biol 203 exam 1

Mass and charge of a proton

1 Da (Dalton (or amu)) and +1

Mass and charge of a neutron

1 Da (dalton (or amu)) and 0 charge

Mass and charge of an electron

0 Da and -1 charge

Cation forms

Loss of an electron

Anion forms

Gain of an electron

Most common bond type in living organisms

Covalent

Most common bio atoms

C H O N P S

Order of relative electronegativities

O > N > S = C = P = H

O > N > S = C > P = H

Ionic bond

An atom transfers one or more electrons to a second atom, resulting in 2 atoms possessing opposite charges (cation/anion)

Why life revolves around water

Molecule is small, bent geometry, and highly polar

Can form hydrogen bonds

Is a great solvent

Hydrogen bonds

Electrostatic force that occurs between H+ in one molecule and another charged atom (often N- or O-) in another molecule

They are weak individually but powerful in large numbers

Types of molecules water can dissolve and why

Hydrogen bonds/small size of h2o allows polar and ionic to dissolve (but NOT nonpolar)

Hydrophobic (definition and interactions)

Nonpolar molecules that won’t dissolve or interact with water

Stabilized by van der waals forces

Water makes a “cage” around them

Hydrophilic

“Water loving” molecules like polar and ionic that dissolve in water

Van der waals forces

Weak, short-range electrostatic attractions between nonpolar molecules or atoms due to tiny temporary partial charges caused by electron movement between atoms

Cohesive

individual molecules stick to each other (same type of molecule) because of hydrogen bonding

Adhesive

A molecule sticks to other charged or polar surfaces

Water is

Cohesive AND adhesive

Density of ice vs liquid water and WHY

Liquid is denser than ice because the hydrogen bonding pulls water molecules in tight, but in ice the molecules are spread out in a crystal lattice

Ice floats

What is special about water’s specific heat and heat of vaporization

High specific heat

High heat of vaporization

(Protected the original lifeforms in the ocean from energy/heat changes)

Specific heat

Amount of energy it takes to heat something

(High means it takes a lot of energy to heat )

Heat of vaporization

Energy required to go from liquid to gas

(High means it takes a lot of energy)

pH scale math

To compare pH, subtract one from the other and that is the number of zeros after 1

Monomer

The smallest whole subunit (of a polymer)

Monomer of protein

Amino acid (There are 20 most common)

Components of amino acid

Carboxyl group (O=C-OH nonionized or O=C-O- more commonly ionized)

Amino group (H-N:-H nonionized or H3N+ when ionized)

H to central C

(+ a unique side chain)

** amino acids are usually ionized

Resonant stabilization

A double bond flips back and forth between same atom with a single bond to stabilize it

R group

Side chain (amino acids)

Determines reactivity and what the amino acid is

Can make it be nonpolar, polar, or acidic/basic(charged)

Peptide bond

Formed through dehydration synthesis (or condensation rxn)

Links amino acids together (the C in carboxyl group connects to the N in amino group)

Usually very stable, taking on many double bond characteristics (like planar geometry)

Dehydration synthesis

Aka condensation rxn

Results in some product and H2O

Residues

The individual amino acids linked together in a peptide chain

Oligopeptide

Short chain

<50 amino acids

Polypeptide

Long chain

Anything >50 amino acids

Protein

Any length of residues (reserved for only fully functional molecules usually)

Peptide chain reading direction

From N-terminus (amino group end) to C-terminus (carboxyl group end)

Why life is organic (carbon based)

C provides molecular skeleton (with 4 valence e-)

C can form links, chains, and rings

Functional groups attach easily to define chemical behavior

primary structure (proteins)

The unique sequence of amino acids in a protein, determining its SHAPE, function, and properties.

dictates the likeliness of alpha helices or beta sheets

secondary structure (proteins)

the alpha helix or beta pleated sheets (distinctly shaped sections of linear sequence stablized by hydrogen bonding between functional groups in the peptide bond backbone

tertiary structure (proteins)

comes from interactions between r-groups or backbone AND r-groups located relatively far apart in primary sequence

