HonorsBiology Ch. 6

HonorsBiology Ch. 6

Chemistry in Biology

Chemistry in Biology

I. Atoms, Elements, and Bonding

I. Atoms, Elements, and Bonding

- Living and nonliving things are made of atoms.

A.A.ElementElement- pure substance of only 1

type of atom- 98 natural elements- CHNOPS

The Size of Cells and Their Components

B. AtomsB. Atoms- smallest unit of matter

Atomic ModelsAtomic Models

Hydrogen (H) Helium (He)

Nucleus

ElectronElectronShellShell

B. AtomsB. Atoms- smallest unit of matter

1. Nucleus contains:Charge

Mass - Protonspositive 1

- Neutrons neutral1

2. Electrons negative0

C. IsotopesC. IsotopesC. IsotopesC. Isotopes- forms of an element with varying

number of neutrons- 12C vs. 14C

D.D. Compounds and Compounds and BondingBonding

D.D. Compounds and Compounds and BondingBonding- 2 or more elements chemically

bonded1.Covalent Bonds:

- attraction due to shared electrons- ex. water

Water Is CovalentElectron pair forms covalent bond

Each spends some time w/one, then the other atom

Oxygen Molecule (O2)Oxygen Molecule (O2)

Oxygen Atom Oxygen Atom

2.2. Ionic Bonds:Ionic Bonds:2.2. Ionic Bonds:Ionic Bonds:- attraction due to electrons

transferred from one atom to another creating + and - ions

- ex. table salt (NaCl)

Ionic Bonding in NaClIonic Bonding in NaCl

Sodium can lose 1 electron; Chlorine can gain 1 electron. Sodium becomes a positive ion; Chlorine a negative ion.

Sodium has 1 electron in outer shell;

chlorine has 7.

Ionic Bonding in NaClIonic Bonding in NaCl

ClCl-- ClCl-- ClCl-- ClCl--

ClCl-- ClCl-- ClCl-- ClCl--

ClCl-- ClCl-- ClCl-- ClCl--

ClCl-- ClCl-- ClCl-- ClCl--

NaNa++ NaNa++ NaNa++

NaNa++ NaNa++ NaNa++

NaNa++ NaNa++ NaNa++

NaNa++

NaNa++

NaNa++

NaNa++ NaNa++ NaNa++ NaNa++

Opposites attract.

Sodiums nestle between chlorines.

Perfectly cubical crystals.

ClCl-- ClCl-- ClCl-- ClCl--

ClCl-- ClCl-- ClCl-- ClCl--

ClCl-- ClCl-- ClCl-- ClCl--

ClCl-- ClCl-- ClCl-- ClCl--

NaNa++ NaNa++ NaNa++

NaNa++ NaNa++ NaNa++

NaNa++ NaNa++ NaNa++

NaNa++

NaNa++

NaNa++

NaNa++ NaNa++ NaNa++ NaNa++

Some Elements Are Molecular.

Some Elements Are Molecular.

Hydrogen gasOne electron from each hydrogen atom is shared, forming a single covalent bond

Oxygen gasTwo oxygen atoms share four electrons, forming a double bond

E. Acids, Bases, and pHE. Acids, Bases, and pH1.Acids:

- form H+ ions in solution2.Bases:

- form OH- (hydroxide) ions in solution

3.pH:- measure of how acidic or

basic a solution is- logarithmic scale

The pH ScaleThe pH Scale

NeutralNeutralpHpH++ = pOH = pOH––

Increasingly AcidicIncreasingly Acidic Increasingly BasicIncreasingly Basic

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14Water

LemonJuice

LimeJuice

StomachAcid

Orange Juice

Coffee

Urine

Vinegar

Blood

SeaWater

BakingSoda

Bleach

Ammonia

OvenCleaner

Hand Soap

Universal pH Indicator

Universal pH Indicator

II. WaterII. WaterA.A.Water Is PolarWater Is Polar - water molecules have

positive and negative ends

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

O

H H+ +

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled closer to oxygen.

