unit ii - biochemistry big campbell ~ ch 2-5 baby campbell ~ ch 2-3

UNIT II - BIOCHEMISTRYBig Campbell ~ Ch 2-5

Baby Campbell ~ Ch 2-3

I. CHEMICAL BASIS OF LIFE

• Elementso Cannot be broken down without losing characteristic

propertieso Six elements in greatest concentration in living things are

Sulfur Phosphorus Oxygen Nitrogen Carbon Hydrogen

o Defined by Atomic # which is = #of protons and the #of electrons in most cases

I. CHEMICAL BASIS OF LIFE, cont

• Atomso Smallest unit of matter

that retains properties of that element Protons (+); found in

nucleus Neutrons (neutral);

found in nucleus Electrons (-); found in

electron clouds.

o Atomic Mass = p + no Isotopes – when an

atom has a different atomic mass, Ex: C12, C13, C14

I. CHEMICAL BASIS OF LIFE, cont• Chemical Bonds

o Chemical behavior of atom determined by valence electronso Atoms interact with other atoms to complete their valence shells,

either by transferring or sharing electrons

I. CHEMICAL BASIS OF LIFE, cont

• Types of Chemical Bondso Ionic – Results when one atom has a much stronger

attraction for electrons than another; one atom has a greater electronegativity. Electron(s) are transferred resulting in formation of ions. Bond forms due to charge attraction. Strength is dependent on environment

I. CHEMICAL BASIS OF LIFE, conto Covalent Bonds – More stable;

results from sharing a pair of valence electrons. Forms a molecule. One pair of electrons shared = single covalent bond; two pair of electrons shared = double covalent bond.Non-polar covalent bond –

formed when electronegativity of atoms is the same

Polar covalent bond – formed when one atom is more electronegative; unequal sharing of electrons results in slight charges at either end of molecule

II. WATER• Properties of Water Due to its

Polarityo Hydrogen “bonds”

II. WATERo “Stickiness”

Cohesion Surface Tension

AdhesionCapillary Action

II. WATER, conto Regulation of Temperature

High specific heat High heat of vaporization

o Density of “solid” water _<_ density of liquid water

II. WATER, conto Solvent of Life

Hydrophilic “Water-loving” Polar molecules

“pull apart” ionic compounds & other polar molecules

Hydrophobic “Water-hating” Non-ionic and non-

polar substances are repelled by water

II. WATER, cont

• Dissociation of Watero Rare, but measurable phenomenono (2)H2O → H3O+ + OH- → H+ + OH-

o In aqueous solution at 25˚C, total conc of [H+] [OH-] = 1x10-14

Neutral solution → [H+] = [OH-]; therefore [H+] = 1 x 10-7

o pH = Provides a means for a compressed measurement of [H+] -log10[H+]

o Acid – Substance that dissolves in water to __increase_ [H+] [H+] _>___ 1 x 10-7; pH __<__ 7

o Base - Substance that dissolves in water to _decrease_ [H+] [H+] _<___ 1 x 10-7; pH _>_ 7

o pH of Water = 7

II. WATER, cont

o Buffers Maintain a constant pH by donating, accepting H+

Bicarbonate Buffer System Very important buffer system in blood pH of blood = _7.4_

III. ORGANIC CHEMISTRY – THE STUDY OF CARBON

• Atomic Structure of Co Atomic Number of C = 6

6 protons 6 electrons __4___ valence electrons

o Hydrocarbon – composed on only C-H; impt in fossil fuels. Hydrophobic

o Isomer – compounds with the same #of elements/atoms, but a different structural arrangement. See Ex…

Four Ways Carbon skeletons can vary

III. ORGANIC CHEMISTRY, contFunctional Group Structure Characteristics

Hydroxyl-OH may be written as HO-

Very polar; forms “ –ols” (alcohols)

Carbonyl

C=O, also written -CO Ketone – if carbonyl group is within the carbon skeleton

Aldehydes – if carbonyl group is at the end of the carbon skeleton.

Carboxyl-COOH; c alled carboxylic acids

Acts as an acid; donates H+ to solution

III. ORGANIC CHEMISTRY, cont

Functional Group Structure Characteristics

Amino-NH2; called amines Acts as a base; removes H+

from solution

Sulfhydryl-SH; called thiols Important in stabilizing protein

structure; forms disulfide bridges

Phosphate-OPO3; known as organic phosphates

Gives molecule negative charge; react with water to release energy

Methyl-CH3 Affects the expression of

DNA

IV. THE BIOMOLECULES

• Most are polymers made up of single units called monomers

• Four Main Groups CARBOHYDRATES

LIPIDS

PROTEINS

NUCLEIC ACIDS

IV. BIOMOLECULES, cont• Dehydration Synthesis

o Also called _CONDENSATION REACTION__o Reaction that occurs to build polymerso Forms __COVALENT_ bond between 2 monomerso _WATER_lost as waste producto Requires energy input, enzymes

IV. BIOMOLECULES, cont• Hydrolysis

o “__WATER BREAKING/SPLITTING_”o Covalent bonds between monomers broken Releases energy;

reaction accelerated with enzymes

V. CARBOHYDRATES

• Provide fuel, act as building material• Generally, formula is a multiple of CH2O

• Contain carbonyl group & multiple hydroxyl groups• Monomer = monosaccharides• Monosaccharides – usually found as ringed structures

o PentosesRibose

Deoxyribose

V. CARBOHYDRATES, conto Hexoses

GlucoseFructoseGalactose

V. CARBOHYDRATES, cont• Disaccharides

o 2 monosaccharides covalently bonded together through dehydration synthesis

o ExampleSucroseLactoseMaltose

V. CARBOHYDRATES, cont• Polysaccharides

o Many monosaccharides covalently bonded together through dehydration synthesis

o Two main groups Energy Storage Polysaccharides

Starch – Plants store glucose as starch in cell structures called plastids. Humans have enzymes to hydrolyze starch to glucose monomers.