**only cistine forms disulfide bonds, otherwise all other bond types may occur

quaternary structure (proteins)

**only SOME proteins have this

multiple polypeptide subunits

quaternary structure naming conventions

prefix+ending

Prefixes: homo- (protein subunits are identical) and hetero- (at leats one polypeptide differs from the others

Endings(# of protein subunits): dimer(2), trimer(3), tetramer(4)

functions of proteins

enzymes catylize rxns

form structural components in body

motor/contractile proteins move cells or molecules within cells

signaling proteins send messages between cells

transport proteins help molecules enter/exit cells or carry them through the body

antibodies attack viruses/bacteria

DNA

deoxyribonucleic acid

stores genetic info (long term=stable)

RNA

ribonucleic acid

many many functions(more reactive, more functions=less stable, breaks down over time): transcribe genetic info, assemble proteins, regulate gene expression, and in some viruses acts as genetic material

monomer of nucleic acids

nucleotide

DNA vs RNA

DNA has deoxyribose sugar (an H on 2’ Carbon) and thymine (extra methyl group)

RNA has ribose sugar (an OH on 2’ Carbon) and uracil

Components of Nucleotides

5 carbon sugar

phosphate group

nitrogenous base (the unique part)

nucleotide to nucleic acid

a phosphodiester bond forms via dehydration synthesis (or condensation rxn)

the O on one phosphate group attaches to the C on 5-carbon sugar

sugar-phosphate backbone

chain of nucleotides making up DNA and RNA, with the nitrogenous bases hanging off

nucleic acid order conventions

sequence of nucleotides written in 5’→3’ direction

(new nucleotides get added to the 3’ end)

how to tell difference in nucleic acid ends

5’ carbon has a free phosphate group

3’ carbon has a free hydroxyl group

secondary structure (DNA)

Nitrogenous bases are flat and perpendicular to sugar-phosphate backbone

twists into a helix—minimizes contact w/ water

complementary base pairs:

thymine—adenine

cytosine—guanine

bond type between complementary base pairs

hydrogen bonds

what do the arrows in a DNA diagram represent

the arrows are the 3’ end, the plain line is the 5’ end

adenine

purine (2 rings)

thymine

pyrimidine (1 ring) & has an extra H3C and O

guanine

purine (2 rings) with an extra O

cytosine

pyramidine (1 ring) with an extra NH3

uracil

pyramidine (1 ring) and no extra stuff

tertiary strucure (DNA)

when too tight/loose it can coil on itself to form supercoils

(in eukaryotes and some archea) may wrap around binders called histones

histones

dna binder

why is DNA stable

phosphodiester linkages, h-bonds, hydrophobic interactions

base stacking & twisted helical shape prevent many functional groups from being exposed to chemical reactions

why complementary base pairs

fixed nucleotide pairs means DNA’s structre provides a mechanism for copying the primary sequence, even with only one strand

protein spontaneous folding process

molecular chaperons facilitate, prevent formation of nonfunctional aggregates

primary structure contains all the info to predictably become fully functional with correct structure, though many do not become fully functional until they interact with something to trigger a change/activation

**structure shapes function

molecular chaperons

assist in protein folding by temporarily binding to nonpolar regions of unfolded proteins

(protects nonpolar parts from hydrophobic interactions with water)

prevents formation of nonfunctional aggregates

infectious prions

induce changes in normal protein prions leading to misfolding and aggregation

beta pleated sheets tend to be compact/aggregate

(positive feedback loop so as more turn, more get infected)

RNA secondary structure

RNA is FLEXIBLE and CAN TWIST BECAUSE OF steric hinderance, so its base pairing occurs within a single strand of nucleotides, sometimes looping into a hairpin loop

steric hinderance

the extra OH on 2’ carbon (ribose vs deoxyribose) prevents RNA from coiling into double helix, leaving reactive functional groups exposed

RNA tertiary structure

complementary base pairing from nucleotides located far apart from each other in the primary sequence (ex: pseudoknots)

