the basics of chemistry for biology

The Basics of Chemistry for Biology

• Atoms: The units of elements

• Bonding:Covalent vs. Ionic

• Water:Water‘s unique properties

The Chemistry of Life

• Matter – (anything that takes up space)– Composed of atoms

• Atom– Smallest unit of an element that

has the properties of the element– 2 regions

• Nucleus• Electron cloud

Inside the Atom: Subatomic Particles

• Protons: positive charged particles found in the nucleus (p+)

• Neutrons: neutral particles found in the nucleus (nº)

• Electrons: negative particles found in the electron cloud (e-) – Move around the nucleus in energy levels

Energy Levels of the Electron Cloud

The number of electrons on each level is given by the formula 2n2

where n is the level number

Number/Name # of e- it can hold

1-K 2

2-L 8

3-M 18

4-N 32

5-O 50

6-P 72

7-Q 98

Info from the Periodic Table

• Symbol • Atomic Number

(Z)– = Number of p+

• Mass Number (A)– = p+ + nº

Nuclides

A

Z XCopper

Oxygen

Practice SetSymbol/

NameAtomic Number

Atomic Mass

Nuclide Protons Neutrons Electrons

OOxygen

AuGold

NaSodium

KPotassium

ClChlorine

FFluorine

CaCalcium

Let’s Draw an Atom

1. Write the nuclide.2. Draw the Energy levels.3. Write the number of protons and

neutrons in the nucleus.4. Place the correct number of electrons on

each energy level.5. Leave unused energy levels empty.

Practice Drawing

Ions

• For a neutral atom, protons = electrons• Ion: an atom with more or fewer

electrons than it should normally have, causing a charge– Loss of electrons forms a positive ion

• Cation– Gain of electrons forms a negative ion

• Anion

Isotopes

• Isotopes: atoms of the same element with different masses due to different # of neutrons

• radioactive isotopes: unstable nuclei breakdown over time (nuclear decay)

Summary ChartSubatomic

particle number to be changed

How changed Atom is now a __ of the original

atom

Electron

Gained

Lost

Anion (negative ion)

Cation (positive ion)

Neutron Gained or Lost Isotope

Bonding and Compounds

• Compound: two or more atoms bonded together due to electron exchange (give & take) or electron sharing

Metals

• Metals are found mainly in columns I to III

• They give away electrons to bond– This forms positive ions: cations

Non-metals

• Non-metals are found mainly in columns III to VIII– They can take in electrons from a metal to

bond and form negative ions: anions– They can share electrons with another non-

metal and form molecules

Ionic Bonding

• Ionic Bonding: involves the giving of electrons by metals and the taking of electrons by non-metals– Examples

• Sodium chloride• Calcium chloride• Sodium oxide

– Forms IONS

Ionic bonding

Covalent Bonding

• Covalent Bonding: the sharing of electrons between two non-metals– Carbon dioxide– Methane– Nitrogen dioxide– Diphosphorus pentoxide

– Forms MOLECULES

Covalent Bonding

Polarity

• Polar: electrons are not shared equally between the two non-metals in a covalent bond

• Non-polar: electrons are shared equally between the two non-metals in a covalent bond

Polar covalent bond

Polar/nonpolar bonds

• van der Waals forces: forces of attraction between molecules– Weak forces

van der Waals forces

van der Waals interactions• Weak interactions between molecules or

parts of molecules that are brought about by localized change fluctuations

• Due to the fact that electrons are constantly in motion and at any given instant, ever-changing “hot spots” of negative or positive charge may develop

Hydrogen bonds• Hydrogen atom

covalently bonded to one atom is also attracted to another atom (oxygen or nitrogen) on another molecule– Strong– Water is best example

Cohesion

• Cohesion: attraction of molecules of the same substance to each other– Example water molecules to other

molecules in a glass

Water’s Properties• Polar~ opposite ends, opposite charges• Cohesion~ H+ bonds holding molecules

together (same substance, water to water)• Adhesion~ H+ bonds holding molecules to

another substance• Surface tension~ measurement of the

difficulty to break or stretch the surface of a liquid

• Specific heat~ amount of heat absorbed or lost to change temperature by 1oC

• Heat of vaporization~ quantity of heat required to convert 1g from liquid to gas states

• Density……….

