Chapter 2: Biochemistry & the Chemical Basis of

Life

Chemistry: ◦Branch of science studying the composition

of matter and how it changes Biochemistry:

◦Branch of science studying how chemistry affects living organisms

◦Focuses on carbon molecules called macromolecules

◦Ex: nucleic acids, lipids, proteins, carbohydrates

Introduction

Element: ◦A chemical substance with only one type of

atom◦ Ex: oxygen, hydrogen, carbon, nitrogen

110+ known (92 naturally found) Usually combine to form compounds and molecules

Living organisms require about 20 elements◦ Ex: O, C, H, N (95% of biomass)◦ Others: Ca, K, S, Cl, Na

Elements and Atoms

Atoms: ◦Smallest particle of an element which still

retains properties of that element◦Made of subatomic particles: 1) Proton: + charge, in nucleus (middle of atom) 2) Neutron: neutral, in nucleus 3) Electron: - charge, circles the nucleus in

cloud/shells◦Atoms vary in weight, chemical properties and

physical properties Form attractions to other atoms (chemical bonds)

Elements and Atoms

Chemical bond:◦Def: an attraction between two or more

atoms ◦Will form between atoms of same element

or atoms of differing elements Same element: Example – Nitrogen gas

(N2 – two atoms of nitrogen) Different elements: Example – Water

(H2O – two atoms of hydrogen, one of oxygen)

Chemical bonds

Bonding involves the sharing or transfer of electrons

Atoms will bond to fill their electron shells◦1st shell(closest to nucleus): 2 electrons

needed to fill Ex: Hydrogen in water bond

◦2nd shell: 8 Ex: Oxygen in water bond

(fills 1st level with 2, then fills the 2nd level with 8)

◦3rd shell: 8

Chemical bonds

Three types of bonds:◦1) Ionic:

Bond that forms between two charged atoms (ions)

Atoms involved have transferred electrons – giving them opposite charges

Ex: NaCl (Na+ lost electron, attracted to Cl- (gained elec.))

FORMS BETWEEN atoms of the SAME MOLECULE

Chemical bonds

Three types of bonds:◦2) Covalent:

Bond that forms when two atoms SHARE electrons

Polar: unequal sharing of electrons, ex: water Nonpolar: equal sharing of electrons, ex: N2, H2 Forms BETWEEN atoms of the SAME MOLECULE

Chemical bonds

Three types of bonds:◦3) Hydrogen:

Bond that forms between hydrogen atom and the negative atom of another molecules

Ex: between water molecules, connects two strands of DNA, important in protein folding

Chemical bonds

Chemical reactions:◦Reactants: Molecules/compounds which

start a reaction◦Products: Molecules/compounds which are

formed during a reaction

Chemical reactions

Chemical reactions:◦Def: Form or break bonds between atoms,

ions, or molecules; generates new chemical combinations

◦Ex: digestion, macromolecule synthesis, cellular respiration, photosynthesis

Chemical reactions

Types of chemical reactions: 1) Synthesis:

When two or more atoms bond to form a more complex structure; requires energy input

Ex: DNA replication, condensation reaction (formation of macromolecules)

2) Decomposition: When bonds within a reactant break to form

simpler molecules; energy is released Ex: Digestion

3) Exchange reaction/double displacement: When two types of molecules trade atoms Ex: Acid/Base reactions form water and salts

Chemical reactions

Synthesis

Decomp

Double displacement

Many are reversible ◦ Shown with a double-

arrow◦ Reversible reactions

meant that the products of the reaction can change back into the reactants

Chemical equilibrium:◦ When the concentrations

of both reactants and products do not change

◦ Reaction continues!

Chemical reactions

Chemical reaction rates:◦ Dependent upon a variety of

environmental variables Ex: pH, temperature, concentrations of

reactants/products, energy availability, salt/salinity

◦Catalyst: Def: A molecule that can change the rate

(usually increase) of a chemical reaction Ex: enzymes Human body relies upon these to sustain life

Ex: Enzymes involves in DNA replication (helicase, DNA polymerase, ligase)

Chemical reactions

Electrolyte:◦Substances that release ions in water◦The solution then can conduct electricity

Acids:◦ Def: An electrolyte that release hydrogen ions

(H+) in water◦ Ex: Hydrochloric acid (HCl) releases H+ and Cl-

ions in water Base:

◦ Def: An electrolyte that release hydroxide ions (OH-) in water

◦ Ex: Sodium hydroxide (NaOH) releases OH- in water

Acids and Bases

Concentrations of H+ and OH- ions in body fluids can greatly affect chemical reactions◦ Ex: Blood pressure, breathing rate

We measure these ion concentrations using pH scale ◦ pH scale: Measurement of H+ ion concentration◦ Scale range: 0-14◦ Each number represents 10-fold difference in H+

ions Ex: pH of 6 has 10X H+ ions than pH of 7

pH of 7 means there is an equal concentration of H+ and OH- ions (neutral)

pH scale

Acid: pH = 0-7ish◦ Ex: hydrochloric acid in stomach, battery acid,

vinegar◦ More H+ ions (than OH-) = lower number

Ex: pH of 2 has MORE H+ than pH of 5 Neutral: pH = 7ish (optimal for most life)

◦ Ex: Distilled water, cow’s milk (6.6), human blood (7.4)

Base: pH = 7ish-14◦ Ex: bleach, egg white, ammonia◦ More OH- (than H+) = higher number

