Biochemistry. All Matter is composed of Atoms The Structure of the Atom Electrons: Negative...

Biochemistry

All Matter is composed of

Atoms

The Structure of the AtomElectrons: Negative electrical charge

Protons: Positive electrical charge

Neutrons: No net electrical charge

Molecules

• Two or more atoms held together by

Chemical bonds

Chemical Bonds

• form because of the interactions between the electrons of the atoms

The atom’s ELECTRONEGATIVITY

(ability to attract electrons)

• Determines the type and strength of the Chemical bond

Ions• Ions are atoms that have either a

positive or negative

electrical charge because the

electron number is NOT equal to

the proton number

IONIC BONDS

• Form between atoms when electrons are TRANSFERED

from one atom to another forming ions of opposite

electronic charges• http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/

anim/anim0904.htm

Covalent Bonds• Form when atoms share

electrons• Occur when the

electronegativities between the atoms are similiar

• http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/anim/anim0904.htm

• Some molecules have Single Covalent Bonds… which means

the atoms share one pair (a single pair) of electrons

• Some molecules have Double Covalent Bonds… which means

the atoms share two pairs of electrons

• Some molecules have Triple Covalent Bonds… which means the atoms share Three pairs of

electrons

Nonpolar Covalent Bonds

• Occur when the electronegativities of both atoms are identical and the

electrons are shared equally

Polar Covalent Bonds

• Occur when the electronegativities of both atoms are Different and the

electrons are shared unequally

Negative Pole

Positive Pole

Hydrogen Bonds

• Hydrogen bonds are weak bonds which form between molecules

Hydrogen Bond

Bond Strengths• Ionic Bonds are weak and are easily

broken in water

• Covalent Bonds are generally strong

• Hydrogen Bonds are very weak

The Properties of Water

• 1. Water is the UniversalUniversal Solvent.

• Ionic compounds and Polar covalent molecules readily

dissolve in water

Hydrophilic Molecules (water-loving)

• Are substances that dissolve in water…. Salts,

sugars, etc….

Hydrophobic Molecules (water-fearing)

• Are substances that do not dissolve in water… oils,

waxes, etc…

Water Has A High Specific HeatCapacity…. The capacity of a

substance to change temperature in response to a gain or loss of heat… water changes temperatures very

slowly• Specific Heat - the amount of heat needed to

raise 1 g of the substance 1 degree C.

• Why? ……… Hydrogen bonding.

Water Has A High Heat Of Vaporization

• Heat of Vaporization: the quantity of heat a liquid must absorb for 1g of it

to convert to a gaseous state.

Liquid Water Is Cohesive

• Water sticks to water.

• Why?

Because the polarity of water results in hydrogen bonding.

Liquid Water is Adhesive

• Water sticks to other molecules.

• Why?

Hydrogen bonding.

Water transport in trees uses Cohesion and Adhesion

Water Has A High Surface Tension• The surface

of water is difficult to stretch or

break.

• Why?

• Hydrogen bonding.

Water Stabilizes Temperature

• Water can absorb and store a huge amount of heat from the sun.

• Result - climate moderation

• Result - organisms are able to survive temperature changes.

Evaporative Cooling

Result:• Water cools organisms from

excessive heat buildup.

• Why?

As water evaporates it takes the heat with it.

Water Expands and becomes less dense when It Freezes….so

it floats

• The distance between water molecules INCREASES from the liquid to the solid form.

• Why?

• Hydrogen bonding

Water Benzene

Floats Sinks

Result

• Ice floats and forms an blanket of insulation during the

winter……….Aquatic life

can live under ice.

Water is used to make Solutions

• A Solution is a Homogeneous mixture of two or more

substances.

• Solvent + Solute Solution

• Sugar water, Saltwater, Pepsi

Solvent

• The dissolving agent

• Present in a greater proportion

Examples:

• Water

• Methane

Solute

• The substance that is dissolved.