Density• Less dense as solid

than liquid1. Due to hydrogen

bonding2. Crystalline lattice

keeps molecules at a distance

Mixtures• Combination of 2

or more elements physically but not CHEMICALLY (not bonded together)

Wet MixturesSoution All components are

distributed evenly Parts1. Solute: is dissolved2. Solvent: does the

dissolving

Example: Kool-aid dissolved in water

Suspension Components are distributed

unevenly, just mixed together

Parts1. Supernant: liquid2. Precipitate: solid

Example: snowglobe

Acid/Base & pH• Dissociation (breaking apart)

of water into a hydrogen ion and a hydroxide ion

• Acid: increases the hydrogen concentration of a solution

• Base: reduces the hydrogen ion concentration of a solution

• pH: “power of hydrogen”• Buffers: weak acids or bases

that react with strong acids or bases to prevent changes in pH

pH Scale

Acid Neutral Base

0 1 2 3 4 5 6 7 8 9 10 1112 13 14

Stronger Weaker WeakerStronger

Human body prefers pH of 6.5 to 7.5

Acids vs. BasesAcid• “Acidic”• More H+ than OH-

• Tastes sour• Turns litmus paper red• Found in coffee, tea, soft

drinks, and fruit juices

Base• “Alkaline”• More OH- than H+

• Tastes bitter• Turns litmus paper blue• Found in cleaners and

soaps

NeutralizationWhen Acids and Bases are mixed

chemically, they produce salt and water. This reaction is called neutralization because the end products are not acidic nor alkaline, they are neutral!

2006-2007


What are living creatures made of?

Why do we have to eat?

• 96% of living organisms is made of: carbon (C) oxygen (O) hydrogen (H) nitrogen (N)

Elements of Life

Molecules of Life• Put C, H, O, N together in different

ways to build living organisms• What are bodies made of?

– carbohydrates • sugars & starches

– proteins– fats (lipids)– nucleic acids

• DNA, RNA

Why do we eat?• We eat to take in more of these chemicals

– Food for building materials• to make more of us (cells)• for growth• for repair

– Food to make energy• calories• to make ATP

ATP

What do we need to eat?• Foods to give you more building blocks &

more energy• for building & running bodies

– carbohydrates– proteins– fats– nucleic acids– vitamins– minerals, salts– water

• Water– 65% of your body is H2O– water is inorganic

• doesn’t contain carbon

• Rest of you is made of carbon molecules– organic molecules

• carbohydrates• proteins• fats• nucleic acids

Don’t forget water

2006-2007

How do we make these molecules?

We build them!

How do we make these molecules?

We build them!

How to take large molecules apart• Digestion

– taking big molecules apart– getting raw materials

• for synthesis & growth– making energy (ATP)

• for synthesis, growth & everyday functions

+

ATP

Example of digestion

starch glucose

ATP

ATP

ATP

ATP

ATP

ATPATP

• Starch is digested to glucose

Building large molecules of life• Chain together smaller molecules

– building block molecules = monomers

• Big molecules built from little molecules– polymers

• Small molecules = building blocks

• Bond them together = polymers

Building large organic molecules

Building important polymers

sugar – sugar – sugar – sugar – sugar – sugar

nucleotide – nucleotide – nucleotide – nucleotide

Carbohydrates = built from sugars

Proteins = built from amino acids

Nucleic acids (DNA) = built from nucleotides

aminoacid

aminoacid–

aminoacid–

aminoacid–

aminoacid–

aminoacid–

How to build large molecules• Synthesis

– building bigger molecules from smaller molecules

– building cells & bodies• repair• growth• reproduction

+

ATP

How to take large molecules apart• Digestion

– taking big molecules apart– getting raw materials

• for synthesis & growth– making energy (ATP)

• for synthesis, growth & everyday functions

+

ATP

Example of digestion

starch glucose

ATP

ATP

ATP

ATP

ATP

ATPATP

• Starch is digested to glucose

Example of synthesis

amino acids protein

amino acids = building blockprotein = polymer

Proteins are synthesized by bonding amino acids

Old Food Pyramid

New Food Pyramid

Carbon, the Backbone

Carbon is special in the world of elements because it is able to bond to 4 other atoms at the same time!