DNA vs RNA: diversity of reactivity & 3D shape

RNA has more level of reactivity and can generate more diverse 3D shapes

carbohydrate functions

energy storage (ex:photosynthesis), structural support(ex:cellulose), cell identification(ex: glycoproteins & glycolipids)

(can vary widely structurally to perform wide variety of tasks in variety of places in body/cells/etc)

monomer of carbohydrates

monosaccharide

monosaccharide basic structure

ALL HAVE: carbonyl group (C=O), several hydroxyl (—OH), and several C—H bonds

monosaccharide distinguishing features

—location of carbonyl group (aldose vs ketose)

—size of monomer (# of carbons… 2 min, 9 max, 3-7 average)

—3D spatial arrangement of atoms/bonds

aldose

any monosaccharide with the carbonyl group at the END of the carbon chain

ketose

any monosaccharide with the carbonyl group WITHIN the carbon chain

how do monosaccharide rings form?

if they have 5+ carbons, they spontaneously take shape when put in aqueous solutions

α configuration, generic structure & purpose

goes BELOW plane

long chain begins to form a helical shape

generally for energy storage

β configuration, generic structure & purpose

goes ABOVE plane

long chain looks planar

generally used structurally

disacharride

smallest polymer of a carbohydrate

2 monosaccharides linked with glycosidic linkages made through dehydration synthesis reaction

glycosidic linkage

(—O—) forms between the hydroxyl groups to connect a carbon on each monosaccharride (alway 1’ carbon and any other carbon, creates partial + charge increasing reactivity)

the location and geometry can vary widely in overall polysaccharide bc of variation in monomers

naming conventions of glycosidic linkages

“(alpha/beta)—1,(#)—glycosidic linkage”

carbs as energy storage plants vs animals

starch for plants has no (alpha-1,4) or rare (some alpha-1,6) branching in glucose residues, takes up less space

glycogen for animals has a lot of branching (alpha-1,4 and many alpha-1,6), makes it easier to break/access energy quickly

carbs as structural polymers

beta monomers linked in planar structure, with hydrogen bonding cross-linking adjacent parallel strands to add strength and rigidity

ex: cellulose, chitan, peptidoglycan

lipids

catch-all term for water-insoluble/hydrophobic compounds with lots of C—C or hydrocarbon C—H bonds

includes steroids, fats, phospholipids, pigments, waterproof coatings, vitamins in cellular processes

bond saturation

number of H a lipid contains relative to max potential amount given a set number of C linked in a chain

unsaturated lipid

at least one C=C in chain, means less H can be attatched

can have bends in structure

saturated lipid

all C—C, max amount of H attatched

linear structure

steroids

type of lipid

function: chemical signals(hormones) & parts of cell membrane

structure: 4 carbon rings w/ functional group to determine purpose

examples: cholesterol, estrogen, testosterone

fats

type of lipid

function: energy storage (2x more than sugars)

structure: long carbon chain w/ carboxyl group & lots of hydrogens

example: fatty acid

phospholipids

type of lipid

function: component of plasma membrane

structure: (charged head) choline—phosphate group—glycerol—nonpolar tail

*are amphipathic & are most common lipid in body

amphipathic

molecule with both both hydrophilic & hydrophobic regions

lipid micelles

circular structure (np tail in, p head out) formed by small amphipathic lipids with single hydrocarbon chains in water

studied via lab-made artificial vesicles called liposomes

forms spontaneously (high entropy)

lipid bilayers

two rows, tails in, heads out; made of bulky phospholipids; have selective permeability

studied via lab-made artificial planar ___

forms spontaneously (high entropy)

factors affecting selective permeability

-molecule size (smaller > bigger)

-molecule polarity/charge (nonpolar > polar; NO charged/ionic cross at all)

-bilayer structure (short tail > long) (unsaturated > saturated) (*cholesterol hinders)

-temperature (high temp=more movement > low temp=slow or even stop)

*in general, it is greatest when phospholipids are freely moving and loose