AP BIO Unit 1

Topics: data collection, functional groups, properties of water, organic chemistry (macro molecules, isomers, etc.).

mean vs median

mean is affected by outliers, median is not

mean > median

outliers on the high end of the data

mean < median

outliers on the low end of the data

standard deviation

shows the spread of the data

high standard deviation

high variation in data

low standard deviation

data is consistent

standard error (of means)

compare our data to all possible data

low standard error of means

our data is similar to all the data

high standard error of means

our data is different than all possible data

covalent bonds

sharing of electrons

non-polar covalent bonds

electrons are shared equally

polar covalent bonds

electrons are shared unequally

functional group

group of atoms within a molecule that interacts in predictable ways with other molecules (hydroxyl, amino, carboxyl, carbonyl, methyl, sulfhydryl, phosphate)

hydroxyl group

OH, consists of a hydrogen atom covalently bonded to an oxygen atom, represented as (-OH); polar, weakly acidic (donates proton H+), can form H bonds (water soluble), high BP, ex. ethanol, methanol, etc.

carbonyl group

-CO, consists of a carbon atom double bonded to an oxygen atom (C=O); reactive and versatile, polar, high BP, can form H bonds (water soluble), used to make new bonds with other molecules, ex. aldehydes, ketones, carboxylic acids, esters, amides

aldehyde

an organic molecule with a carbonyl group located at the end of the carbon skeleton

ketone

when the carbonyl group is in the center of the carbon skeleton

carboxyl group

COOH, functional group consisting of a carbonyl group (C=O) and a hydroxyl group (OH) bonded to the same carbon atom; weak acid (bc of hydroxyl group donating H+), polar, H bonding (donor H in OH and acceptor O in C=O), high MP and BP

amino group

NH2, functional group that can accept a proton (H+) from a solution, becoming positively charged (NH3+); basic, classified based on R groups, polar, can form H+ bonds, water soluble, high BP and MP

sulfhydryl group

-SH, strong, unpleasant odor, low BP, limited H+ bonds, can form disulfide bridges with other sulfhydryl groups (-S-S-), strong slightly polar covalent bond (S more EN than H), low water solubility, ex. cytesine, glutanthoine, etc.

phosphate group

PO4, soluble in water, added and removed from molecules easily, gives molecule a negative charge, polar, low BP

polymer

large compound formed from combinations of many monomers

monomer

a simple compound whose molecules can join together to form polymers

ionic bonds

the transfer of electrons

electronegativity

how strongly an atom pulls electrons towards itself, EN increases diagonally up right, noble gases not included bc they achieve octet rule, F is the most EN

hydrogen bond

a weak attraction between a hydrogen atom and a highly electronegative atom (O, N, F) in another molecule or within the same molecule

water molecule properties

high polarity, can form H bonds, high heat capacity and heat of vaporization, can act as a solvent

cohesion

water molecules sticking to water molecules

adhesion

water molecules sticking to other molecules

surface tension

cohesion causes a film of surface water

c+a capillary action

due to cohesion and adhesion, water climbs narrow tubes

high specific heat (water)

how much energy it takes to raise the temp; stabilizes the temp

high vaporization point (water)

takes effort to move molecules fast

why is water able to stick to itself and other molecules?

bc the H bonds between H and O has a charge to it; it is bc the polar covalent bonds (sharing electrons)

why is ice less dense than water?

bc water is slightly polar (H+) and (-), forming hydrogen bonds; molecules slow down, ice created more space with it’s bonds, they push farther apart

organic chemistry

the study of structure, properties, composition, preparation, and reactions of carbon containing compounds; these elements might include other elements such as CHONPS

properties of carbon

only has 4 VE (needs 8), forms 4 covalent bonds with other atoms, can be single, double or triple bonds

why do bonds matter?

types of bonds change the shape; shape gets smaller with more bonds (single, double or triple)

properties of an acid

more H+ ions, pH below 7

properties of a base

more OH- ions, pH above 7

CHONPS

key elements found in living things; carbon (is the central element), hydrogen (is often used in energy exchange, used to create energy gradients as an ion, basis of acidity/alkalinity), phosphorus (in phosphate groups such as ATP), nitrogen, oxygen, sulfur

carbon skeleton

forms long chains containing single and/or double bonds; forms ring structures, hydrocarbons

isomers

molecules with the same molecular formula, but different structural formula (which indicates different properties)

dehydration synthesis (condensation rxn)

enzymes pull a hydroxyl group (an -OH) off of one monomer (or a group of already connected monomers); a hydrogen atom is pulled off the other; pulling out water

hydrolysis

enzymes insert a water molecule between the monomers making up the polymer; breaks the polymer apart

structural isomers

have different bonding patterns and organization

stereo isomers

different bond angles

cis-trans isomers

cis (same), trans (opposite); cis bonds are on the same side (I), trans bonds are on opposite sides (diagonal \)

enantiomers

one pair of molecules that are mirror images of each other; inverted, essentially (KL | LK)

what is the relationship between monomers and polymers?

