Biochemistry:

Polar Molecules

electrons distributed unevenly

charged molecules (ions)

Non-Polar Molecules

electrons distributed evenly

uncharged molecules -neutral molecules or atoms

Polar:

salts

ions

water

acids

bases

Non-polar:

gasoline

oil

lipids

fats

Organic Chemistry:

mostly in or from living things

(some can be formed without life)

All contain

C

Most contain O H

Some contain

N S P

A few contain

Fe Ca Na Cl Mg K

S P O N C H

6 most common elements in organic compounds

(not in order)

Note:

water H₂O

carbon dioxide CO₂

calcium carbonate CaCO₃

are inorganic compounds

(even if produced by living organisms)

WATER-

most important solvent

-polar

water

-cohesion (attraction between molecules of the same substance)

holds drops together

Water

-Adhesion

(force between one substance and another)

makes water a great solvent

explains capillary action

Carbon has 4 vacancies in its outer orbit

Forms bonds in 3 D in a tetrahedral shape

Carbon can form chains

Carbohydrates:

mono saccharides

di saccharides

poly saccharides

starches

Lipids:

chains of C and H

saturated

unsaturated

fatty acids

fat + acid

fat = chain of non-polar C and H

acid = COOH

carboxylic acid group

glycerol (glue for fats)

triglycerides

3 fatty acids + glycerol

hydrolysis

hydro lysis

hydro = water

lysis = break apart

dehydration synthesis

dehydrate=remove water

synthesis=put together

Nucleic Acids

P & N in addition to CHO

chemically, they are- surprise- acidic

2 kinds of nucleic acids

RNA

DNA

RNA=ribonucleic acid

DNA=deoxyribonucleic acid

DNA is the hereditary material of almost all life on earth

(exceptions some viruses like HIV)

Like a code the information to form a living organism is in the nucleic acid sequence

Nucleic acids first isolated from the nucleus of cells

DNA (and RNA) are long chain molecules with repeating subunits called nucleotides

Nucleotide=

5 C sugar

(ribose or deoxyribose)

phosphate group

(PO₄)

nitrogen base

Nitrogen base is an organic base with -surprise- nitrogen in it

In DNA there are only 4 kinds of bases

adenine

thymine

cytosine

guanine

In RNA there are only 4 kinds of bases

adenine

uracil

cytosine

guanine

purine

Adenine and guanine have two rings in the base

pyrimidines

Thymine, uracil and cytosine have only 1 ring

In forming the classic (Read "The double helix") double helix or when DNA and RNA bond the distance between the sides of the helix determine that you can only have 3 rings.

That is one pyrimidine

and one purine

Due to the bonding structure (3D structural formulas) for hydrogen bonds (polar molecules)

adenine can only bond to thymidine (or uracil) and

cytosine can only bond with guanine

Due to the structure of the ribose sugar (as opposed to the deoxyribose sugar) two strands of RNA can not form a long lasting double helix

RNA is the "translator" from the language of nucleotides to the language of proteins

roteins

N in addition to C, H, O

General Structure

In higher life on earth 20 different kinds of R groups

Like letters in the alphabet, the combinations are what make proteins different

Smallest proteins are chains of 50 amino acids

(1000 atoms)

Really big ones can be 100,000 aa's and millions of atoms

(one molecule)

Examples:

1

dehydration synthesis (remember)

H from the amino group

OH from the carboxylic acid

makes water and bonds two amino acids together

dipeptide

with an amino group

and a carboxylic acid group

polypeptide

Proteins do things

They are hormones,

enzymes, and structural components (muscle).

Enzymes:

function as biological catalysts, speeding up reactions, and controlling them inside a cell

names

usually (not always) end in -ase

lipase

protease

amylase

pepsin (oops)

Some enzymes work inside the cell others (digestive enzymes) work outside (are secreted from) the cell

Substrate

(what it acts on)

How they work

active site

enzyme-substrate complex

see diagrams page 69

3D lock and key fit

catalyzes reaction by reactant placement

induced fit-enzyme 3D shape changes slightly as bonding takes place, catalyzing reaction

Key points/Factors that affect enzyme action

1-small amounts of enzyme can cause the reaction of large amounts of substrate

2-reactions occur at normal cell temperatures

3-work best at specific temperatures

4-work best at specific pH

5-rate depends on substrate and enzyme concentration, but saturates if one concentration is held constant

6-coenzymes needed

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