Ex: pH of 14 has MORE OH-/less H+ than does 11

pH scale

Two groups of chemicals produced and used in chemical reactions:◦1) Organic:

Def: those that contain both carbon and hydrogen atoms

Ex: macromolecules, methane Nonelectrolytes (usually do NOT release ions in

water)◦2) Inorganic:

Def: the remaining molecules Usually dissolve in water or react with water to

form ions Electrolytes (Ex: acids, bases)

Cellular compounds

Water (H2O):◦ Most abundant compound in living organisms◦ 2/3 of the biomass of an adult human◦ Major component of blood and other body fluids◦ Important solvent (many substances dissolve

easily within it)◦ Plays important role in moving chemicals (ex:

oxygen, salts, sugars, vitamins)◦ Can absorb and transport heat

Oxygen (O2):◦ Enter body through respiratory organs and

transported via blood◦ Organelles use oxygen to release energy from food

Inorganic substances

Carbon dioxide (CO2):◦ Produced as waste product during cellular respiration

(breakdown of food molecules to produce energy)◦ Exhaled via lungs

Salts:◦ Compound composed mainly of oppositely-charged

ions◦ Ex: Na+ and Cl- = NaCl (table salt)◦ Abundant in cells and tissues◦ Provide necessary ions important to

chemical/metabolic processes Ex: nervous system action potential, muscle contraction

Inorganic substances

Made of monomers which combine to form polymers

4 macromolecule groups:◦1) Carbohydrates Ex: sugar, starch, cellulose

◦2) Proteins Ex: enzymes, antibodies, cell surface receptors

◦3) Lipids Ex: fats, steroids, phospholipids (cell membrane

component)◦4) Nucleic acids Ex: DNA and RNA

Organic substances

Carbohydrates Made of C, H, and O (twice as many hydrogen as oxygen)◦Ex: C6H12O6

Often involves chains or rings of carbon atoms joined with atoms of hydrogen and oxygen

Functions: ◦Provide much of energy that cells

require,◦Supply materials to build cell structures, ◦Stored as energy reserves

Carbohydrates Monomers (ONE sugar)

◦Monosaccharide ◦Examples: glucose, fructose, galactose

Dimers (TWO sugars)◦Disaccharides◦Examples: sucrose and lactose

Polymers (MANT sugars)◦Polysaccharides◦Examples: starch, glycogen, chitin, and

cellulose Dimers/Polymers are considered complex carbohydrates

Carbohydrates

Carbohydrates

Chitin Cellulose

Lipids Made of C, H, and O (phospholipids have P)◦Smaller proportion of Oxygen atoms than do

carbs◦Ex: Fat tristearin (C57H110O6)

Do not dissolve in water◦Will dissolve in ether or chloroform

Functions:◦Primary energy storage molecules (fats)◦Insulation (fats)◦Primary component of cell membrane

(phospholipids)◦Used to synthesize other fats (steroids)◦Important to development of gametes

(steroids – sex hormones)

Lipids Parts of Fat molecule:

◦1) Glycerol molecule◦2) Fatty acid chains

◦Fatty acid chains are what make fats diverse Differ in:

# of chains Types of chains

Lipids Triglyceride fats

◦1 Glycerol, 3 Fatty Acid Chains◦Examples: Fats found in adipose tissue

Phospholipid◦1 Glycerol, 2 Fatty Acid Chains◦Example: Molecules found in cell

membrane Steroid

◦4 Carbon ring structure◦Example: cholesterol, testosterone,

estrogen, and other hormones

Lipids (cont)

Lipids (cont)Phospholipid

Lipids (cont)

Cholesterol

Progesterone

Testosterone

Steroids

Protein Made of C, H, O, N, S (not all) Functions:

◦ Structural materials◦ Energy sources◦ Hormones◦ Can combine with carbs to function as cell

surface receptors◦ Detect foreign substances in body◦ Catalysts to speed up chemical reactions

Protein Monomer

◦ Amino Acid (20 found in body) Polymer

◦ Polypeptide chain◦ Amino acids are held together by peptide bond

(covalent bond)◦ Polypeptide chain folds to become a functional protein

Primary (simple chain of amino acids) Secondary (forms alpha/beta chains) Tertiary (alpha/beta chains fold up-on themselves) Quaternary (more than one chain)

◦ Conformation (folding of protein) determines its function

Amino Acid Structure

Polypeptide

H3N+

R

COOH

H

CH3N

+

R

COOH

H

CH3N

+

R

COOH

H

CH3N

+

R

COOH

H

C

Peptide bonds b/t Amino acids

Protein Folding

Protein Folding (cont)

Protein Folding (cont)

Protein Folding (cont)

Nucleic Acid Made of C, H, O, N, and P Functions:

◦Energy source (molecule is broken apart to release energy)

◦Genetic source Monomer- Nucleotide

◦Parts of a nucleotide: 1) 5-carbon sugar 2) phosphate group 3) nitrogenous base

Phosphate

Sugar

Nitrogen Base

Nucleic Acid DNA

◦ Sugar- Deoxyribose◦ Nitrogen Bases- A, T, G, C

RNA◦ Sugar- Ribose◦ Nitrogen Bases- A, U, G, C

ATP◦ Sugar- Ribose◦ Nitrogen Base- A◦ Contains three phosphate groups

A = TG = C

A T

G C

Nucleic Acid - DNA

•Single-stranded

Nucleic Acid - RNA

Ribose

Phosphates

High Energy BondsAdenine

Adenosine

Nucleic Acid - ATP