Foundations of Biology (1411) University of Iowa Exam 1

proton

-positive charge

-found in the nucleus

neutron

-no charge (neutral)

-found in the nucleus

electron

-negative charge

-found outside the nucleus in e- shells

isotope

-atoms of the same element that differ in number of neutrons

ion

an atom with a net charge

ionic bond

-forms when electrons are completely transferred between 2 atoms

-large difference in electronegativity

covalent bond

-forms when electrons are shared

non-polar covalent

electrons are shared equally because atoms have same electronegativity, or the geometry of the molecules negate polarity

polar covalent

electrons are not shared equally. the more electronegative atom hogs the electrons, they are still shared.

can a polar substance and a non-polar substance form a hydrogen bond?

no, because there are no charges to create attractive force

hydrogen bond

attraction between a slightly positive hydrogen atom and a slightly negative atom.

van der waals interaction

attractions between oppositely charged atoms in nonpolar molecules. (movement of electrons result in small temporary dipoles)

dipole

a molecule that has two regions with opposite charges

dipole-dipole interaction

an attraction between regions of polar molecules that have partial charges of opposite sign

electronegativity

the ability of an atom to attract electrons when the atom is in a compound

____________ is required to break a bond, but ___________ is also released once a bond is broken.

energy, energy

electronegativity in non-polar covalent bonds

less than 0.4, which results in no dipole

electronegativity in polar covalent bonds

between 0.5-1.7, which results in a slight dipole

electronegativity in polar ionic bonds

anything greater than 1.7, resulting in a significant dipole

-------------------->

^ 1 ^|^ 2 ^|^ 3 ^

increasing ionic character: label 1, 2, and 3.

1. non-polar covalent bonds

2. polar covalent bonds

3. ionic bonds

what bonds create partial charges on the molecule?

polar covalent

what do polar bonds indicate?

electrons spend more time orbiting the more electronegative atom

since electrons spend more time orbiting the more electronegative atom in a polar bond, what does this cause?

the more electronegative atom will be slightly negatively charged (d-) and the less electronegative atom will be slightly positive (d+)

what can polar bonds form?

hydrogen bonds

what can non-polar molecules not form?

hydrogen bonds

where can hydrogen bonds form?

between molecules or between polar regions of large molecules. (protein folding)

what do functional groups allow us to predict?

-how molecules react to each other

-molecular shape

can large molecules have more than one functional group?

yes

properties of water

-highly polar

-capable of making multiple hydrogen bonds

-universal solvent

-cohesion and adhesion

-high surface tension

-high heat capacity

-changes in density

polar bonds

-unequal sharing of electrons because of different electronegativities, therefore the atom that is more electronegative hogs the electron. this causes d+ and d- regions (partial charge regions). this matters because polar molecules can form hydrogen bonds with other polar molecules or other polar regions in the same molecule.

in bio: cells are aq and water is polar which determines how molecules act in a cell. this informs proteins form, and shape is important for protein function.

non-polar bonds

-electrons are shared equally, this is because atoms have very similar or the same electronegativities or the same geometry of the bonds in the molecules, which creates symmetry and negate any electron sharing inequities. this all causes a neutral molecule with no d+ or d- regions. this matters because non-polar molecules cannot form hydrogen bonds with polar molecules.

in bio: fatty acids cannot dissolve in aq solutions, basis of cell formation.

biomolecules

built of monomer subunits, carbon is a major component of these

average composition of cells

70% water

30% chemicals

of that 30%, 15% proteins, 7% nucleic acids, 4% small molecules (ions), 2% lipids, 2% carbohydrates

polymerization

creation of biomolecules by bonding multiple molecules together

polymer

long chain of smaller molecules (monomers) joined by covalent bonds

monomers

small molecular subunit chained together in larger molecules

examples of monomers

nucleotide, amino acid, sugar

examples of polymers

nucleic acid, protein, carbohydrates

examples of non-polymers

carbon-hydrogen chains, glycerol, lipids

condensation

reaction that joins monomers together to build a polymer

(energy in, water out)

hydrolysis

reaction that breaks polymers apart into constituent monomers (water in, energy out)

what is condensation sometimes referred to as?