Polar Covalent Bonds in a Water Molecule

Polar Covalent Bonds in a Water Molecule

II. WaterII. Water

Hydrogenbonds

+

+

H

H+

+

–

–

––

Hydrogen Bonds between Water Molecules

Hydrogen Bonds between Water Molecules

A.A.Water Is PolarWater Is Polar - hydrogen bonds form

between water molecules

A.Water Is PolarA.Water Is Polar- polarity gives special properties

OO

OO

HH

HH

HHHH

++

++

++

––

––

++

++

Hydrogen Bonds

Hydrogen Bonds

How Polarity Makes Water Behave Strangely (3:52)

- solvent of life

Negative oxygen regions of polar water molecules are attracted to sodium

ions (Na+). +

+

+

+Cl –

–

–

–

–

Na+

Positive hydrogen regions

of polar water molecules cling to chloride ions (Cl–).

+

+

+

+

–

–

–

–

–

–Na+

Cl–

A Crystal of Table Salt Dissolving in Water

A Crystal of Table Salt Dissolving in Water

- strong cohesion and adhesionWater surface tension

Water is transported great heights up the stem.

Water conducting cells

100 µm

Cohesion among Water MoleculesCohesion among Water Molecules

- strong cohesion and adhesion

Meniscus

Meniscus Capillarit

yCapillarit

y

Adhesion among Water Molecules

Adhesion among Water Molecules

- high specific heat- good evaporative coolant

- less dense when frozen

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds are stable

Hydrogenbond

Ice: Crystalline Structure and Floating

Barrier

Ice: Crystalline Structure and Floating

Barrier

III. Organic CompoundsIII. Organic Compounds - Living organisms are made up of

organic compounds.

A.Major Differences Between:Living vs.Nonliving

Systems Systems

complex simplecompounds compoundshigh energy low energy

- All organic compounds contain carbon.- Exceptions: CO2, CO, CaCO3

- Carbon can form 4 covalent bonds.

- Carbon based molecules form chains, branched chains, rings, etc.

Chlorophyll AChlorophyll A Chlorophyll BChlorophyll B

Buckminsterfullerene

Buckminsterfullerene

B. 4 Classes of Organic Compounds:

B. 4 Classes of Organic Compounds:1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids

IV. CarbohydratesIV. Carbohydrates- contain C, H, O (1:2:1) - include sugars, starches, cellulose - used for energy storage and to

build cell walls - names usually end in "-ose"

A. Monosaccharides:A. Monosaccharides:- single (simple) sugar

A. Monosaccharides:A. Monosaccharides:- single (simple) sugar - C6H12O6, C5H10O5

- ex. glucose (source of energy in cells), fructose (fruit sugar), galactose

B.Disaccharides:B.Disaccharides:- double sugar

B.Disaccharides:B.Disaccharides:- double sugar - C12H22O11

- ex. sucrose (table sugar), lactose (milk sugar)

C. Polysaccharides :C. Polysaccharides :

C. PolysaccharidesC. Polysaccharides- many sugars1. Starch

- Made of many 10 - 1000 glucose molecules

- in plants (potatoes, grains) - Glycogen: animal starch

Storage polysaccharides of plants and animals

Storage polysaccharides of plants and animals

Mitochondria Glycogen granules

Chloroplast

Starch

AmyloseAmylopectin

1 m

0.5 m

Starch: a plant polysaccharideGlycogen: an animal polysaccharide

Glycogen

2. Cellulose:2. Cellulose:

- long starch chains bonded side by side

- very strong - found in the plant cell walls

The Arrangement of Cellulose in Plant Cell

Walls

The Arrangement of Cellulose in Plant Cell

Walls

Cellulosemolecules

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

OO

OHOCH2OH

OO

OHO

CH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

OO

OH CH2OH

OH

Glucose monome

r

O

O

O

O

O

O

Parallel cellulose molecules areheld together by hydrogen

bonds between hydroxylgroups attached to carbon

atoms 3 and 6.