Glycogen – Storage form of glucose in animals. More highly-branched than starch. In humans, found mainly in liver, muscle cells

V. CARBOHYDRATES, cont Structural polysaccharides

Cellulose – polymer of glucose. Every other glucose is upside down – forms parallel strands of glucose molecules held together with H-bonds

V. CARBOHYDRATES, contStructural polysaccharides• Chitin – found in arthropod

exoskeleton, cell walls of fungi

VI. LIPIDS• Very diverse group• Non-polar, hydrophobic molecules• Hydro_phobic__• Not true polymers• Four groups

Fats & oils phospholipids steroids waxes

VI. LIPIDS, cont

• Fats& Oilso Composed of

glycerol + 3 fatty acids

o Glycerol = 3-C alcohol

o Fatty acids – long hydrocarbon chains ending with carboxyl group

o AKA triglycerideso Used for energy

storage

VI. LIPIDS, cont

Saturated fats – “Saturated with hydrogens”; contain all single bonds. Typically from animal source, solid at room temp. Associated with greater health risk.

Unsaturated fats – Contain double bonds, fewer H-atoms. Results in “kinked” hydrocarbon chain. Typically from plant source, liquid at room temp.

Fats, cont.

• Saturated fat • Unsaturated fat

VI. LIPIDS, cont

• Phospholipids 2 fatty acids

attached first 2-carboxyl groups of glycerol.

Negatively-charged phosphate group is attached to 3rd carboxyl

Partially polar and partially non-polar

Found in all cell membranes.

Phospholipid, cont.

VI. LIPIDS, cont• Waxes – One fatty acid attached to an alcohol. Very

hydrophobic. Used as coating, lubricant• Steroids – Consist of 4-rings with different functional

groups attached. o Cholesterol – steroid found in animal cell membranes;

precursor for sex hormones

Steroids, cont.

VII. PROTEINS

• Important part of virtually all cell structures, processes, reactions

• Amino Acids – Proteins are large polymers made up of amino acid monomers. All amino acids have the same basic structure:

o Amino groupo Carboxyl groupo Carbon, known as alpha carbono R group → variable component; gives each amino acid its unique

properties. Determines whether amino acid is classified as polar, non-polar, acidic, or basic.

VII. PROTEINS, cont

VII. PROTEINS, cont

VII. PROTEINS, cont

VII. PROTEINS, cont

• Amino Acid → Proteino Dehydration synthesis results in formation of a peptide bondo Polypeptide – many amino acids covalently bonded together

VII. PROTEINS, cont

• Protein Conformation o Protein’s shape is related to its function. Generally, a

protein must recognize/bind to another molecule to carry out its function.

o Denaturation - A change in a protein’s shape. Results in a loss of protein’s ability to carry out function.

o Four levels of protein structurePrimarySecondaryTertiaryQuaternary

VII. PROTEINS, cont

Primary – Sequence of amino acids

VII. PROTEINS, cont Secondary – Coiling of polypeptide chain due to formation of H-bonds

between H of amino end of one aa and OH of carboxyl end of another aa Alpha helix – created from H-bonds forming within one pp chain Beta pleated sheet – H-bonds form between aa in parallel pp chains

VII. PROTEINS, cont Tertiary - Involves

interactions between R groups of amino acids. Helps to give each protein its unique shape.

VII. PROTEINS, cont

Quaternary – Proteins that are formed from interactions between 2 or more polypeptide chains folded together. Examples include hemoglobin, collagen, chlorophyll

VII. PROTEINS, cont• Enzymes

o Biological catalysts that act by lowering activation energy; that is, the amount of energy needed to get the reaction going

o Only catalyze reactions that would normally occuro Recycled – not used up or changed by the reactiono Temperature and pH sensitiveo Substrate specific

VII. PROTEINS, cont

o Induced fit – As enzyme envelops substrate, a slight change takes place in bond angles, orientation of atoms. Allows chemical rxns to occur more readily

o Inhibition of Enzyme Function Competitive inhibitor – mimics

normal substrate Non-competitive inhibitor –

attaches to another part of enzyme; changes shape of active site

VII. PROTEINS, conto Regulation of enzyme

function Allosteric Regulation –

binding of a molecule to enzyme that affects function of protein at another site

Feedback Inhibition – as end product is synthesized and accumulates, enzyme is inactivated → switches off metabolic pathway

VIII. NUCLEIC ACIDS

• Nucleic acid group includes DNA, RNA, ATP

• Monomers = _NUCLEOTIDES_ Composed of

Pentose deoxyribose (DNA) ribose (RNA)

Phosphate group Nitrogen base

• Polymers formed through _dehydration synthesis__ Phosphate group of one

nucleotide covalently binds to sugar of next

VIII. NUCLEIC ACIDS, cont Nitrogen Bases

Pyrimidines – Single-ringed structure

Thymine Cytosine Uracil

Purines – Double-ringed structure

Adenine Guanine

VIII. NUCLEIC ACIDS, cont• DNA