• Present in smaller quantity

Examples:• Salt in saltwater

• Sugar in sugar water

Solution Concentration

• Usually based on Molarity

• Molarity - the number of moles of solute per liter of solution.

• A mole is = 6.021x1023

One Mole of each

Sulfur

Sugar

Copper Sulfate

Mercury Oxide

Copper

Sodium Chloride

Dissociation of Water

• Water can sometimes split into two ions.

• In pure water the concentration of each ion is 10-7 M

• Adding certain solutes disrupts the balance between the two

ions.

• The two ions are very reactive and can drastically affect a cell.

Acids• Materials that can release H+

Example: HCl HCl H+ + Cl-

Hydrochloric acid, vinegar, etc…

Effects of Acid Rain

Bases

• Materials that can absorb H+

• Often reduce H+ by producing OH-

Example: NaOH NaOH Na+ + OH-

Drano, Soaps, etc…….

pH Scale

• A logarithmic scale for showing H+ concentration in a solution.

pH = - log [H+]

pH Scale

Acids: pH < 7Acids: pH < 7Neutral: pH 7Neutral: pH 7Bases: pH >7Bases: pH >7

• Acids: pH <7 etc.

• Bases: pH >7 etc.

Each pH unit is a 10x change in H+

Buffers• Materials that have both acid

and base properties.• Resist pH shifts.• Cells and other biological

solutions often contain buffers to prevent damage.

Organic Molecules

• Contain carbon atoms, exceptions are carbon monoxide and carbon dioxide

• Carbon has 4 electrons available to form 4 chemical bonds….therefore large molecules

are easily formed using carbon as the backbone.

• Large carbon based molecules are usually found as long chains or rings.

Macromolecules

• Most macromolecules are “polymers”“polymers” ….molecules that consist of a single unit (monomermonomer) repeated many times.

Functional Groups

• Many organic molecules share similar properties because they have similar clusters of atoms, called the….. Function GroupsFunction Groups

• Each Functional Group gives the Each Functional Group gives the molecules a particular property, molecules a particular property,

such as acidity or polarity.such as acidity or polarity.

Functional Groups

Four Main Types Of Macromolecules

• CarbohydratesCarbohydrates

• LipidsLipids

• ProteinProtein

• Nucleic acidsNucleic acids

Carbohydrates

• Used for fuel, building materials, and receptors.

• Made of C,H,O

• General formula is CH2O

• C:O ratio is 1:1

Types Of Carbohydrates

• Monosaccharides

• Disaccharides

• Polysaccharides

Monosaccharides• Mono - single• Saccharide - sugar• Simple sugars.• Can be in linear or

ring forms.• Glucose, Fructose,

Galactose…. all with the chemical formula C6H12O6….. Same chemical formula, different shapes.

• Most words ending with the letters OSE are carbohydrates.

Glucose, Fructose, Galactose

Disaccharides

• Sugar formed by joining two monosaccharides together thru the process of Dehydration

Synthesis….(removing water)…aka…. Condensation Synthesis.

• all with the chemical formula C12H22O11

• glucose + fructose = sucrose (table sugar) + H2O

• glucose + galactose = lactose ( the sugar in milk) + H2O

• glucose + glucose = maltose + H2O

Condensation Synthesis or

Dehydration Synthesis • The chemical

reaction that joins monomers into polymers.

• Covalent bonds are formed by the removal of a water molecule between the monomers.

Hydrolysis

• Reverse of condensation

synthesis.• Using water (Hydro),

to split (Lysis)• Breaks polymers

into monomers by adding water

Examples of Disaccharides produced through Dehydration Synthesis

• Maltose = glucose + glucose

• Lactose = glucose + galactose

• Sucrose = glucose + fructose

Polysaccharidesall with the chemical formula (CH2O)n

• Many joined simple sugars.• Used for storage or structure.

• Examples: Starch - a polymer of -glucose molecules, principle

energy storage molecules in plants Glycogen - a polymer of -glucose molecules, principle

energy storage molecules in animals, stored in the liver and muscles cells

Cellulose - a polymer of -glucose molecules, principle structural molecules in plant cell walls…. Major component of wood

Chitin - a polymer of -glucose molecules, each modified with a nitrogen group, principle structural molecule in the cell walls of fungi and the exoskeletons of the arthropods.

