Learn: BIO 002 MIDTERM I

six core elements in biomolecules

NOCHPS

electronegativity

tendency to hold onto outermost valence electrons

- greater electronegativity = greater attraction

- determines bonds between atoms

- increase L to R across periodic table

formation of an ionic bond

TRANSFER of electrons

- equal balance of opposite charges

- electroneg difference LARGE (>2)

formation of covalent bond

SHARING of electrons

- partial charges and dipoles

- strongest type of bond because do not break as easily as ionic in aqueous solutions

- solid lines

polar bonds

- NO CHPS rule: N & O both high electronegativity, so they will always have polar bonds

- high electronegative difference (0.5-2)

- UNequal sharing of electrons

nonpolar bonds

slight/no electronegative difference (

hydrogen bonds

- between multiple molecules

- UNequal sharing of electrons

- formed between water molecules

- H and other electroneg atom

dipoles

- partial charges due to differences in electronegativity

- arrows pointing towards more electronegative atom (or +/- delta)

hydroxyl group

R-OH

- alcOHol

- polar, hydrophilic, H bonds with water

methyl

- R-CH3

- nonpolar, hydrophobic

carbonyl

- C=O with two R groups

- polar, H bonds with water

carboxyl group

- -COOH aka O=C-OH

- negative charge, ionizes to release H+

- acidic

- H bonds with water

amino group/amine

R-NH2

- positive charge, accepts H+ to form NH3

- basic

- H bond swith water

phosphate group

P bound to four oxygen atoms

- ionizes to release H+

- acidic

- H bonds with water

sulfanyl

R-S-H

- moderately polar

amiDe

Double bonded oxygen to carbon with an amine

good hydrogen bond DONOR

polar functional groups have partial positive charges to have available H to donate

interactions between functional groups and water

water molecules rearrange themselves for more H-bonds --> condense --> expand (less dense)

- especially at lower temps

change interactions between functional groups WITHIN and BETWEEN molecules

1) reactions and dynamic equilibrium

2) pKa

3) pH

protonated vs deprotonated

protonated: HA, has H proton on it to donate

deprotonated: A-, molecule + H+

dynamic equilibrium

- ROC stops changing, rates are equal and remain constant

- ratio is 1

pKa

= -logKa

- STICKINESS for protons

- increase pKa = more sticky = hold onto H+ more = more protonation

- how often protonation occurs based on [H+]

- dif functional groups have dif level of stickiness for protons --> differenct functions of molecules and interactions

pH

H2O

pH = -log10[H+]

- increase [H+] = decrease pH = more acidic

- in presence of H2O, carboxyl group can lose H+ to form H3O+

- 1 unit pH change = a factor of 10 change in [H+]

what happens to BONDS if pH DECREASES dramatically

- INCREASE [H+] (more avail) --> deprotonated carboxyl group can become MORE protonated

- neutralize the neg charge of carboxyl group --> ionic bond undone/eliminated --> protein unfolds (lost ability to bind)

- decrease pH = less binding

- in terms of functional groups because they determine how proteins bind

- pKa determines pH tolerance

glycosidic bond

link monosaccharides into long carbohydrates / disaccharides

carbohydrate

LOTS of C and OH (1 C : 2 H : 1 O)

rings or linear

glycosidic bonds

lipids

- fatty acid tails: long lipid tails

- polar, hydrophilic head & nonpolar, hydrophobic tails

- triglycerol: 3 fatty acid chains

- overall hydrophobic: lots of nonpolar hydrocarbonds

- low solubility in water

glycerophospholipid

glyc- = carbohydrate glycerol

lipid = 2 fatty acids

phospho = phosphate with R group

hydrophilic head, hydrophobic tails

* be able to draw

saturated vs UNsaturated fatty acid

- sat: long, linear carb chain with SINGLE covalent bonds to maximize hydrogens attached

- unsat: double bonds that create kink in straightness --> bent tail

- sat acids in membrane: temp decreases --> straight tails compress --> dense rigid membrane

