AP Biology - Biochemistry

Characteristics of Water

Polar covalent, adhesive, cohesive, high specific heat, surface tension, has hydrogen bonding

Water - Adhesion

Water can stick to other things

Water - cohesion

Water can stick to itself

Water - Surface tension

Not about density, as long as something doesn’t break the water’s surface tension, it can stay on top (how bugs are able to walk on water)

Water in plants

Photosynthesis happens in the leaves but water comes from the roots, water evaporates through the stomata (hole in the bottom of the leaf), water molecules are pulled up through tree trunk through cohesion and adhesion

Density when water freezes

When water freezes, it becomes less dense, ice sits on top of the water, gives underwater insulation in winter which is important for aquatic life

Solvent

Part of solution that does the dissolving (water is a universal solvent)

Solute

Part of a solution that is dissolved

Hydrophilic

Attracted to water (through charges), usually other polar molecules

Hydrophobic

Doesn’t like water, usually nonpolar

Water - High specific heat

Helps maintain homeostasis because water doesn’t boil out of our body

Carbonic acid (H₂CO₃)

Important buffer in living organisms

CaCO₃

Coral, increased acidity of the ocean results in more carbonate interaction with the Hydrogen, less coral can be formed

Hydrocarbon

Carbon bonded to hydrogen

Isomer

Same number and type of atoms in different arrangements

Cis isomer

Isomer where similar atoms are on the same side

Trans isomer

Isomer where similar atoms are on opposite sides

Monomer

One block

Polymer

Many blocks hooked together

Dehydration synthesis

Removing a water to bond two molecules

Hydrolysis

Adding a water to break a molecule

Carbohydrates

Sugars, have a 1:2:1 C-H-O ratio, can be mono, di, or polysaccharide

Glucose, fructose, galactose

Common monosaccharides, fructose is pentagon-shaped, glucose and galactose are hexagon shaped, isomers of each other

Ribose

Monosaccharide, the R in RNA, pentagon shaped

Disaccharide

Two monosaccharides hooked together by an oxygen (glycosidic linkage)

Sucrose

Disaccharide of glucose and fructose

Lactose

Disaccharide of glucose and galactose

Maltose

Disaccharide of glucose and glucose

Cellulose

Polysaccharide important for plant structure, aka fiber

Chitin

Polysaccharide important for structure in insects and fungi

Starch

Polysaccharide important for energy storage in plants

Glycogen

Polysaccharide important for energy storage in animals

Lipids

Fat, oils, waxes, steroids

Triglycerides

Three fatty acid molecules, glycerol head and three tails, tails attach to head through dehydration synthesis

Saturated fat

All single bonds in tails, all tails are straight, holding as much hydrogen as possible, solid at room temperature

Unsaturated fat

Bent tail due to double bond, can’t be packed as tightly, liquid at room temp (monounsaturated=1 tail bent, polyunsaturated=multiple tails bent), healthier than saturated fat

Phospholipids

Made up for phosphate polar head, which is hydrophilic, and two non-polar tails, which are hydrophobic, used to create membranes of cells and organelles, hay have led to first simple cell (protocells), can be saturated or unsaturated

Steroids

Four fused rings and a tail, used as messengers within the body

Proteins

Chains of amino acids

Amino acids

Made up of an amino group, a carboxyl group, and a “R” side chain group, all amino acids have a N-C-C chain, 20 amino acids, 9 are essential

Essential amino acids

Amino acids that our bodies can’t produce, we have to get them through food

Peptide bond

Bond between amino acids

Primary structure of amino acids

Order the amino acids are hooked together and the number of each

Secondary structure of amino acids

Due to hydrogen bonding, can either get an alpha helix, where the primary structure starts to twist, or a beta pleated sheet, which is a wavy pattern

Tertiary structure of amino acids

Secondary structure can be bent due to side chains, 3D, the parts start to attract/repel each other, occurs in large proteins

Quaternary structure of amino acids

Multiple polypeptide chains coming together

Conformation

Structure and shape of a protein, proteins must have a specific conformation to do their job

Denatured protein

When a protein loses its shape, due to high temperatures and extreme pH

Chaperonins

Envelopes polypeptide chain, allows the side chains to interact without interacting with other proteins

Enzyme

Type of protein that speeds up reactions by lowering the amount of energy needed for the rxn to run, are specific and controlled, don’t get used up in a reaction

Enzymes are specific

Enzymes target a specific substrate (where the enzyme attaches)

Enzymes are controlled

Substances in the cell can cause enzymes to become more or less active

Active site

Area where the enzyme hooks onto the substrate, active site and substrate must be the same shape for the enzyme to work

Catalase

Breaks down hydrogen peroxide

Lipase

Breaks down lipids

Protease

Breaks down proteins

Lactase

Breaks down lactose

Cofactors

Modifies active site shape by attaching so enzyme can attach to substrate

Inhibitors

Control enzymes (turn them off), competitive inhibitors attach at active site, noncompetitive inhibitors attach somewhere else, both turn off the active site

Key elements in living things

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorous, Sulfun (SPONCH or CHONPS)

Nucleic acids

Code for life, make up DNA and RNA, made of a sugar, phosphate, and base

DNA

Double helix, the sides go in opposite directions, sugar is 3’ end, phosphate is 5’ end, one side goes 3’ to 5’ and the other 5’ to 3’, sugar is deoxyribose (one less oxygen than ribose)

RNA

Single strand, sugar is ribose

Phosphodiester bond

The bond between DNA or RNA molecules

DNA bases

Adenine, Thymine, Cytosine, Guanine (A and G two rings - purines, C and T one ring - pyrimidines)

RNA bases

Adenine, Uracil, Cytosine, Guanine (A and G two rings - purines, C and U one ring - pyrimidines)

Bonding of DNA bases

Hydrogen bonds between bases (A and T = 2 H bonds, G and C = 3 H bonds)

Benedict’s Solution

Used to test for simple carbohydrates

Iodine

Used to test for complex carbohydrates

Biuret Solution

Used to test for proteins

Ethanol test

Used to test for lipids

Benedict’s negative result

Blue when testing for simple carbohydrates

Benedict’s positive result

Orange when testing for simple carbohydrates

Iodine negative result

Dark red when testing for complex carbohydrates

Iodine positive result

Black when testing for carbohydrates

Biuret negative result

Blue when testing for proteins

Biuret positive result

Dark purple/black when testing for proteins

Ethanol test negative result

No separation when testing for lipids

Ethanol test positive result

Separation when testing for lipids