About 80 cellulosemolecules associateto form a microfibril, themain architectural unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Starch and Cellulose Structures

Starch and Cellulose Structures

Cellulose: 1– 4 linkage of glucose monomers

H O

O

CH2OH

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4 OH

CH2OH

O

OH

OH

HO41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OH

O

OH

OH

HO4

O1

OH

O

OH OHO

CH2OH

O

OH

O OH

O

OH

OH

and glucose ring structures

Starch: 1– 4 linkage of glucose monomers

1

glucose glucose

CH2OH

CH2OH

1 4 41 1

V. LipidsV. Lipids- fats, oils, waxes, steroids - not soluble in water - more energy (calories) in lipids

than in carbohydrates- energy storage, insulation, cell

membrane, coatings, and many hormones

Triglycerides

Triglycerides

GlycerolGlycerol

3 Fatty Acids .

3 Fatty Acids .

Lipid Structure Lipid Structure

Animal fat

Animal fat

Vegetable oil

Vegetable oil

Saturated vs. UnsaturatedFatty Acids

Saturated vs. UnsaturatedFatty Acids

Carcinogenic

Carcinogenic

‘Natural’‘Natural’

What Are Trans Fatty Acids?

What Are Trans Fatty Acids?

Phospholipid Bilayer

Phospholipid Bilayer

Cell MembraneCell Membrane

Steroids

Steroids

CholesterolCholesterol

EstradiolEstradiol Testosterone

Testosterone

Progesterone

Progesterone

AldosteroneAldosteroneCortisolCortisol

VI. Proteins:VI. Proteins:- the most abundant and varied of

organic compounds- contain C, H, N, O (S)

A. Types of ProteinA. Types of Protein1.Structural:

- keratin (hair, fingernails)- collagen

2.Contractile:- actin and myosin (muscle)

3.Pigments:- melanin (in skin, hair, iris)

4.Hormones:- regulate body functions (insulin)

5.Antibodies:- fight disease

6.Enzymes:- amylase (in saliva), lactase

B. Structure of ProteinsB. Structure of Proteins- very complex

1. Amino Acids- building blocks of proteins

- 20 different amino acids- proteins contain between

50 - 2000 amino acids

2. Peptide Bond2. Peptide Bond- joins 2 amino acids - polypeptide: many amino acids

Peptide Bond

Peptide Bond

3. Levels of Protein Structure3. Levels of Protein Structure

Primary Structur

e

Primary Structur

e

Secondary

Structure

Secondary

Structure

Tertiary Structur

e

Tertiary Structur

e

Quaternary

Structure

Quaternary

Structure

3. Levels of Protein Structure3. Levels of Protein Structurea) Primary Structure:

- sequence of amino acids

b) Secondary Structure:- helix or pleated sheet

c) Tertiary Structure:- amino acids interact to form the polypeptide into a 3 dimension shape

d)Quaternary Structure:- 2 or more tertiary polypeptides

C. Enzymes C. Enzymes - protein catalysts- speed up chemical reactions- each enzyme catalyzes only one

specific substrate- most function at a specific

temperature and pH

C. Enzymes C. Enzymes

C. Enzymes C. Enzymes

VII. Nucleic AcidsVII. Nucleic Acids- 2 major types:

A.DNA- contains

hereditary information (genes) - double helix

VII. Nucleic AcidsVII. Nucleic Acids- 2 major types:

A.DNA- contains hereditary

information (genes) - double helix

B. RNA- controls protein synthesis - single helix

Information Flow:

Information Flow:

DNA

RNA

Protein

TheTheTheThe

EndEndEndEnd

ƒ2-6Chapter

2 65

NaCl Dissolved by WaterNaCl Dissolved by Water

NaCl is ionicly bonded

NaCl is ionicly bonded

Water is polar and charged

Water is polar and charged

O sticks to Na+

O sticks to Na+

H sticks to Cl-

H sticks to Cl-

Universal pH Indicator

Universal pH Indicator

pH 4.0

pH 5.0

pH 6.0

pH 7.0

pH 8.0

pH 9.0

pH 10.0

Information Flow:Information Flow:DNA RNA ProteinDNA RNA Protein