dehydration reaction

true or false? carbon comprises 18% of the body by weight (but only 0.03% of earth's crust)

true

why is carbon so prevalent in the body

-it can form four covalent bonds

-can form single, double, or triple bonds

-can build small (CO2) and very large (biopolymers) molecules

-makes polar and non-polar covalent bonds

carbohydrates

polymers of simple sugars (monosaccharides)

what does saccharide mean

sugar

what are polysaccharides

polymers of sugars, small (3C to 6C)

monosaccharides

-ringed (joined together to make polymers)

-location and presence of OH groups indicate type

general formula of a polysaccharide

Cn(H2O)n

what bonds are monosaccharides joined by to build complex carbohydrates?

gyclosidic

reaction used to join monosaccharides to form di-, oligo-, and polysaccharides

condensation (dehydration)

disaccharide

two monosaccharides linked by covalent bonds

oligosaccharides

3-20 monosaccharides

polysaccharides

hundreds or thousands of monosaccharides

i.e. starch glycogen, cellulose

what do monomer bonding patterns determine

polysaccharide branching

linear polysaccharide branching

β - 1,4 glycosidic bonds

branched glycosidic branching

α - 1,4 and α - 1,6 glycosidic bonds

proteins

amino acid monomers joined by peptide bonds

how are proteins formed

amino acids are joined together by condensation (dehydration), covalently joined by peptide bonds

when can functional groups ionize

in neutral ph

ph of pure water

1x10^-7 (ph of 7)

zwitterion

both a positive and negative charge, it is able to act as both a base or an acid depending on the situation

(positive can give H+ atoms, and negatives can accept H+ atoms)

amino acids being zwitterions means what for proteins?

this makes them a useful buffer

amino acids with electrically charged hydrophilic side chains

positive: arginine, histidine, lysine

negative: aspartic acid, glutamic acid

amino acids with polar but uncharged side chains (hydrophilic)

serine, threonine, asparagine, glutamine, tyrosine

amino acids with nonpolar hydrophobic side chains

alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, valine

monomer

amino acids

special cases

cysteine, glycine, proline

levels of protein structure

primary, secondary, tertiary, quaternary

primary structure

order of amino acids (monomers) in a chain (polymer)

secondary structure

first step 3-d folding. hydrogen bonds between carboxyl + amino functional groups of amino acids

α helix

right handed coil resulting from hydrogen bonding between adjacent amino acids

β pleated sheet

two or more polypeptide chains are aligned; hydrogen bonds from between the chains

tertiary structure

2nd step of 3-D folding stabilized by disulfide bridges, van der waals forces, ionic bonds, and hydrogen bonds between R-side chains of AA

quaternary structure

tertiary structures (subunits) bond together. final functional form of protein. this results from the interaction of subunits by hydrophobic interactions, van der waals forces, ionic bonds, and hydrogen bonds

protein function depends on ________.

structure (3-D shape)

proteins must be correctly _________ into specific, 3-D shapes to function correctly.

folded

true or false: proteins can denature and refold

true

denaturation

loss of 3D structure is sufficient to cause loss of function

what can most proteins be denatured by

heat, pH, salt, and solvents (can refold if correct conditions are met)

________ can be predicted based on amino acid order and known interactions between the side chains.

shape

titin

huge protein that adds flexibility to muscle fibers (34,000 amino acids)

thyrotropin

releasing hormone; a short polypeptide that controls secretion of thyroid hormone - 3 amino acids.

protein's roles in biology

- support regulation of DNA + RNA

- enzymes: biochemical reactions

- transport

- immune system: antibodies

- second source of energy

- coordinate response to hormones

monomers: __________ = phosphate + nitrogenous base + sugar backbone

nucleotides

nucleotides join by phosphodiester bonds to build what?

nucleic acids

what does dna stand for

deoxyribonucleic acid

what does rna stand for

ribonucleic acid

what are dna and rna joined together by

phosphodieter bonds

functions of nucleotide monomers in cells

ATP, cAMP, and GTP

what are nucleotides held together by

strong covalent bonds called phosphodieter

what holds base pairs together

hydrogen bonds

what does dna do?

stores information to make proteins

what does dna form

double helix

what does rna do

uses DNA info to make proteins, enzymes, gene regulatory units, signaling, etc.

what forms does rna come ine?

various

what stores information and carry out protein synthesis

nucleic acids

lipids are __________ but not __________.

macromolecules, polymers

lipids

- mostly build by nonpolar covalent bonds between hydrogen and carbon

- hydrophobic

-structurally varied in size and arrangement of atoms

- typically bond to polar functional group at one end

fatty acids are ___________

amphipathic molecules