AP Biology: Unit 1 - Biochemistry

Chemical Properties of Water

- polar molecule

- attract to opposite sides

- water's polarity allows it to hydrogen bond with other water molecules or other polar molecules

Water's Importance

- transports substances, needed for chemical reactions, keeps temperature constant

- universal solvent

Surface Tension of Water

- cohesion and adhesion

- resists being ruptured

- hyrdogen bond with nearby water molecules

Cohesion

water molecules attract and bond to other water molecules

Adhesion

water molecules are attracted and bond to other polar or charged molecules

Capillary Action

- Water adheres to the side of tubes that are lined with polar/charged molecules and "crawls" up the tube. The water molecules do not separate because of cohesion

- helps plants pull water from its roots

Water Resists Temperature Changes

- individually weak, collectively strong

- lots of hydrogen bonds

- a LOT of energy to break

- High Specific Heat Capacity

- maintain constant internal temperature for homeostasis

Solvency

substance that dissolves other chemical

Solvency of Water

- excellent solvent because it is polar

- pulls ionic compound into ions

Covalent Bonds

chemical bonds that involves the sharing of electrons to form electron pairs between atoms

Ionic Bonds

type of linkage formed from the electrostatic attraction between oppositely charged ions in a chemical compound

Hydrogen Bonds

- An attraction between two atoms that already participate in other chemical bonds.

- One of the atoms is hydrogen, while the other may be any electronegative atom

Electronegativity

- different atoms attract electrons more than others

- atoms that pull electrons closer to them are more electronegative

- flourine, oxygen, nitrogen

Biomolecules

- organic molecules

- primarily made from carbon and oxygen

- required for life: carbohydrates, lipids, proteins, nucleic acids

Carbon's Importance

- form 4 covalent bonds

- more structures = more shapes = more functions

Dehydration Synthesis

water is released to create a bond and forms a longer polymer

Hydrolysis

opposite of dehydration synthesis; water is used to break chemical bonds

Biomolecule Metabolism

series of chemical reactions that build up or break down biological molecules

Biomolecule Catabolism

- Reactions that break down materials

- Catabolic reactions break down polymers and release energy

Biomolecule Anabolism

- Reactions that make or build up materials

- Anabolic reactions make polymers and store energy

Carbohydrates

sugars; ratio of 1:2:1 (carbon, hydrogen, oxygen); linear and ring form structures

Monosaccharide

monomer of carbohydrates; joined via a glycosidic bond

Polysaccharide

polymer of carbohydrates; energy storing; in humans - glycogen, in plants - starch

Functions of Carbohydrates

short term energy source; energy storage; structure

Structural Polysaccharide

- linear structure and can stack to form stable structures

- used to make cell walls for plants

- we do not have enzymes to break glycosidic bonds

Functional Groups

clusters of atoms on a molecule that give the molecule polarity or acidity

pH

- how acidic something is

- acids give up H+ ions

- bases accept H+ or create OH-

Lipids

fats, oil, waxes; long carbon-hydrogen chains; hydrophobic/nonpolar nature; insoluble in water

Triacylglycerols

glycerol head, 3 fatty acids

Phospholipids

- also glycerol head but with phosphate group and 2 fatty acids

- used to form cell membrane

- Hydrophilic head and hydrophobic tail

Steroids

4 fused hydrocarbon rings; often used a signaling molecules

Saturated Fats

no carbon-carbon double bonds; long hydrocarbon chains can stack and have more intramolecular attraction; solids at room temperature

Unsaturated Fats

double bonds leading to bends in the chain; bends prevent stacking; liquids at room temperature

Proteins

- found in meats and muscles

- 20 amino acids

- 4 different structures

- carbon, hydrogen, oxygen, nitrogen

- wound repair, catalyzing chemical reaction

- enzymes speed up chemical reactions; maintain homeostasis

- found in cell membrane; transportation of materials

Basic Amino Acid Structure

carboxyl group (carbon double bonded to oxygen and OH), amino group (2 hydrogens bonded to a carbon), R-side chain

Primary Structure of Protein

sequence of amino acids determine how protein folds; change in sequence causes protein to misfold and not function properly

Secondary Structure of Protein

folding into alpha helices and beta sheets after the functional groups hydrogen bond; R-side chains are not involved

Tertirary Structure of Protein

finished folding; caused by interactions between R-side chains

Quaternary Structure of Protein

multiple polypeptide chains come together (not all proteins have this)

Protein Directionality

C-terminal (ends in carboxyl group) and N-terminal (ends in amino group)

Hydrophobic

scared of water

Hydrophillic

not afraid of water

Hydrophobic Collapse

major driving force behind the structure; hydrophobic inside the molecule and away from water

Other R Group Interactions

- hydrogen bonding between side chains

- charge attraction between acidic (-) and basic (+) charges

- hydrogen bonds are sensitive to temperature and pH

DIsulfide bridges

strong bonds between sulfure atoms on cystine amino acids (increase stability)

Denaturalization

changes in temperature causing disruption ahd breaks the protein

Nucleic Acids

genetic materials; carbon, hydrogen, oxygen, nitrogen, phosphorous

Nucleotide Structure

phosphate group, 5 carbon sugar, nitrogen-containing organic base (A, T, C, G)

Function of Nucleic Acids

- store genetic information

- DNA and RNA

- antiparallel (5` and 3` ends)

- carbons in sugars are labeled by direction

DNA Structure

- eukaryotes - long structure, prokaryotes - circular structure

- deoxyribose

- more stable than RNA

- found in nucleus

- sugar phosphate formed by phosphodiester (covalent) bonds

- twisted into a double helix due to repulsion of negative charge

- linked together by hydrogen bonding

Pyrimidians and Purines

- A, G and purines and have double carbon rings

- C, T, U are pyrimidines and have single carbon ring

Base Pairing Rules

A - T, C - G

C - G are connected with 3 hydrogen bonds so they are stronger

RNA

- single-stranded

- A, U, C, G

- ribose

- used as a copy of DNA to make proteins

- make ribosomes, bring amino acids together