Carbon, the BackboneSince Carbon can form so many bonds, it is considered the “backbone” of many compounds, that is Carbon is what the other atoms are all attached to

Special Covalent Bonds1. Single bond: one pair of electrons is

shared between two atoms2. Double bond: two pair of electrons

are shared between two atoms3. Triple bond: three pair of electrons

are shared between two atoms

Who can do these special cases?

C, N, O, and S can all form double bonds.

Only C and N can form triple bonds!

Carbon’s ShapesWhen Carbon bonds to other Carbon atoms, the resulting bond can take one of the following shapes:

1.Straight chain (in a straight line)2.Branched chains (like the straight chain,

but with a fork in the road3.Ring structures

Carbohydrates

Biochemical molecules that are used as both sources of energy and as short term energy storage• commonly called sugars and starches

Glucose

C6H12O6

Carbohydrates, I

Monosaccharides CH2O formula; simple sugars multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldoses) ketone (ketoses) raw material for amino acids and fatty acids

Carbohydrates, II

Disaccharides glycosidic linkage (covalent bond) between 2 monosaccharides; covalent bond by dehydration reaction

Sucrose (table sugar) most common disaccharide

Carbohydrates, III• Polysaccharides

(Storage) Starch~ glucose monomers Plants: plastids Animals: glycogen

• Polysaccharides (Structural)Cellulose ~ most abundant

organic compound; Chitin ~ exoskeletons; cell

walls of fungi; surgical thread

Monomers and Polymers

• -mer: building blocks • Monomer: one building block

• Polymer: many building blocks

Proteins• Importance:

instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known

• Monomer: amino acids (there are 20) ~ carboxyl (-COOH) group, amino group (NH2), H atom, variable group (R)….

• Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base

• Three-dimensional shape (conformation)• Polypeptides (dehydration reaction):

peptide bonds~ covalent bond; carboxyl group to amino group (polar)

Primary Structure• Conformation:

Linear structure

• Molecular Biology: each type of protein has a unique primary structure of amino acids

• Ex: lysozyme

• Amino acid substitution:hemoglobin; sickle-cell anemia

Secondary Structure

• Conformation: coils & folds (hydrogen bonds)

• Alpha Helix: coiling; keratin• Pleated Sheet: parallel;

silk

Tertiary Structure

Conformation: irregular contortions from R group bonding

hydrophobicdisulfide bridgeshydrogen bonds ionic bonds

Quaternary Structure

• Conformation: 2 or more polypeptide chains aggregated into 1 macromoleculecollagen (connective tissue)hemoglobin

Lipids• No polymers; glycerol and fatty acid• Fats, phospholipids, steroids• Hydrophobic; H bonds in water exclude fats• Carboxyl group = fatty acid• Non-polar C-H bonds in fatty acid ‘tails’• Ester linkage: 3 fatty acids to 1 glycerol

(dehydration formation)• Triacyglycerol (triglyceride)• Saturated vs. unsaturated fats; single vs.

double bonds

Lipids, II

Phospholipids

• 2 fatty acids instead of 3 (phosphate group)

• ‘Tails’ hydrophobic (water fearing); ‘heads’ hydrophilic (water loving)

• Micelle (phospholipid droplet in water)

• Bilayer (double layer);cell membranes

Steroids

• Lipids with 4 fused carbon rings• Ex: cholesterol:

cell membranes;precursor for other steroids (sex hormones); atherosclerosis

Nucleic Acids, I• Deoxyribonucleic acid (DNA)• Ribonucleic acid (RNA)• DNA->RNA->protein• Polymers of nucleotides

(polynucleotide):nitrogenous basepentose sugarphosphate group

• Nitrogenous bases: pyrimidines~cytosine, thymine, uracilpurines~adenine, guanine

Nucleic Acids, II

• Pentoses:√ribose (RNA)√deoxyribose (DNA)√nucleoside (base + sugar)