- unsat acids in membrane: temp decreases --> kinked tails elbow other lipids away --> still space between lipids --> fluiditiy

digestive enzymes

help digesting by catabolizing nutrients into monomers

transport proteins

carry substances through the blood

structural proteins

construct dif structures (cytoskeleton)

hormones (protein)

coordinate activity of different body systems

defense proteins

protect body from pathogens and foreingers

contractile proteins

muscle contraction

storage proteins

nourishment in early development and seedling

amino acid

amino group, side chain (R group and alpha carbon), carboxyl group

- side chain determines how proteins interact iwth each other and in water

- NCC backbone structure

- R group determines amino acid characteristics

- condensation: 2-->1, H of one bonds with OH of another), product is H2O

- hydrolysis: reactant is H2O, breaks bonds 1-->2

- peptide bonds: carboxyl + amine = H2O and peptide chain

secondary structure

- H bonds on the NCC backbone (NOT R groups)

- alpha helix (coiled): H bonds between helices

- beta pleated sheet

- continued NCC pattern with condensation

tertiary structure

- 3D shape of protein FOLDING

- H bonds, covalent bonds, ionic bonds, hydrophobic interactions, disulfide bridges

- between R groups

- hydrophobic effects!

structure begets function

functional variety

same backbone --> 20 dif amino acids --> dif variations and orders of AA --> tons of dif proteins and functions

Energy Story

1) identify start and end in process: states of matter and energy (who, where, when)

2) changes of matter during process (what)

3) changes of energy during process (why)

4) mechanisms driving changes (how)

energy

- conserved, transferred, FLOWS through systems

- changein energy --> chagne in system

- neither created nor destroyed

entropy

- energy dispersal/spread

- more ways for E to spread = more ways for E to be used

- increases in the universe (local decrease is compensated by greater increase elsewhere)

enthalpy

internal energy (bio systems have constant pressure and volume)

gibbs

deltaG = deltaH - TdeltaS

deltaG < 0 (neg): spontaneous rxn

deltaG > 0 (pos): NOT spontaneous rxn

G: DIRECTION of energy flow

H: internal energy

S: how energy is ORGANIZED

T: scales the relationships (in K)

catalyst

- increases rate of reaction

- recycled

- lowers Ea

- does NOT change eqbm

enzymes and substrates

- enzyme: protein catalyst (-ase) that have active sites for specific substrates

- substrate: reactant of enzyme

- substrates must have correct orientation to collide into the active site (only certain molecules can enter/fit) --> release product

- together: enzyme-substrate complex

cofactors, coenzymes, prosthetic groups

- non-protein molecules that provide additional chemistries to enzymes and other proteins

- help enzymes do job and catalyze

environmental influences on enzyme function

- substrates can only fit under chemical environments of the amino acid functional groups

- influenced by *pH* : enzymes are made of AA therefore have certain pKa and can de/protonate

- influenced by (optimal) *temperature* : enzymes find/collide with substrate faster at higher temps --> Ea reached and crossed more often

identifying amino acids

1) find backbone, ignore it

2) look at R group: nonpolar&hydrophobic, polar&hydrophilic, charged(acidic&basic)

- nonpolar & hydrophobic: C and H

- polar & hydrophilic: neutral/uncharged (O or S), acidic (carboxyl/H donor), basic (amine/H acceptor)

active site

unique chemical environment of certain R groups on amino acids for a substrate to uniquely fit into

- reach a transition state to catalyze the reaction and make products

induced fit

enzyme active site and substrates undergo slight conforming/adjustments when in contact --> binding

- dynamic interaction --> mild shift in enzyme structure for better binding to maximize catalysis

- substrates together in optimal orientation

- compromise bond structure of substrate to break bonds more easily

- provide optimal chemical environment conditions

- form covalent bonds with substrates

regulate enzyme action

- change cell external conditions

- change locations within the cell

- inhibitors: preventing reactions

- activators: regulate enzymes with metabolic feedback

noncompetitive vs competitive inhibitors

noncompetitive: binds to enzyme at allosteric site --> change enzyme shape (cannot be overcome by more substrate)

competitive: block enzyme active site --> compete with substrate (can be overcome by more substrate

allosteric inhibition vs activation

Allosteric = Away from Active site

bind away from active site --> shape change

inhibit: reduce substrate affinity (turns off/slows down enzyme activity)

activation: increases substrate affinity (turns on/speeds up)

prokaryotes

single-celled, no membrane bound nucleus, no membrane-bound organelles

- bacteria and archaea

- wide inhabitability

- cytoplasmic membrane holds all reactions that are supposed to be membrane-bound

