BIO 181 - Chemistry of Life

atoms

smallest unit of matter

nucleus composed of

protons and neutrons

electron shells

contain electrons

atomic number

number of protons

mass number

protons and neutrons

proton charge

positive +1

neutron charge

neutral 0

electron charge

negative -1

across rows

electrons are added until the outer (valence) shell is full

groups

columns (I)

periods

rows (—)

valence electrons

electrons residing in the outermost electron shell

atoms are more stable when

their valence shells are completely full (have 2 electrons in the inner shell or 8 electrons in the outer shells)

the number of unpaired valence electrons

determines how many bonds can be formed

bond types

polar covalent, nonpolar covalent, ionic

covalent bonds

electron sharing (includes polar and nonpolar)

nonpolar covalent bonds

equal sharing of electrons, no charge

polar covalent bonds

unequal sharing of electrons, partial charge

ionic bonds

transfer of electrons, full charge

electronegativity

the tendency for an atom to attract electrons towards itself

higher electronegativity

holds onto electrons more, partial charges depending on atom

how to determine bond type

1. find electronegativity of both atoms

2. subtract the smaller from the larger

3. determine type of bond from result

bond type calculation for nonpolar covalent

0-0.4

bond type calculation for polar covalent

greater than 0.4 and less than 1.8 (determine partial charges from this)

bond type calculation for ionic

greater than or equal to 1.8

nonpolar covalent bond between 2 hydrogen molecules

electrons are halfway between the 2 atoms, shared equally

properties of water

1. polar

2. a partial negative charge on the oxygen

3. a partial positive charge on the hydrogens

4. can dissolve other polar and ionic compounds (due to polar bonds and partial - and + charges)

   
   

hydrogen bonds form

1. bonds between water molecules

2. between 2 water molecules where the partial positive of the H is attracted to the partial negative of the O

3. bonds between H and O in water are polar covalent

states of water

1. ice - molecules are spread apart

2. warm water - molecules move past one another

3. cold water - molecules slow down and pack more tightly

what do the kinks (unlabeled atoms) in the lines between molecules indicate

carbon atoms and hydrogen atoms (H fills in)

how many bonds can carbon form

4

how many bonds can hydrogen form

1

lewis structures

show how valence electrons are arranged around atoms (dots = electrons; lines = bonds)

what are the 4 macromolecules

carbohydrates, lipids, nucleic acids, and proteins

what should you know about each macromolecule

1. it’s major function(s) in living organisms

2. how to identify it

3. how it interacts with water

4. the monomer and polymer

hydrophilic molecules

water loving (water soluble), have similar properties to water (polar or charged), usually has an oxygen

hydrophobic molecules

water-fearing, have opposite properties of water (nonpolar), usually has hydrogen chains

monomer

1 part, small, single molecules that can combine to form bigger ones

polymer

many monomers bonded together

how to identify carbohydrates

look for C, O, OH rings/chains; H-C=O or C=O

how carbohydrates interact with water

hydrophilic, polar, water soluble, bonds to water via hydroxyl (-OH) groups

carbohydrates monomer

monosaccharides (ex. glucose, fructose)

carbohydrates polymer

polysaccharides (starch, glycogen, cellulose, chitin)

carbohydrates major function in living organisms

energy storage (quick energy), plants use starch, animals use glycogen; structure/support (ex. cellulose in plants)

nucleic acids main function in living organisms

dna and rna; stores genetic information

nucleic acids monomer

nucleotides

nucleotides structure

phosphate group, sugar (ribose or deoxyribose), and a base (ATCGU)

where are nucleic acid bases connected

they’re connected to the sugar

pyrimidine bases

(CUT); cytosine, uracil, thymine

purine bases

(Georgia)(GA); guanine, adenine

bonds between nucleotides

phosphodiester bonds

nucleic acids polymer

dna/rna

how are nucleic acid bases bonded

horizontally via hydrogen bonds

what is the backbone of dna made of

sugar-phosphate

how nucleic acids interact with water

hydrophilic, like water, usually has oxygen molecules, polar

rna vs dna

ribonucleic acid has an O on the ribose; deoyribonucleic acid does not have an O on the ribose

lipids include

fatty acids, phospholipids, steroids

lipids major function(s) in living organisms

1. energy storage (long term)

2. membranes (structure)

3. hormones (regulation)

4. insulation

how to identify lipids

hydrocarbon chain plus a carboxyl group (HC chain + O=C-OH)

types of fatty acids

saturated and unsaturated

saturated fatty acids

only C-C, packed with H atoms, tightly packed, solid at room temperature

unsaturated fatty acids

at least 1 C=C, bent/kinked, liquid at room temperature, not tightly packed, less H atoms

phospholipids major function

forms cell membranes

van der waals forces

“glue” that holds the tails together; weak but a lot of them so it is stronger

phospholipids structure

hydrophilic phosphate head, hydrophobic tail

lipids monomer

fatty acids and glycerol

lipids polymer

triglycerides/phopholipids

protein main functions in living organisms

includes enzymes, hormones does transport, structure, defense, and contraction

enzymes function (protein)

catalysts for reations like digestion; breakdown, rearrangement, or synthesis

hormones function (protein)

growth, development, metabolism signals (e.g. insulin)

protein structure determines

protein function

protein monomer

amino acids

protein polymer

protein/polypeptide

how to identify proteins

amino group (H2N) + side chain (r group) + carboxyl group (O-C=O)

peptide bonds

connect the carboxyl group of 1 amino acid to the amino acid of another

r groups (side chains)

what makes amino acids unique; they have different properties

peptide chains

backbone made up of r groups hanging from it

when amino acids are bonded via dehydration synthesis, the ends are called

amino end including H and N (n-terminal) and carboxyl end including C and O (c-terminal)

what determines a protein’s shape

the interactions between amino acids

proteins are also known as

polypeptides

primary protein structure

chain of amino acids (each connected by peptide bonds)

secondary protein structure

hydrogen bonds hold the helix together; evenly spaced; local, repeating, 3-D folding of a polypeptide backbone (alpha helixes and beta-pleated sheets); hydrogen bonds hold parallel or antiparallel strands together

tertiary protein structure

occurs due to side chains (r groups) interacting; very diverse; r groups bond together by disulfide bonds

disulfide bonds

strong covalent linkages (-S-S-) bonds r groups

quaternary protein structure

consists of more than 1 amino acid chain; arrangement and assembly of 2 or more individual folded protein chains, called subunits, into a single, larger functional complex

sickle cell protein structure

1 single dna base difference changes 1 amino acid in the primary structure; glutamic acid (a negatively charged amino acid) is changed to valine (a non polar amino acid)

enzymes

proteins that catalyze (speed up) reactions

substrate-enzyme interaction

substrate enters the active site of the enzyme, slightly changing the shape of the enzyme; the enzyme releases products created from the substrate and they leave the enzyme

protein denaturation

temperature matters; the protein loses its native 3-D shape and biological activity due to external stress; effects the secondary, tertiary, and quaternary structures

nonpolar

no charge, hydrophobic

polar

charged, hydrophilic

when it comes to charge

opposites attract