AP Biology - Biochemistry

Atoms

Building blocks of matter

• 25 elements are essential for life

• 4 of those elements make up 96% of living matter

• Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N)

Valence shells

The electrons in the outermost portion

• This guides reactions

Guiding reactions

Tendency for atoms to fill or empty their valence shells

Covalent bond

Two atoms that share a pair of electrons

• Strong, stable

• Both atoms holding onto electrons

• forms molecules

Nonpolar

Pair of electrons shared equally by two atoms

• Atoms involved have similar electronegativity

Polar

Pair of electrons shared unequally by two atoms

• Ex: H20

• Oxygen is way more electronegative than water

Hydrogen bond

Intermolecular force (Happens between molecules)

• Weak bond

• Polar water creates molecular attractions

• Attraction between positive H in one H2O to a negative O in another H2O

Cohesion/Adhesion

H2O to H2O (Cohesion)

• H bonding between H2O molecules

• Surface tension

H bonding with other (Adhesion)

• Capillary action

Water is a good solvent

Polarity makes water a really good solvent

• Easy for things to be dissolved in water

• Things that aren't polar or don’t have charge can’t dissolve in water (oils)

• H2O surrounds + and - ions

Density

Why is ice floating important?

• Ice insulates water below allowing life to survive winters

If ice sank 

• Bodies of water would freeze

High specific heat

Amount of energy required to 1g to 1 degree (C)

• H2O moderates temperatures on earth

• Lots of water in the air stabilizes temperatures in the air

• If water got hot really fast it would be hard to live on Earth

High Heat of Vaporization

Takes a lot of energy to get water to move from liquid to gas taking heat with it

• When we sweat, water molecules absorb lots of heat from our body to evaporate which cools us nicely

• Large bodies of water (oceans, lakes) absorb and release heat slowly, moderating Earth’s climate.

pH scale

Water ionizes 

• H(+) splits off from H2O, leaving OH(-)

• if [H+] = [-OH], water is neutral

• if [H+] > [-OH], water is acidic

• if [H+] < [-OH], water is basic

Buffer

A solution that resists significant changes to its pH when small amounts of strong acid or base are added

• Maintains a stable environment

Why is carbon so special?

All life is built on carbon

• Organic = carbon based 

• Tetravalent (4 bonds) = good builder

What is an isomer?

Molecules with the same molecular formula but different structures

• Different chemical properties

• Different biological functions

• FORM FITS FUNCTION

Functional groups

Parts of an organic molecule that give it distinctive properties

Hydroxyl

• C-C-O-H

• Alcohols, names end in -ol

• Donates H+. acidic

• Increase polarity

Carbonyl 

• C double bonded to O increases polarity

Amino

• -NH2

• Amines are basic, they pull H+ out of a solution

Sulfhydryl

• Compounds with SH = thoils 

• SH groups stabilize the structure of proteins = tertiary structure

• Polar

Phosphate 

• P bonded to 4 O

• Lots of negative charge

• Highly reactive

• Transfers energy between organic molecules

• Acidic, releases H

Carboxyl 

• Acids, they donate H+

• COOH

Polymers

Long molecules built by linking repeating building blocks in a chain.

Monomer

The building blocks themselves

How to build a macromolecule/polymer

Condensation ←→Dehydration

• Joins monomers by “taking” H2O out

• One monomer donates -OH

• Other monomer donates H+

• Together this forms H2O

How to break a macromolecule/polymer

Hydrolysis (Opposite of dehydration synthesis)

• Use H2O to breakdown polymers 

• Cleave off one monomer at a time

• H2O is split into H+ and -OH

• H+ and -OH attach to ends

What are the main purposes of carbs?

• Energy 

• Energy storage

• Raw materials

• Structural materials (building) 

Main formula for carbs

(CH2O)x

• Composed of C, H, and O

• Similar carbons and oxygens

Where is the energy stored?