Lipids (Fats)

• Diverse hydrophobic molecules which are insoluble in water (and other polar molecules) and

soluble in non-polar molecules like ether and chloroform

• Made of C,H,O• No general formula.

• C:O ratio is very high in C

Types of Lipids (Fats)

• Triglycerides

• Phospholipids

• Steroids

Triglycerides

• Three fatty acids joined to one glycerol.

• Joined by an “ester” linkage between the -COOH of the fatty acid and the -OH

of the alcohol.

• Differ in which fatty acids are used.

• Used for energy storage, cushions for organs, insulation.

Acid Fat

Fats and Oils

• Fats - solid at room temperature.

• Oils - liquid at room temperature.

• Saturated - solid at room temperature.

• Unsaturated - liquid at room temperature.

Saturated Fats

• Saturated - no double bonds.

Unsaturated Fats• Unsaturated - one or more C=C

bonds. Can accept more Hydrogens.

• Double bonds cause “kinks” in the molecule’s shape.

Question ?

• Which has more energy, a kg of fat or a kg of starch? …. (Hint) in Fats there are more C-H bonds which provide more energy per mass.

• Answer… carbohydrates (starch) have 4 calories per gram, lipids have 9 calories per gram

Phospholipids

• Similar to fats, but have only two fatty acids.

• The third -OH of the glycerol is joined to a phosphate group replacing a fatty acid

• Major component of the Plasma

Membrane of all cells

Result

• Phospholipids are amphipathic which means they have a nonpolar, hydrophobic tail, but a polar, hydrophilic head.

• Self-assembles into bilayers, an important part of cell membranes.

Steroids

• Characterized by a backbone of four fused carbon rings.

• Differ in the functional groups attached to the rings.

• Examples:

–cholesterol

–sex hormones

Proteins

• Made of C,H,O,N, and sometimes S.

• No general formula

• Polymers of amino acids

Uses Of Proteins

• Structural Proteins: used to make skin, hair, muscles, etc…

• Enzymes: Control Metabolism• Antibodies: Provide protection

against foreign substances• Transport Proteins: Transport

molecules across membranes• Storage: such as ovalbumin in

eggs

Proteins

Proteins are Polypeptide chains of Amino Acids

linked by peptide bonds.

Amino AcidsAmino Acids• All have a Carbon

with four attachments:

-COOH (acid)

-NH2 (amine) -R group• 20 different kinds

of amino acids because there are 20 different kinds of R groups

Amino GroupCarboxyl Group AKA: Acid Group

Amino Acids

Amino Acids

R groups

The properties of the R groups

determine the

properties of the protein.

Polypeptide Chains

• Formed by dehydration synthesis between the carboxyl group of one

amino acid and the amino group of the second Amino Acid.

Levels Of Protein Structure

• Organizing the polypeptide into its 3-D functional shape.– Primary– Secondary– Tertiary– Quaternary

Primary Structure

• Order of amino acids in the

polypeptide chain.

• Many different sequences are possible with

20 AAs.

Secondary Structure• 3-D structure

formed by hydrogen bonding between the R groups.

• Two main secondary structures:

helix

- pleated sheets

Tertiary• 3D shape as bonding

occurs between the R groups.

• Examples:

– Hydrophobic interactions

– Ionic bonding

– Disulfide bridges– Hydrogen Bonding

Quaternary• When two or more polypeptides

unite to form a functional protein.

• Example: hemoglobin

Is Protein Structure Important?

Denaturing Of A Protein

• Events that cause a protein to lose structure (and function).