• Polynucleotide:phosphodiester linkages (covalent); phosphate + sugar

Nucleic Acids, III

• Inheritance based on DNA replication

• Double helix (Watson & Crick - 1953) H bonds~ between paired bases van der Waals~ between stacked bases

• A to T; C to G pairing• Complementary

Give the complimentary DNA strand:

A G T C T G C A

Give the complimentary RNA strand:

A G T C T G C A

Biochemical Type

Carbohydrates Lipids Proteins Nucleic Acids

Monomers Monosaccharides

Sugars

Fatty acids and glycerol

Amino acids nucleotides

Polymers Polysaccharides

Starches

NONE Polypeptides, aka proteins

polynucleotide

Forces holding together

Glycosidic linkages Ester linkages

Peptide bonds Bonds and van der Waals

phosphodiester linkages

Uses Energy storage and structural

support

Energy storage,

hormones, membranes

Structural building

materials

Genetic information

transfer

Biochemical Test

Carbohydrates Lipids Proteins Nucleic Acids

Biuret's Reagent

Blue turns violet in

proteins, and pink with

short-chain polypeptides

Benedict’s Solution

Simple sugars heated with

Benedict’s turns from blue to red

Iodine Starches turn dark purple or black

Brown Bag Test/ Sudan III

stain

Leaves spot on brown bag/ turns

fats red

http://en.wikipedia.org/wiki/Proteins

http://en.wikipedia.org/wiki/Polypeptides

Conformation Test Lab

Lab Information

In the laboratory investigation you will perform known tests using known reagents in order to obtain positive results for comparison with an unknown. Be sure to follow your lab directions exactly!

IDENTIFYING MACROMOLECULES

IN FOODLAB

Introduction

Carbohydrates, proteins, and fats are all essential nutrients.

We cannot manufacture these nutrients so we must obtain them from our environment.

Introduction In this lab, with the use of indicators as

chemical detection tools, you will analyze a variety of foods for the presence of nutrients.

Detection is based upon observing a chemical change that takes place most often a change in color.

Objective

Identify the presence of major nutrients such as simple carbohydrates (glucose), complex carbohydrates (starch), protein and fat in

common foods.

What is an indicator?

• Indicators are chemical compounds used to detect the presence of other compounds.

Background InformationINDICATOR MACRO-

MOLECULENEGATIVE

TESTPOSITIVE

TEST

Benedict’s solution

simple carbohydrate

blue orange

IKI solution complex carbohydrate

dark red black

Biuret solution

protein blue violet, black

Sudan IV lipid dark red reddish- orange

What is a Standard?

• An acknowledged measure of comparison for quantitative or qualitative value; a criterion.

Test for Simple CarbohydratesBenedict’s solution

• Benedict's solution is a chemical indicator for simple sugars such as glucose: C6H12O6.

• Aqua blue: negative test; yellow/green/brick red, etc.: positive test

Test for Simple CarbohydratesBenedict’s solution

• Unlike some other indicators, Benedict’s solution does not work at room temperature - it must be heated first.

Test for Complex CarbohydratesIKI solution

• IKI solution (Iodine Potassium Iodine) color change = blue to black

Test for Complex CarbohydratesIKI solution

• Iodine solution is an indicator for a molecule called starch.

• Starch is a huge molecule made up of hundreds of simple sugar molecules (such as glucose) connected to each other.

Test for Protein (amino acids)Biuret solution

• Biuret solution dark violet blue to pinkish purple

Test for Fats (lipids)Sudan IV

• Like lipids, the chemical Sudan IV is not soluble in water; it is, however, soluble in lipids.

• In this test dark red Sudan IV is added to a solution along with ethanol to dissolve any possible lipids.

Test for Fats (lipids)Sudan IV

• If lipids are present the Sudan IV will stain them reddish-orange (positive test).

QuestionWhy didn’t the test tube containing sucrose

change colors?

QuestionWhy didn’t the test tube containing starch

change colors?

ProcedureSimple carbohydrate

1. Add 5ml distilled H2O using pipette to test tube

2. Add 1ml of food sample to test tube3. Add 20 drops of Benedict solution4. Place test tube in a hot water

bath for 10 minutes.