Energy is stored in C—C bonds 

• This is a direct relationship to potential ATP (Energy currency)

• More bonds = more potential 

Simple to complex carbs

Monosaccharides (1)

• Simple on monomer sugars

• glucose 

Disaccharides 

• 2 monomers 

• sucrose 

Polysaccharides 

• Large polymers 

• starch

What is the bond type for carbohydrates?

Glycosidic linkage

• Disaccharides seem to hold hands

• Monosaccharides seem to be more independent

Diversity of polysaccharides

Costs little energy to build

• Easily reversible = easy to break/build

Function of polysaccharides

Energy storage 

• Starch (plants) 

• glycogen (animals) 

• Alpha formation glycosidic linkage (Enzyme)

Structure

• cellulose (plants) 

• chitin (athropods, fungi) 

• NO Human enzyme (Beta formation glycosidic)

Cellulose

Most abundant organic compound on Earth

• Herbivores have developed a mechanism to digest cellulose (mutualistic)

• Most carnivores have not

What are the primary purposes of lipids (fats)?

Fat

• Long term energy storage 

• Insulation 

• Shock absorption 

Lipids are nonpolar due to the hydrocarbon chains (H-C)

• Lack oxygen so electronegativity is similar

Monomer base

Fatty acids

• DO NOT FORM POLYMERS

What is the bond name for a lipid?

Ester linkage

Types of fats

Saturated

• All C bonded to H

• NO double C-C bonds

• long, straight chains

Unsaturated

• C-C double bonds

• Kinks in the chain

Phospholipids structure

Glycerol + 2 fatty acids + PO4

• Polar “head” 

• Nonpolar “tails”

This makes phospholipids amphipathic (polar and nonpolar)

• They are found in cell membranes

Cholesterol/steroids structure

4 fused carbon rings

• Different steroids are created by attaching different functional groups to rings 

• Different structures creates different functions

Purposes and functions of proteins

Most structurally and functionally diverse group

• Enzymes

• Structure

• Carriers and transport

• Cell communication

• Defense

• Movement 

• Storage

Monomer for proteins

Amino Acid

• 20 different amino acids

Polymer for proteins

Polypeptide

Bond name for proteins

Peptide bond

• Amino group (NH2) to Carboxyl (COOH) of another

Primary (1st degree)

Order of amino acids in a chain

• Sequence is determined by gene (DNA)

• Slight change affects function

Secondary (2nd degree)

“local folding”

• folding short sections of polypeptide

• Hydrogen bonds between folded section

Forms sections of 3D structure

• Alpha Helix

• Beta pleated sheets

Tertiary (3rd degree)

“Whole molecule folding”

• Interactions between distant amino acids

• These interactions are nonpolar 

• Covalent bonds in sulfhydryls stabilize the protein’s shape

Every protein folds to this level

Quaternary (4th degree)

More than one polypeptide chain folded together

• Only then does polypeptide become functional protein

Most proteins fold to this level

Denature/renature

Unfolding of a protein

• Conditions that disrupt H bonds, ionic bonds, disulfide bridges

• pH, temp, salinity

• destroys functionality

Function/purpose of nucleic acids

Genetic material

• stores information

• Transfers information

Monomer of nucleic acid

Nucleotide

• Nitrogen base, pentose sugar, phosphate group

Polymer of nucleotide

DNA - double helix

RNA - single helix

Types of nitrogen bases

Purines

• Double ring as N base 

• Adenine (A)

• Guanine (G)

Pyrimidines

• Single ring as N base

• Cytosine (C)

• Thymine (T)

• Uracil (U)

Bond name for Nucleic Acids

Phosphodiester bond (Covalent)

• Sugar to PO4 bond

Base pairings

Nucleotides between DNA strand

• Purine::Pyrimidine

• A::T/U (2 H bonds)

• G::C (3 H bonds)

When does DNA need to be replicated?

2 strands are complimentary to each other

• Have one, can build other

• Have one, can build the whole/

ATP

Adenosine Triphosphate 

• Energy carrying molecule in cells 

• Nitrogen base, sugar, and phosphate