Bio Unit 1 The Chemistry of Life

element v compound

element

• pure substance

• can’t be broken down by ordinary means

• ex: hydrogen, nitrogen

compound

• 2 or more different elements combined in a fixed ration

• ex: h20, co2

elements of life

carbon, hydrogen, nitrogen, oxygen, phosphorous, sulfur

how to read element chart

isotopes

number of neutrons varies, but same number of protins

covalent bonds

strong bonds

sharing of electrons

polar and nonpolar

polar covalent bonds

between atoms that differ in electronegativity

ex: h20

nonpolar covalent bonds

electrons shared equally

exL 02, H2

ionic bonds

transfer of electrons between atoms

2 ions bond between givers and takers
ex: Na+Cl-

affected by environment

hydrogen bond

weak bond

h of polar covalent molecule bonds to electronegative atom of other polar covalent molecules

van der waals interactions

weakest bond

slight, fleeting attractions between atoms and molecules close together

ex: gecko toe hairs + wall surface

purposes of different bonds

chemical reactions

reactants → products

some are reversible

chemical equibilibrium

point at which forward and reverse reactions offset one another exactly

no net change in concentrations of reactants/products

radioactive isotopes

An unstable form of a chemical element that releases radiation as it breaks down and becomes more stable. Radioisotopes may occur in nature or be made in a laboratory. In medicine, they are used in imaging tests and in treatment.

valence electrons

the electrons in the outermost or valence shell, are important

provide insight into an element's chemical properties and are the ones gained, lost, or shared during a chemical reaction. In general, atoms are most stable and least reactive when their outermost electron shell is full.

single v double bond

A single bond involves one shared pair of electrons between two atoms, while a double bond involves two shared pairs of electrons between the same two atoms. Single bonds are longer and weaker than double bonds. 

hydroxyl group

-OH

alcohol

specific name usually ends in -ol

carbonyl group

sugars

compound name: ketone or aldehyde (if carbonyl group is at end of a carbon skeleton

carboxyl group

-COOH

acts as an acid (can donate H+)

compound name: carboxylic acid or organic acid

amino group

-NH₂

compound name: amine

acts as a base

sulfhydryl group

-SH

two sulfhydryl groups can react to form a “cross link” that helps stabilize protein structure

compound name: thiol

phosphate group

-OPO₃

contributes negative charge

compound name: organic phosphate

methyl group

-CH₃

affects the expression of genes when on DNA or on proteins bound to DNA

compound name: methylated compound

water is a polar/nonpolar molecule

polar

why is water polar?

because of the unequal sharing of electrons between oxygen and hydrogen since oxygen has a higher electronegativity than hydrogen and h20 has a bent/assymmetrical shape

in h20, region around oxygen has a partial ? charge, region near the hydrogen has a partial ? charge

negative, positive

bonds in H20

cohesion

hydrogen bonding between like molecules (polar)

ex: surface tension - measure of how difficult it is to break or stretch surface of liquid

adhesion

hydrogen bonding between unlike molecules

ex: capillary tubes, water & plants; water is attracted to the glass walls of the tube so water is able to “climb upwards through the capillary tubes. this counters the downward pull of gravity

transpiration

movement of H20 up plants and evaporation of water from leaves and evaporation of water from leaves

cohesion and adhesion occurs

thermal energy (heat)

the total amount of kinetic energy in a system

temperature

measure intensity of heat due to the average kinetic energy of molecules

high specific heat of water

it takes a significant amount of energy to raise its temperature compared to other substances

most of the heat is used to disrupt hydrogen bonds

changes temp less when it absorbs or loses heat

larger bodies of water absorb and store more heat

a person swimmming in a pool has a higher temperature than the pool but the water has a higher amount of heat

helps regulate temperatures on Earth and in living organisms

water has a high heat of vaporization

requires a large amount of energy to transition from a liquid to a gaseous state

this is due to the strong hydrogen bonds in water

evaporative cooling

molecules with greatest kinetic energy leave as gas (molecules are moving fast enough to overcome attractions of like-like molecules)

this is a reduction in temperature resulting from evaporation of liquid

ex: human sweat

insulation by ice: ice is less dense

when water freezes, the molecules expand due to hydrogen bonds, sicne the molecules move slower, the kinetic energy decreases

the molecules move further apart so it becomes less dense

hydrophilic

affinity for H20

polar, ions

cellulose, sugar, salt, blood

hydrophobic

repels H20

non-polar

oils, lipids, cell membrane tails

water dissociation

h20 breaks into H+ (acts as acid) and OH- (acts as base)

reverisible equilibrium reaction

acids ? H+ concentration

bases ? H+ concentration

increase, reduce

pH formuka

pH = -log(H+)

(H+)(OH-) = 10^-14

if H+ = 10^-2 -log(10^-2) = -(-2) = 2'

if OH- = 10^-10 H+ = 10^-4 -log(10^-4) = -(-4) = 4

buffers

minimize changes in concentrations of H+ and OH_ in a solution (makes weaker acids and bases)

carbonc acid-bicarbonate buffer system - a critical mechanisms for maintaining a stable pH in the blood and other body fluids (blood has to be at pH ~7.4)

4 emergent properties of water

• cohesive/adhesive behavior

• ability to moderate temperature

• expansion upon freezing

• versatility as a solvent

heat must be ? in order to break hydrogen bonds

heat must be ? when hydrogen bonds form

absorbed

released

water is a universal solvent

due to polarity

can dissolve ionic compounds because the partially negative charge of the oxygen attracts cation and the hydrogen is attracted to anions

carbon has ? valence electrons so it can form up to ? covalent bonds

4

4 classes of macromolecules

carbohydrates

proteins

lipids

nucleic acids

isomers

molecules have same molecular formula, but differ in atom arrangement

• structural: Differ in the covalent arrangement of atoms and often in the location of double bonds.