ProcedureComplex carbohydrate


2. Add 1ml of food sample to test tube3. Add 20 drops of IKI solution

ProcedureProtein (amino acids)


2. Add 1ml of food sample to test tube3. Add 20 drops of Biuret solution

ProcedureFats (lipids)

• Add 5ml distilled H2O using pipette to test tube

• Add 1ml of food sample to test tube• Add 20 drops of Sudan IV

LAB SAFETY and CLEAN UP

WEAR safety goggles and apron

at all times

THOROUGHLY CLEAN lab area and

equipment

NO EDIBLE products in lab

Enzymes

Enzymes & Their Function

Reactions (Chemical Changes)

• Bonds are made or broken• Energy is used or released• Starting material: Reactant• Ending material: Product

Enzymes

Catalytic proteins: change the rate of reactions w/o being consumed

Free E of activation (activation E): the E required to break bonds

Substrate: enzyme reactant

Active site: pocket or groove on enzyme that binds to substrate

Induced fit model

EnzymesLearning objective: to examine what enzymes are anddescribe how they work.

Enzymes

What are they?

Why do we need them?

Name some examples ?

EnzymesGlobular proteins that catalyse chemical reactions in living organisms

Properties

Enzymes

Properties

Specific

Enzymes

Properties

Specific

Increase rate of the reaction

Enzymes

PropertiesSpecific

Increase rate of the reaction

Unchanged at the end of the reaction


PropertiesSpecific

Increase rate of the reactionUnchanged at the end of the reaction

Need them


PropertiesSpecific

Increase rate of the reactionUnchanged at the end of the reaction

Need them Reactions too slow to maintain lifeCan’t increase temperatures/pressure in cells (fatal)

Enzymes Are ProteinsThe enzyme binds to the substrates by its active site

The active site is a pocket formed by the folding of the protein where the substrates bind.

Enzymes Are ProteinsThe enzyme binds to the substrates by its active site

The active site is a pocket formed by the folding of the proteinwhere the substrates bind.

Active site

The active site involves a small number of key residues that actually bind the substratesThe rest of the protein structure is needed to maintain these residues in position

How do enzymes work?

An Example

An Example

Sucrose + H2O

Glucose + Fructose

An Example

Sucrose + H2O

Glucose + Fructose

Substrates

Products

For a reaction to occur the sucroseand water would have to collide with

enough energy to break and form bonds

For a reaction to occur the sucroseand water would have to collide with

enough energy to break and form bonds

This is the activation energy

Sucrose + H2O Glucose + Fructose

++

Substrates Products

Energy

Progress of reaction

Energy


Substrates

Energy


Substrates Products

Energy


Substrates Products

High energy intermediate

Energy


Substrates Products


Activation energy

The minimum amount of energy needed to start the reaction, leading to the formation of a high energy intermediate

= The Activation energy

Energy


Substrates Products


Activation energy

Enzymes reduce the height of the energy

barrier

“Activation Energy”

In a ‘natural’ reaction the product has a lower energy than the substrate so equilibrium will take it in the direction of the product.

However there is an energy ‘barrier’ to be overcome

Enzymes lower the activation energy required to bring about a reaction.

Ex. catalase reduces the activation energy for the reduction of H202 86-fold

Enzyme ActionWhat are the different models for enzyme action and which factors which control the rate of an enzyme reaction?

Lock and Key

Lock and Key

However certain substances can bind to the enzyme at sites other than the Active site and modify its activity (inhibitors/co-factors)

Idea that the enzyme is flexible

E

S

E

S

E

P P

Induced Fit

How do enzymes work?

• Reaction Mechanism

– In any chemical reaction a substrate is converted into a product.

– In an enzyme catalysed reaction the substrate first binds to the active site of the enzyme to form the enzyme-substrate complex

Molecule Geometry

• Substrate molecule fits into the enzyme like a lock & key.

