY 22 MODULE 1 – Chemical Basis of Life

v2.0

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

o

Subatomic particles – neutrons, electrons, protons

o

Atoms

o

Compounds

o

Complexes of compounds

o

Organelles – bodies within cells that perform specific functions

o

Cell

Specific combination of organelles

Can metabolize and reproduce

Least elaborate living structure

Significance of Chemistry/Physics in Biology

o

Biology based on chemistry

o

Chemistry based on physics

Important Concept in Chemistry

o

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

 

Nucleus

Proton

Neutron

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

o

Elements

Compounds / Molecules

Pure substances made of one kind of atom

Cannot be decomposed

o

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.

H2O)

o

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

Types

 

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

o

o

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

Anabolism

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

 

AB A + B

Catabolism

Exchange reaction

 

Double displacement

AB + CD AC + BD

Reversible reaction

End product can revert to the original combining reactants

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

o Water

Abundance

 

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

Structure

Tetrahedral

Polar covalent bond of H and O

Hydrogen bond between H2O molecules

Ice = crystalline structure

Properties

 
 

Water molecules are highly dipolar

 

Excellent solvent + suspending medium

Participant in many chemical reactions

Lubricant

 

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

Functions

 
 

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

Acids

Substances that give off H+ in solutions

Proton donors

pH < 7

Bases

Substances that give off OH- in solutions

Proton acceptors

pH > 7

pH

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

o

Salts

Yield neither H+ nor OH-

Do not affect pH

Formed by reaction of acid and base

o

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

o

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

o

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

o

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

o

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

Group

Name

Characteristics

H-C-H

Hydrocarbon

= insoluble in H2O

 

= nonpolar

does not form H bonds

=

= shared electrons

 

-OH

Hydroxyl

= soluble in H2O

 

= forms H bonds

= in alcohols, sugars

 

-C= O

Carbonyl

= forms H bonds

 

= in sugars

= C=O + H = aldehyde

= C=O w/o H = ketone

 

-COOH

Carboxyl

= forms H bonds

 

= acid

= ionized to COO-

= in lipids

 

-NH2

Amino

= forms H bonds

 

= base

= ionized to NH3+

 

-PO4

Phosphate

= very soluble

 

= forms H bonds

= always ionized

 

HS

Sulfhydryl

= forms weak H bonds

 

= HS + HS S-S

= in polypeptides

o

Isomers

Definition

Molecules with same elemental ratios occur in different

spatial arrangements/structures Biological molecules = amazing variety of forms

Types

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

 

Enantiomers

 

Isomeric forms that form when carbon is bonded to 4

different functional groups Form a 3D tetrahedron

o

Carbohydrates

Definition

 

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

Formula = Cx(H2O)y

Functional groups – hydroxyl, carbonyl

Bonds – glycosidic

Classification

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)

Glycogen

100s or 1000s of glucose units

Animal starch

Highly branched

Unstable, metabolizable, decomposable

Starch

Principal storage product in plant

Moderately branched

Unstable, decomposable

Cellulose

2000 glucose units

Plant cell wall

Unbranched

Very stable

Digested by cellulose

Chitin

Tough structural nitrogenous polysaccharide

Exoskeleton of insects, cell wall of fungi

 

Glycosaminoglycans

 

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.

Mechanisms

 
 

Condensation reaction

 

Formation of carbohydrates by removal of H2O

Dehydration synthesis

 

Hydrolysis

 
 

Breaking of carbohydrates by addition of H2O

 

Polymerization

 
 

Series of dehydration synthesis of simple sugars

resulting in polysaccharides

Functions

Structural building blocks of DNA and RNA deoxyribose

and ribose Energy rich molecules glycogen

Major component in connective tissue matrix glycosaminoglycans

o

Lipids

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

Classification

 
 

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

 

Sphingolipids

 

Myelin sheath

 

Waxes

 

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

Mechanisms

 
 

Esterification – removal of H2O formation of fats

Ester bond holds fats together

Glyoxidic cycle – conversion of fatty acids to glucose

Functions

Fats

Energy storage 2x more than glycogen

Cushioning and protection of organs

Insulation adipose tissue

Phospholipids

Diffusion through cell membrane

Sphingolipids

Impulse conduction

Waxes

Water repellent

Cell wall protection in mycobacteria

Steroids

Message transmission

Membrane fluidity

o

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

 

Functional

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

Mechanisms

 

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

Denaturation

 

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

 

Examples

Catalytic – speed up chem rxn

= enzymes

Storage

= ovalbumin

 

= casein

= seed protein

 

Transport

= 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

 

Toxins

= hemotoxin

 

= neurotoxin

 

Hormones – regulation

= insulin

 

= ACTH

= GH

 

Structural – support/strength

= collagen most abundant

 

= elastin

= glycoproteins

= keratin hair, nails

Enzymology

Enzyme

 
 

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

Models

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

Reversibility

Enzymes form complexes with substrate but retain

their identity after the reaction Enzymes may detach from substrate

o Nucleic Acids

Definition

 
 

First isolated by Meischer from pus cell nuclei

Secret to life (NOT PROTEIN)

Polymer of nucleotides

Functional groups – hydroxyl, carbonyl, phosphate

Bonds – phosphodiester bonds

Structure

 
 

Pentose sugar component deoxyribose / ribose

Phosphate group

Nitrogenous bases

 

Purines – adenine, guanine

Pyrimidines – cytosine, thymine, uracil

 

Structures

 

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

Structure

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

Types

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