Biochemistry

Chapter 6

Atoms and their interactions

Elements

Substances that cannot be broken down into simpler chemical substances90 naturally occurring 25 essential to life

Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) 96% of human bodyTrace elements present in small amounts Iron, magnesium, iodine

Atoms

Smallest particle of an element that has the characteristics of that elementNucleus central portion Protons positive charge Neutrons no charge

Atoms cont.

Electron cloud surrounds the nucleus Negative charge Travel in energy levels 1st level 2e- 2nd level 8e- 3rd level 8e- (18e- total)Most atoms have equal numbers of protons and electrons no net charge

Isotopes

Atoms of the same element containing different numbers of neutronsEffects mass only (not charge)Some are unstable radioactive

Carbon 12 6p and 6nCarbon 14 6 p and 8n

Compounds and bonding

Compound

Composed of atoms of 2 or more different elements that are chemically combinedWater H2O

Bonding occurs between atoms to reach stabilityStability = outermost energy level is full

Covalent bonding sharing e-

H2O: O 6e- in 2nd level H 1e- in 1st level

Most compounds in living organisms have covalent bonds strong

Ionic bonding gaining or losing e-

Produces ions charged particlesNaCl: Na 1e- in 3rd level Cl 7e- in 3rd level

Chemical reactions

Breaking and forming bondsAtoms are rearranged to form new substancesMetabolism all the chemical reactions in an organism

Chemical reactions cont.

Represented by chemical equations2H2 + O2 2H2O

2H2 + O2 are the reactants

2H2O is the product

The numbers of each atom must be = on each side of the equation

Mixtures and solutions

Mixture

Combination of substances that each retain their own propertiesCan easily be separatedSalt and pepper

Solution

1 or more substances (solutes) are distributed equally in another (solvent)Cannot easily be separatedKool-Aid sugar dissolved in water

Acids and bases

The pH scale

Water and diffusion

The importance of water

Essential for most life processesUniversal solventMeans of transport

Polarity unequal distribution of charge

e- not shared equally positive and negative ends to a moleculePolar molecules attract other polar molecules and ions (opposites attract)

Polarity continued

Form weak hydrogen bonds Cohesion water molecules stick together Adhesion water sticks to other molecules Capillary action water creeps up thin

tubes

Water resists temperature changes

Requires a lot of heat to increase water temperatureInsulator helps maintain homeostasisExpands when freezes ice is less dense that water and floats

Diffusion

Movement of particles from an area of high concentration to an area of lower concentrationDue to random movement of all molecules slowContinues until equilibrium is reached equal concentration on each side

Diffusion Demonstration

http://www.indiana.edu/~phys215/lecture/lecnotes/lecgraphics/diffusion2.gif

Diffusion cont.

Concentration gradient difference in concentration No energy required to move with the

gradient

Rate is affected by

Concentration higher concentration of molecules = faster diffusion

Temperature higher temperatures = faster diffusion

Pressure higher pressure = faster diffusion

Life substances

Role of carbon organic compounds (C-H bonds)

Can form 4 different bonds versatile Straight chains, branched chains,

rings Any number of C atoms infinite

number of structures Isomer same formula, different

structures

Role of carbon cont.

Polymers long chains of repeating units Made from smaller molecules bonded

together by the removal of water dehydration synthesis

Hydrolysis breaking apart polymers by adding water

Opposite ReactionsDehydration Synthesis Hydrolysis

Carbohydrates C:H:O in a 1:2:1 ratio

Used to store and release energyMonosaccharides simple sugars Building blocks of carbs Glucose C6H12O6

Forms of glucoseLinear (dry) form Ring (dissolved) form

Disaccharides 2 monosaccharides linked together Glucose + glucose maltose

Carbs cont.

Polysaccharides polymers of monosaccharides Used for food storage Starch (plants), glycogen (animals),

and cellulose

Lipids CHO

Less O than carbsUsed for energy storage, insulation, protection, cell membrane components

Nonpolar insoluble in waterBuilding blocks 3 fatty acids and 1 glycerol moleculeFats, oils, and waxes

Lipids cont.

Saturated fats C-C bonds are single Maximum amount of H Solid at room temperature Increase cholesterol levels cardiovascular

disease

Unsaturated fats some C-C double bonds Liquid at room temperature Plant products Hydrogenation converting unsaturated to

saturated by adding hydrogen

Proteins CHON

Used for tissue structure and cell metabolismBuilding blocks amino acids Humans need 20 different amino

acids Held together by peptide bonds

Proteins cont.

Number and order of amino acids determines the protein Each protein has a specific 3-D shape Shape determines function Denaturation changing the shape of

a protein impairs it’s function

Proteins cont.

Enzymes protein catalysts that change the rates of chemical reactions, but are not changed themselvesMost reactions will not occur without enzymesHighly specific 1 enzyme per substrate Lock and key model enzyme and substrate

fit together precisely to form an enzyme-substrate complex

Proteins cont.

Factors affecting enzyme action:Concentrations of enzyme and substrateTemperature 37oC (human body temp.)pH of environmentHomeostasis must be maintained in order for enzymes to function

Nucleic acids DNA and RNA

Store cellular information in code formBuilding blocks nucleotides 5-C sugar Nitrogenous base Phosphate group

Nucleic acids cont.

DNA deoxyribonucleic acid Double helix structure Watson and

Crick Sugar is deoxyribose Bases: cytosine, guanine, adenine,

thymineRNA ribonucleic acid Single strand Sugar is ribose Bases: cytosine, guanine, adenine,

uracil