Ap Bio Organic chemistry

Covalent

Shares electrons

Ionic

donate electrons

Protons

positive charge in nucleus

Neutron

neutral, in the nucleus, determine isotopes (C-12)

radioisotope

radioactive and synthetic, chemical element that releases radiation as it breaks down and becomes more stable. used in imaging

Cation

Ionic that donates electrons (+)

Anion

Ionic that accept electrons (-)

molecule

group of two or more atoms held together

compound

A specific molecule that needs at least two different type of atoms

Non polar covalent bond

electrons are equally shared

Polar covalent bond

unequal sharing of electrons, both side are slightly positive or negative

GC-content

In DNA, it is harder to seperate than AT because it has 3 H bonds

AT-content

have 2 H bonds

Hydrophilic

Having an affinity for water.

Hydrophobic

Having an aversion to water; tending to coalesce and form droplets in water.

Acids

are proton (h+) donors

bases

are proton (h+) acceptors

Buffers

a set of chemicals that stabilize ph

Universal solvent

Water can dissolve lots of different solutes, such as polar solutes and ionic salts, but not good at dissolving non-polar solutes

Density

water is very dense in its liquid form than its solid form

Heat capacity

Water stores a lot of energy, such as removing heat from sweating, and releasing sun's energy from hurricane

Transparent

photosynthesis can happen in aquatic marine environment

Cohesion

the sticking together of particles of the same substance. ex: forming surface tension of H2O

adhesion

attraction between molecules of different substances, ex: xylem and pholem, moving water and nutrients

5 H2O properties

Universal solvent, Density, Heat Capacity, Transparency, Cohesion and adhesion

What is organic chemistry primarily based on?

Carbon-based chemistry

How many binding sites does carbon have?

Four binding sites

Are most organic molecules simple hydrocarbons?

Very few are just simple hydrocarbons

What are functional groups in organic molecules?

The reaction centers of the molecules

Methyl

CH4, it is in fatty acids and can be in amino acids, non polar such as butter

alcohol hydroxyl

OH, it is in carbohydrates, alcohol, and can be in amino acids, polar such as sugar

amino

H2S, it is in amino acids, basic and accepts H+ and polar

carboxylic acid

COOH, it is in amino acids, and it is acidic and polar

phosphate

POOOHH, it is on nucleotides and phospohlipids, it is polar and holds energetic bonds

Sulfhydryl

SH, it can be in amino acids such as cystenine, it forms bonds between amino acids

Keto

C=O, it is in sugars and amino acids, it is polar

Condensation

Water forming reaction, condensation is the chemical mechanism used in many anabolic processes, making peptide bond

hydrolysis

Water breaking reaction, making polymer into monomer, meaning that it is catabolic

how does condensation and hydrolysis work together?

condensation makes polymers and forms H2O, hydrolysis, which uses water to break down polymer and form monomer

4 main classes of biomolecules

carbohydrates, lipids, proteins, nucleic acids

1. Carbohydrates

extremely abundant, primary used for enegy and structure

Monosaccharides

monomer of carbohydrates and can be easily dissolved in water, such as glucose, which is a primary energy source that forms ATP

Disaccharide

Formed by monosaccharides by condensation, forming moltose or sucrose with a byproduct of water

What is the bond that put carbs together?

glycosidic bond

Polysaccharide

A polymer of many monosaccharides, can form starch, glycogen, and cellulose

Starch

excess glucose in plants for energy use, very branched, and humans have amylase to break down. Ex. potatoes

Glycogen

Excess glucose in animals, stored in the liver and muscle, ,more branched than starch

Cellulose

glucose polymer forms the structure of the plant, straight chains. Ex wood

2. Lipids

such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

What is the monomer of lipid called?

fatty acid

Saturated fat

Single bonds and carbons are saturated in hydrogen, consist of acid group (polar) and a methyl group (non-polar), in solid form

How does lipid become more polar?

The longer the carbon chain is, the more non-polar it becomes

Unsaturated fat

Double bonds, in liquid form

Triglycerides

Consists of 3 fatty acids and glycerol, bound with ester bond with a byproduct of H2O, they are also a polymer of lipid

Phospholipid

The main component of the cell membrane, consists of 2 fatty acids (hydrophobic, non-polar) and phosphate (hydrophilic, polar, facing in and out of the cell)

Steriods

Classified as lipids, consist of 4 rings of carbon and based on cholesterol

Cholesterol

It can be converted into testosterone, estrogen, and progesterone

Who manufactures lipids

Endoplasmic reticulum

3. Protiens

Polymer of amino acids, which consists of an acid group and an amino group

Amino acid

There are 20 standard amino acids, and DNA provides the code for which amino acid to use in a protein

How do amino group and a carboxyl group bond together

Peptide bond

Primary sturcture of Protein

sequence of amino acids by peptide bond creating polypeptide chain

Secondary structure of Protein

The R group starts interacting with each other and creating an intermolecular bond (H-bond). They twist and turn to create alpha helix and Beta pleated sheet

Tertiary sturcture of Protein

The polypeptide form into a 3D shape by x-helix and beta pleated sheet with a domain

Domain

created in the tertiary structure that it is the reaction center for the protein(ex heme in red blood cells)

Quanternary structure of Protein

tertiary structure combined to form a protein

4. Nucleic acid

polymer of nucleotides: phosphate group, sugar, base, used to control reactions, basis for hereditary info DNA/RNA, energy currency, messenger molecule

ATP

adenosine triphosphate, the main energy source that is created in the cytoplasm (glycolysis) and mitochondria(aerobic respiration)

DNA/RNA

backbone of phosphate and sugar, purine pairs to a pyrimidine base with H bond

DNA

have the base T and its sugar is deoxyribose, forming double stranded polymer

RNA

have the base U and its sugar is ribose, forming single single-stranded polymer