• geometric: Same sequence of covalently bonded atoms but differ in spatial arrangement due to the inflexibility of double bonds

hydrocarbons

organic molecules consisting of any carbon and hydrogen. they are major components of petroleum. they can undergo reactions that release a relatively large amount of energy

cis-isomers

same atoms attached to double bonded carbons on the same side of the double bond

trans isomer

Unlike Cis, this has atoms attached on opposite side of double bond

enatiomers

isomers that are mirror images of each other and differ in shape due to the prescence of an asymmetric carbon

asymmetric carbon

covalently bonded to 4 different kinds of atoms or groups of atoms, whose arrangements can result in mirror images

polymer

a long molecule consisting of many similar or identical building blocks, linked by covalent bonds

monomers

building blocks of polymers

dehydration synthesis

a reaction in which 2 molecules are covalently bonded to each other with the loss of a water molecule

polymerization

the repetition of monomers added to the chain, making a polymer

hydrolysis

polymers are disassembled to monomers by the addition of a water molecule

carbohydrates

include sugars and polymers of sugars

monosaccarides

carbohydrate monomers

ex: glucose, fructose, galactose

disaccharides

double sugars with 2 monosaccharides joined by a covalent bond

ex: maltose, lactose, sucrose

most stable form of sugars

rings

cellular respiration

cells extract energy from glucose molecules by breaking them down in a series of reactions

glycosidic linkage

the covalent bond formed by a dehydration reaction

because disaccharides are joined together by dehydration synthesis, they have the chemical formula of ? bcause one hydrogen is removed

C₁₂H₂₂O₁₁

polysaccharides

many monosaccharides joined by glycosidic linkage

some are used for storage, some are used as uilding material for structures that protect the cell

ex: starch (storage), cellulose (protection for planst), glycogen (storage for animals), chitin (insect protection)

examples of lipids

fats, oils, phospholipids, waxes, steroids, fat soluble vitamins

fat

constructed from the monomers glycerol and fatty acids

fatty acid structure

long carbon skelton, usually 16 or 18 carbon atoms

end of skeleton has functional group carboxyl

rest of skeleton consists of a hydrocarbon chain

fatty acids are hydrophobic because:

nonpolar C-C bonds in the hydrocarbon chains

ester linkage

bond formed by a dehydration reaction between an -OH group and a carboxylic acid

joins fatty acid molecules to glycerol

triacylglycerol

3 fatty acids connected to one glycerol

saturated fatty acids

no double bonds between carbon atoms

typically solid; ex: butter and waxes

unsaturated fatty acids

have one or more double bonds with one fewer hydrogen on each double bond

bend in hydrocarbon chain caused by double bond

typically liquid; ex: oils

main function of fats

energy storage

phospholipids

making up a huge component of the cell membrane

made up of 2 fatty acids, a glycerol and a phosphate group

hydrophilic head and hydrophobic tail

protein

a biologically functional molecule made up of polypeptides into different structures

ex: enzymatic, defensive, storage, transport, hormonal, receptor, motor, structural

proteins are all constructed from the same set of ? amino acids

20

amino acids

building blocks/monomers of proteins

made up of amino group and carboxyl group

polypeptide

polymers of protein

peptide bond

bond that connects amino acids

covalent bond formed between the carboxyl group of one amino acid and the amino acid group of another

importance of side chains

physical/chemical properties of the side chain deterime the unique characteritics of an amino acid

• nonpolar side chains are hydrophobic amino acids

• polar side chains are hydrophilic

• acidic amino acids have side chains that are negative charged (due to carboxyl) (hydrophilic)

• basic amino acids have positive charge (hydrophilic)

polypeptide backone

the repeating sequence of amino acids

primary protein structure

a linear chain of amino acids. it has an amino and carboxyl end and the precise structure is determined by inherted genetic infromation

secondary protein structure

region stabilized by hydrogen bonds between atoms of the polypeptide backbone.

segments of polypeptide chains repeatedly coiled (to make a helix) or folded (to make a pleated sheet)

tertiary protein structure

3d shape; stabilized by interactions between side chains (hydrogen, ionic, van der waals, disulfide bridges)

hydrophobic side chains usually end up in the clusters at the core

disulfide bridge

strong covalent bond between suflfur atoms of two cysteine amino acids

helps stabilize tertiary protein’s 3d structure

quaternary structure

association of 2 or more polypeptides

ex: collagen, hemoglobin

factors that can lead to protein denaturation

pH, temperature

denaturation

protein is now biologically inactive, caused by chemicals that disrupt bonds

monomer of nucleic acids

nucleotides

gentic information flows from:

DNA → RNA → protein

DNA

deoxyribonucleic acid

carries genetic instruction, directions for its own replication, controls protein synthesis

messenger RNA (mRNA)

carries genetic information from the DNA in the nucleus to the ribosomes in the cytoplasm where the proteins are synthesized

where does protein synthesis occur?

ribosomes

polymers of nucleic acids

polynucleotides

structure of nucleotide

nitrogenous base, 5 carbon sugar (deoxyribose), and phosphate group

nucleoside

portion of a nucleotide without any phosphate group (base+sugar)

2 families of nitrogen bases

purines (as good as gold) - double ringed

pyrimidines (cut the umbrella)

bond that joins nucleotides

phosphodiester linkage (creates sugar phosphate backbone)