ap bio: unit 2

organic chemistry

organic chemistry

branch of chemistry that specializes in the study of carbon compounds

major elements in organic compounds

CHNOPS

organic compounds

contains carbon and hydrogen

diversity of carbon

it has 4 valence electrons

how many bonds can carbon form?

4 covalent bonds

carbon's most frequent bonding partners

hydrogen, oxygen, nitrogen

what types of bonds can carbon form?

single, double, or triple

what are the 4 macromolecules?

carbohydrates, lipids, proteins, nucleic acids

isomers

molecules that have the same molecular formula but differ in atom arrangement

structural isomer

varies in covalent arrangement

cis-trans isomer

differ in spatial arrangement

enantiomers

mirror images of molecules

functional groups

behavior of organic molecules depends on these

hydroxyl function

can form hydrogen bonds with water molecules helping to dissolve sugars

carbonyl function

found in sugars and gives rise to ketoses and aldoses

carboxyl function

acts as an acid and can donate H ion

amino function

acts as a base, can pick up an H+ from the surrounding solution

sulfhydryl function

cross-linking to stabilize protein structure

phosphate function

forms ATP

methyl function

affects DNA expression

dehydration synthesis

synthesizes a polymer by removing a water molecule

hydrolysis

breaks down a polymer by adding a water molecule

carbohydrate monomers

monosaccharides (glucose, fructose, galactose)

monomers

building blocks of polymers

hydrogen:oxygen ratio in carbs

2:1

dissaccharides

two monosaccharides joined by glycosidic linkage

glycosidic linkage

covalent bond by a dehydration reaction

common dissacharides

maltose, sucrose, lactose

maltose

glucose + glucose

sucrose

glucose + fructose

lactose

glucose + galactose

polymers

chains of monomers

glycogen

found in animals for energy storage

starch

found in plants for energy storage

cellulose

found in plants for structure

chitin

found in insects for structure

functions of proteins?

enzymes, storage, hormones, movement, defending, transport, receptors, structural

enzymatic proteins

selective acceleration of chemical reactions

storage proteins

storage of amino acids

hormonal proteins

coordination of an organism's activities

contractile and motor proteins

movement

defensive proteins

protection against disease

transport proteins

transport of substances

receptor proteins

response of cell to chemical stimuli

structural proteins

to support

how many amino acids are there?

20 amino acids

what is the bond between amino acids?

peptide bonds

protein monomer

amino acid

amino acid

organic molecule with both an amino group and a carboxyl group

alpha carbon

the central carbon atom of each amino acid

chemical and physical properties depend on what?

amino acids, which affect polypeptides

nonpolar amino acids

hydrophobic

polar amino acids

hydrophilic

acidic amino acids

negatively charged due to carboxyl group (hydrophilic)

basic amino acids

positively charged due to carboxyl group (hydrophilic)

amino acid polymers

polypeptides

polypeptides

amino acids bonded trhhough dehydrationg, forming a peptide bond

why do proteins spontaneously fold?

due to bonds (like hydrogen, ionic, disulfide bridges)

a proteins function depends on what?

its ability to recognize and bind to other molecules (very specific)

primary structure

the sequence of amino acids

secondary structure

either an alpha helix or beta pleated sheet.

tertiary structure

results from interactions between side chains.

quarternary structure

the protein chains in a closely packed arrangement

what determines protein structure?

conditions like pH, salt concentration, temperature

denaturation

loss of normal shape of a protein due to heat or other factor

when is denaturation common?

when proteins are transferred from an aqueous environment to a nonpolar solvent

serious diseases are linked to what?

misfolded proteins

gene

sequence of DNA that codes for a protein and determines a trait

nucleic acid

DNA and RNA

nucleic acid monomer

nucleotide

DNA (full name)

deoxyribonucleic acid

RNA (full name)

ribonucleic acid

functions of DNA

directs RNA synthesis, replicates, protein synthesis

DNA

genetic material inherited from parents

mRNA

messenger RNA, carries instructions from the nucleus to ribosomes to produce proteins

where are ribosomes?

cytoplasm

where is DNA stored?

nucleus

prokaryotes don't have what?

nucleus, they still use mRNA

nucleotide

made a 3 parts

3 parts of a nucleotide

5 carbon sugar (pentose), phosphate (1-3), nitrogenous base

nucleoside

the portion of nucleotide with no phosphate group

nucleic acid polymer

polynucleotide (DNA and RNA)

nitrogenous base

1 to 2 rings that include nitrogen atoms, two families

pyrimidine family

one 6-membered ring of carbon and nitrogen atoms

cytosine

pyrimidine. pairs with guanine. found in both DNA and RNA

thymine

pyrimidine. pairs with adenine. found only in DNA. replaced by uracil in RNA.

uracil

pyrimidine. pairs with adenine. found only in RNA. replaces thymine

purine family

one 6-membered ring fused with one 5-membered ring

adenine

purine. pairs with thymine in DNA and uracil in RNA

guanine

purine. pairs with cytosine. found in both DNA and RNA

what do nitrogenous bases attach to?

sugar, deoxyribose or ribose

what bonds adjacent nucleotides?

phosphodiester linkage

phosphodiester linkage

a phosphate group that links the sugars of two nucleotides

sugar-phosphate backbone

a repeating pattern of sugar-phosphate-sugar-phosphate

how to find 5' and 3'

start from the oxygen and count in a clockwise motion

double helix

two strands of nucleotides wound about each other; structure of DNA

antiparallel

subunits run in opposite directions (5' and 3')