polymers are made up of monomers; dehydration synthesis makes polymers; hydrolysis turns polymers into monomers

monosaccharides

are monomers, carbohydrates

disaccharides

are 2 monomers connected; carbohydrates

polysaccharides

are many monomers connected together; carbohydrates; can be homopolysaccharides or heteropolysaccharides; can be linear or branched

primary function of carbohydrates

production and storage of energy; mechanical support; every sugar ends in “-ose”; molecular recognition

carbohydrate structure

often drawn in linear forms but usually forms a ring structure in aqueous solutions; can be aldose sugars or ketose sugars; have the general formula of 1C: 2H: 1O

carbohydrates

important macromolecule; can be monosaccharides, disaccharides, or polysaccharides (sugars, essentially)

proteins

important macromolecule; made up of amino acids; fully formed and functional polypeptide

protein properties

structural, enzymatic, storage, transport, chemical messengers, receptors, movement, defense

amino acid structure

consists of three parts: amino group, carboxylic acids group, side chain (R group); side chain attaches to the central C atom

non-polar amino acids

have no charge; side chains almost exclusively hydrocarbons; are always hydrophobic

polar amino acids

always hydrophylic, tend to play important roles in active sites of enzymes

electrically charged amino acids

acidic amino acids are negatively charged; basic amino acids are positively charged at body pH; interact with other amino acids bc their charge

peptide bonds

dehydration reaction occurs; carboxylic acid groups of one amino acid connects to amino group of another amino acid

polypeptides

short chains while proteins are long, functional chains of amino acids

4 levels of organization (proteins)

primary, secondary, tertiary, quaternary

primary structure of protein

sequence of amino acids (lvl 1); the chain has an N-terminus and a C-terminus; covalent bonds (peptide bonds) are formed between the carboxyl group of one AA and the amino group of the next, linking them together

secondary structure of protein

forms bc of H bonds between parts of the polypeptide backbone; B sheets form bonds with parallel chains (pleated); A helixes form bonds between every 4th amino acid in a spiral (curly); describes local folded patterns

tertiary structure of protein

3D arrangement of a protein’s polypeptides chain; forms bc of interactions between parts of amino acid side chains

quaternary structure of protein

the organization of multiple polypeptide chains (subunits) into a larger, functional protein complex; interaction between 2 or more seperate proteins to make one complete, functional protein.

what is the name of the monomer and polymer for a protein? what do proteins do for cells?

amino acid; polypeptide - they provide structure, transport, catalysts, etc.

denaturation

the process where a protein or nucleic acid loses its native structure, changing its function; can’t change the primary structure; the shape of the protein is altered

nucleic acids

large biomolecules, essential in all living cells and viruses, that serve as the primary information-carrying molecules

nucleotides

monomer; consists of three things: 5 carbon sugar, nitrogenous base, 1-3 phosphate groups

nitrogenous bases

purines have 2-ring structure; pyrimidines have 1-ring structure; A, T, and U form 2 hydrogen bonds (RNA has U); G, C form 3 hydrogen bonds

pentose sugar

deoxyribose contains one less oxygen than ribose; carbon numbering is extremely important for understanding polymer structure and function

phosphate group (NA)

phosphate groups are unstable, high energy functional groups; addition of groups require energy; removal of groups releases energy

nucleic acid polymers

phosphate group of 1 nucleotide connects to the 3¹ carbon of the sugar in the previous nucleotide; single stranded NA; in double-stranded DNA, the nitrogenous bases form hydrogen bonds between parallel strands; coils into a double-helix structure

deoxyribo nucleic acid (DNA)

double-stranded; used to store and transmit genetic info

ribo nucleic acid (RNA)

used to carry and translate genetic info; controls gene processes, etc.; uses sugar ribose instead of deoxyribose; uses bases G, C, A, U; single-stranded

adenosine triphosphate

stores and carries energy; acts as a coenzyme; can exist as ATP, ADP, or AMP (M is for mono)

lipids

only macromolecule that's not a polymer; hydrophobic; fats, oils, waxes, phospholipids, steroids; long-term energy storage; membrane structure; protection'; chemical messengers; longer energy storage than carbs

triglycerides

composed of glycerol and 3 fatty acids

fatty acids

can be saturated or unsaturated (H vs no H); saturated only have single bonds between carbons; unsaturated have at least 1 double bond between carbons

saturated fatty acid

pack tightly together; form rigid aggregates; solid at room temp

unsaturated fatty acid

packed together loosely depending on # of bonds; greater potential for movement; liquid at room temp; form oils

phospholipids

glycerol with 2 fatty acids and a phosphate group; phosphate group often has other molecules linked to it; has polar head and non-polar tail; used by living things to create membranes; keeps internal and external environment separate bc hydrophobic

steroids

consists of a carbon skeleton of 4 fused rings; have many diverse functions

cholesterol in membranes

embedded within the phospholipid bilayer; makes the membrane more fluid in water

waxes

mixtures of various lipids; play protective structural role; leaf cuticle, cercumen, lanolin, spermaceti