Chapter 2: Biochemistry

Elements and Atoms

• 92 natural elements arranged on a periodic table– cannot be broken down into simpler substances– represented by 1-2 letter symbols– C,H,O, and N

• 4 most abundant elements in living organisms• makes up 96% of the entire mass of the human

body

Trace Elements• ex: Fe, I, and Mg

• are present in very small amounts

• help maintain healthy cells

• elements are made of atoms

–basic building blocks

–smallest particle of an element

• protons: positive charge • neutrons: neutral or no charge • electrons: negative charge

– small– attracted to the nucleus– travel around the nucleus in energy levels

• nucleus: consists of protons and neutrons– the nucleus is always positively charged because of

the positive protons

• energy levels hold a certain amount of electrons

• 1st energy level only holds 2 electrons (e-)

• 2nd energy level holds 8 electrons

• 3rd energy level holds 18 electrons

• an atom’s identity is based on the number of protons it has (atomic number)

• most atoms have no overall charge because the number of protons equals the number of electrons

– ex: Carbon has 6 protons and will have 6 electrons (+6 + -6 = 0)

• ions: charged atoms

– have lost or gained an electron to give the atom an overall + or – charge

• isotopes: atoms of the same element – have the same number of protons but different

number of neutrons– ex: Carbon (normally has 6 protons and 6 neutrons to

equal a mass of 12: C-12)• C-13: 6 protons + 7 neutrons=13• C-14: 6 protons + 8 neutrons=14

• Radioactive isotopes: used in science and medicine– Can be unstable and break apart, giving off radiation

• Compounds: substance composed of atoms of 2 or more different elements that are chemically combined

– Ex: NaCl, H20, C6H12O6

• Covalent: atoms share electrons (nonmetals with nonmetals)

– H20, C6H12O6 (sugars), fats, and proteins

– Weaker bonds– Force that holds atoms together– Molecule: group of atoms held together by covalent

bonds– Has no overall charge

• Ionic: atoms transfer electrons (nonmetals with metals)

• Gain or lose electrons• Ex: NaCl• Attractive force between 2 ions of opposite charge• Stronger bonds• Many ions are very important in living things

– Na and K: help conduct nerve impulses– Ca: help with muscle contraction

Bonding Venn Diagram

Ionic CovalentBoth

Chemical Reactions• Bonds are formed or broken

• Causes substances to recombine into different substances

• Metabolism: all the reactions that occur within a living organism

– Break down and build molecules

Chemical Equations• Reactants (undergo reactions) --------->

Products (formed by reactions)

• EQUATIONS MUST BE BALANCED!!

• Ex: 2H2 + O2 ---------> 2H2O

# of molecules of each substance

# of atoms of each substance

EQUATIONS MUST BE BALANCED!!

Bell Ringer:

1. The nucleus, the center of the atoms, is made up of ___________ and ____________.

2. The negatively charged particles in atoms are called __________.

3. Different isotopes of the same element have different numbers of __________.

4. In a ___________ bond, electrons are transferred from one atom to another.

5. The process that produces a new set of chemicals is called a ___________________.

Water

• The most important compound in living organisms• Makes up 70-95% of most cells• Water is a polar covalent molecule

– Has an unequal distribution of charge• Has a positive end and a negative end• Opposites attract: forms a weak hydrogen bond

• Hydrogen bonds help hold molecules together– Ex: proteins

Characteristics of Water• Cohesion: high surface

tension• Adhesion: able to creep up

tubes (capillary action)• High heat of vaporization

– Resists changes in temperature

– Ex: sweat cooling• High specific heat (internal

and external temperature stability)

• Expands when it freezes (ice floats)

• Great solvent

Mixtures• Different substances

are not chemically combined

– Individual components keep their own properties

– Ex: sand and sugar

Solution• 1 or more substances are distributed evenly in another

substance (well-mixed)

– Can be a solid, liquid, or gas

– Ex: powdered drink mix (Kool-Aid)

– Important in living things

• Solute: what is getting dissolved

• Solvent: what does the dissolving (what dissolves the solute)

– In greater amounts

• Ex: saltwater

– Concentration of the solution:

• Amount of solute

Amount of solvent

Acids and Bases

• pH: a measure of how acidic or basic a solution is

• pH scale: indicates the concentration of H+ ions in solution

• Ex: stomach juice (pH = 2); blood (ph = 7.2)

• pH below 7 acids (form H ions (H+) in H20)• pH above 7 bases (form hydroxide ions

(OH-) in H20)• pH = 7 is neutral (water)

Buffers• pH of fluids in humans must be kept

between 6.5 and 7.5 (to maintain homeostasis)– Higher or lower than this will affect chemical

reactions within cells

• Buffers: weak acids or bases that can react with strong acids or bases – Prevents sharp, sudden changes in pH

Review:1. Match the term with appropriate description:

Polarity Acidic Basic___________ unequal sharing of electrons

___________ lemon juice, pH 1.5

___________ lower concentrations of H+ ions than pure water

___________ ammonia, pH 11.5

___________ a slight negative charge at one end of a molecule, a slight positive charge at the other end

___________ pH values that are below 7

___________ alkaline solutions

2. A dissolved compound that prevents sharp swings in pH is called a __________.

• organic substances contain carbon (found in all living things)

• carbon is the backbone of living things

– has 4 valence electrons

• can bond with other carbon atoms to form chains, branched chains, or rings

• can form single, double, or triple bonds

• C-C C=C C≡C

• Some compounds have the same molecular formula but different structural formulas (called isomers)

– Ex: fructose and glucose- C6H12O6

Macromolecules (polymers)

• Many carbon molecules bond to form long chains• Ex: proteins and starch• Condensation reaction: water molecule is

removed– Dehydration synthesis– □ + □ = □□

• Hydrolysis: breaking down a polymer– Adding water to break bonds– □□ □□ + water □ + □

Organic Molecules• basic units

are called monomers

• 4 major types

Carbohydrates• Elements: Composed of

C,H, and O

• Monomers: Made up of simple sugars called monosaccharides– 2 monosaccharides combine

to make a disaccharide– many monosaccharides

combine to make a polysaccharide

• Function: Used by cells to provide energy

• Special features: examples of polysaccharides– starch (energy storage

in plants)– glycogen (energy

storage in animals)– cellulose (supports cell

walls in plants)

• Examples: breads, pasta, glucose

Lipids• Elements: Made of C,H, and O• Monomer: 3 fatty acids and a

glycerol molecule• Functions:

– Energy storage– Insulation (blubber in some animals)– Waterproof– Important component of the cell

membrane

• Special features:– Insoluble in water– Structure: May be saturated (C-C) or

unsaturated (C=C)

• Examples: fats, oils, waxes, steroids

Proteins

• Elements: Composed of C,H,O,N, and sometimes S• Monomer: Long chains of amino acids (20) joined by

peptide bonds• Functions:

– Structure: hair, nails, hooves, horns, claws, beaks– Contracting muscle tissue– Transport oxygen in blood– Provide immunity

• Special features:– Basic building material for all living things– Enzymes increase reactions

• Examples: Insulin, hemoglobin, enzymes, meat, fish

Enzymes• Proteins that change the rate

of a chemical reaction• Called a biological catalyst

(lowers the activation energy)– Energy needed to start a

reaction

• Enzyme animation

Nucleic Acids• Elements: Composed of

C,H,O,N, and P• Monomer: nucleotides (3

parts)– Nitrogen base (N-base)– Sugar– Phosphate group

• Functions: – Genetic code

• Special features:– DNA: holds all genetic

information– RNA: copies and carries out

instructions from DNA

• Examples: DNA and RNA

How do you test for the presence of organic compounds?

• Carbohydrates:– Starches- Iodine test

• Turns starches blue/black– Sugars- Benedict solution

• Changes from sky blue to orange

• Lipids:– Brown paper bag test-

leaves grease stain• Proteins:

– Biuret: changes from lavender to black

Bell Ringer:

1. The two basic kinds of nucleic acids are ______ and ______.

2. Biological catalysts, or enzymes, act by lowering the _________ required for a reaction.

3. A _______ is a large compound formed by the joining of small compounds called monomers.

4. Protein monomers are called ________.

5. A ______ stores and transmits genetic information.