• Enzyme shape distorts or it changes other factors to make the reaction happen

Enzyme reactions

enzyme + substrate enzyme-substrate complex

Enzyme reactions


E +S ES

Synthesis reaction since you are forming ONE product

Synthesis Reaction

Active site

es

Synthesis reaction

Glucose-1-phosphate

Starch

Enzyme reactions

enzyme + productenzyme-substrate complex

E +PES


E +S ES

Decomposition reaction since you are breaking down one thing into parts

Degradation reactions

animation

http://www.lewport.wnyric.org/jwanamaker/animations/Enzyme%20activity.html

Degradation reactions

Starch

Maltose

Catalase

The enzyme catalase breaks down the waste substance hydrogen peroxide into water and oxygen.

Hydrogen peroxide oxygen + water

(enzyme)

catalase

(substrate) (products)

Degradation reaction

Substrate

Enzyme

Product

Hydrogen peroxide

Catalase

Oxygen and water

Starch Amylase MaltoseMaltose Maltase GlucoseProtein Pepsin PeptidesPeptides Proteas

eAmino acids

Fats Lipase Fatty Acids and Glycerol

Enzyme activity

How fast an enzyme is workingRate of Reaction

Enzyme activity

How fast an enzyme is workingRate of Reaction

Rate of Reaction = Amount of substrate changed (or amount product formed) in a given period of time.

Rat

e of

Rea

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Enzyme activity

Variable you are looking at

Enzyme activity

Four Variables

Enzyme activity

Four Variables

Temperature

pH

Enzyme Concentration

Substrate Concentration

Effects on Enzyme Activity

TemperaturepHCofactors:inorganic, nonprotein helpers; ex.: zinc, iron, copperCoenzymes:organic helpers; ex.: vitamins

Reaction rate factors• Substrate

concentration– Initially rate

increases with substrate concentration

Enzyme activity

Temperature and pH affect the activity of an enzyme.

Rat

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Temperature

Rat

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Temperature

0 20 30 5010 40 60

Rat

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n

Temperature

0 20 30 5010 40 60

40oC - denatures

5- 40oC Increase in Activity

<5oC - inactive

Effect of heat on enzyme activtyIf you heat the protein above its optimal temperature

bonds break meaning the protein loses it secondary and tertiary structure

Effect of heat on enzyme activty

Denaturing the protein

Effect of heat on enzyme activty

Denaturing the proteinACTIVE SITE CHANGES SHAPE

SO SUBSTRATE NO LONGER FITS

Even if temperature lowered – enzyme can’t regain its correct shape

Rat

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n

pH

Rat

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pH

1 3 42 5 6 7 8 9

Rat

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Rea

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n

pH

1 3 42 5 6 7 8 9

Narrow pH optima

WHY?

Rat

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Rea

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npH

1 3 42 5 6 7 8 9

Narrow pH optima

Disrupt Ionic bonds - Structure

Effect charged residues at activesite

Rat

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n


Rat

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Active sites full- maximum turnover

ENZYME INHIBITORSIrreversible (covalent); reversible (weak bonds)Competitive: competes for active site (reversible); mimics the substrateNoncompetitive: bind to another part of enzyme (allosteric site) altering its conformation (shape); poisons, antibiotics

S

S

P P

Shape of the active

site changes

Optimum Condition

Enzymes function best or are most active in specific conditions known as optimum

conditions.

• Enzymes:-– Are defined as a BIOLOGICAL catalyst i.e. something that speeds up

a reaction. Up to 1012 fold– Usually end in ‘…ase’. – Discovered in 1900 in yeasts. Some 40,000 in human cells– Control almost every metabolic reaction in living organisms– Are globular proteins coiled into a very precise 3-dimentional shape

with hydrophilic side chains making them soluble– Possess an active site such as a cleft in the molecule onto which

other substrate molecules can bind to form an enzyme-substrate complex

– Once the substrate has been either synthesised or split, enzymes can be re-used.

– Do not ‘create’ reactions– Widely used in industrial cleaning– Often require co-factors (co-enzymes) to function – metal ions, or

vitamin derivatives

Amylase + starch substrate

the basics of chemistry for biology

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sharing of electrons

giving of electrons

chargeloss of electrons

fewer electrons

correct number of electrons

number of p mass number

number of protons

negative particles