• Example:

–pH shifts

–high salt concentrations

–heat

Nucleic Acids

• Stores the genetic Information

• Polymers of nucleotides

• Made of C,H,O,N and P

• No general formula

• Examples: DNA and RNA

Nucleotides of DNA and RNANucleotides have three parts:

– Nitrogenous Base

– Pentose sugar (Deoxyribose in DNA and Ribose in RNA)

– Phosphate Group

Nitrogenous Bases• Rings of C and N

• Two types:– Pyrimidines (single ring) Thymine, Cytosine– Purines (double rings) Adenine, Guanine

Pentose Sugar• 5-C sugar

• Ribose - RNA

• Deoxyribose – DNA

DNA: Deoxyribonucleic Acid• Double Helix Structure• The two strands of DNA

are antiparallel, oriented in opposite directions… one strand is arranged in the 3’ – 5’ direction while the other is arranged in the 5’ – 3’ direction (5’ means the phosphate group is attached to the 5th carbon on the Deoxyribose molecule.

• Makes up genes.

RNA: Ribonucleic Acid

• Important molecule in protein synthesis.

• Genetic information for a few viruses only.

Differences between DNA and RNA

• RNA is a single strand

• DNA has Deoxyribose, RNA has ribose

• Thymine is replaced by Uracil

Chemical Reactions in Metabolic ProcessesChemical Reactions in Metabolic Processes

• In order for chemical reactions to occur, the reacting molecules must first collide and then have enough energy (Activation energy) to trigger the formation of new bonds.

• Some reactions require catalysts. Catalysts are molecules which trigger or accelerate chemical reactions without being chemically altered themselves.

Metabolism• Chemical reactions which occur within

living organisms are called Metabolic reactions…..

• Two types of Metabolic Reactions:

*Anabolic Reactions:

Build molecules and store energy

*Catabolic Reactions:

Breakdown Molecules and release energy

Chemical Equilibrium

• The net direction of metabolic reactions, forward or reverse, is determined by the concentration of the reactants and the products.

Enzymes: Globular proteins which catalyze metabolic reactions.

• Enzyme: Catalyzes the Reaction

• Substrate: molecule acted upon

• Products: Resulting molecules• Enzyme + Substrate Enzyme – Substrate Complex Enzyme + Products

• Maltase + Maltose Maltase + Maltose Complex Maltase + glucose + glucose

Active Site

Enzymes

• Most Enzymes end with the letters - ASE

• Enzymes are substrate specific….. Examples:

• Maltase can only breakdown Maltose

• Sucrase can only breakdown Sucrose

• Amylase can only breakdown Amylose

EnzymesThe efficiency of Enzymes

is affected by:

- pH shifts: pepsinogen is only activated when stomach acids

lower the pH

- Heat: denatures enzymes

Cofactors• Are nonprotein molecules that

assist enzymes… since they are nonproteins they are used up in the reactions.

• A holoenzyme is the union of a cofactor and enzyme.

• The enzyme is called an Apoenzyme when it’s part of a holoenzyme

Inorganic Cofactors

Are usually metals, like Iron (Fe+2), Magnesium (Mg+2)

CoEnzymes

Are organic molecules which aid in enzyme reactions…….

Some vitamins are coenzymes. Since they are nonproteins they

are also used up in the reactions.

ATPAdenosine TriPhosphate

Source of Activation energy for Metabolic Reactions

Allosteric Enzymes• Have two types of binding sites….

One for the substrate and one for the allosteric effector.

• Two types of Allosteric Effectors:

• 1. Allosteric Activator – binds to the enzyme and changes its shape to induces a reaction

• 2. Allosteric Inhibitor – binds to the enzyme and induces inactivity

Allosteric Enzymes

Competitive Inhibition

Is when an enzyme mimic occupies

the active site preventing a

reaction.

Noncompetitor InhibitorNoncompetitor Inhibitor

Prevents enzyme reactions by binding to the substrate at locations other than the active or allosteric site.

Cooperativity

• Occurs when an enzyme becomes receptive to additional substrate molecules after one substrate molecule attaches to an active site.

• Example: Hemoglobin…… its binding capacity to additional oxygen molecules increases after the first oxygen fills the active site.

Cooperativity