- circular double stranded DNA that floats around

- cytoplasm holds all non-membrane reactions

problems of bacteria and archaea

- transport of nutrients into cell, removal of waste, and need to respond to rapid local environmental changes

diffusion

- especially important for prokaryotes

- passive, down or with the concentration gradient

- passing through the phospholipid bilayer

- get rid of waste

- depends on viscosity of solvent

- diffusion within and of bigger cells: less efficicent

phospholipid bilayer membrane

dynamic membrane of lipid-soluble molecules and proteins embedded

- communicate cell's identity to other cells: receive, transmit, sense signals

- fluid mosaic: changes with temperature; configured of fatty acid tails, sterols, proteins

- semi permeable: selective of what specific compounds transport in and out of the cell

- acts as a barrier

integral membrane protein

- integrate COMPLETELY into membrane

- hydrophobic regions interact with hydrophobic region of phospholipid bilayer

peripheral protein

- only on one side of membrane (intra- or extracellular side)

- OR temporarily on membrane

cholesterol

- between phospholipids in membrane

- dampen effect of temp on membrane by making membrane more stiff or fluid

- low T: space phospholipids apart, less rigid

- high T: takes up space so phospholipids do not dissociate

membrane permeability coefficients (MPC)

- rate of simple diffusion thru membrane (cm/s)

- larger MPC: more permeable

- smaller molecule: fast pass (and vice versa)

- charged molecule: no pass thru membrane b/c ions want to interact with water and not with bilayer

osmosis

- movement of water through semipermeable membrane according to concentration

- depends on tonicity: extracellular solution

active transport

external energy (ATP) required to move substances against the gradient across the membrane

- primary active trasnport: across membrane with differences in charge, depending on ATP hydrolysis

- secondary active transport: movement of material does not require ATP,, it is driven by the electrochemical gradient from the primary exergonic reaction

passive transport

no external energy required to transport stuff across membrane

- high to low (w gradient)

- EXERgonic

- diffusion or facilitated diffusion

factors affecting diffusion

depends on molecule size, shape, environmental factors, thermal energy

- greater difference in concentration = more rapid diffusion (closer to eqbm = slower rate)

- larger = heavier = slow diffusion

- increase T = increase energy = increase movement = increase rate of diffusion

- increase solvent density = decrease rate of diffusion (harder to get thru denser mediums)

- solubility: nonpolar & lipid-soluble pass thru easily

- increase SA = increase diffusion

- thicker membrane = slower diffusion

- increase distance traveled = decrease diffusion rate

facilitated transport

diffuse with the help of transport proteins without the cell expending energy

- type of passive transport

channel proteins

interior passageway that is a low energy barrier for transport

- type of facilitated diffusion

- complementary arrangement of amino acid functional groups

- polar cmpds can avoid nonpolar central layer of membrane

- gated: triggered by attachment of ion, stresses, or changes in voltage

- open: easy pass thru

- catalyst required to speed up the rxn that was already going to occur

carrier proteins

protein binds to substance --> changes the shape of the protein --> bring it into the cell

- selectivity and specificity

- slower transport than transport proteins

- passive or active transport

uni vs sym vs anti porter

- uniporter: carries ONE specific molecule/ion

- symporter: carries TWO different molecules/ions in the SAME direction

- antiporter: carries TWO different molecules/ions in a DIFFERENT direction

Na+/K+ ion pump

maintains electrochemical gradient and corrects the [Na+] and [K+] in animal cells

- 3 Na OUT... 2 K IN

1) protein carrier oriented towards inside cell --> 3 Na bind to protein (high Na affinity)

2) ATP hydrolyzed by the protein carrier --> phosphate group attaches to enzyme

3) ==> carrier changes shape --> reorients towards outside of membrane --> 3 Na ions leave carrier (Na affinity decreases)

4) 2 K bind to protein (increased K affinity) --> phosphate group detaches

5) ==> carrier repositions towards interior

6) 2 K ions leave carrier into cytoplasm (decreased K affinity)

7) ==> higher affinity for sodium ions --> process restarts

pumps

primary active transport mechanism

- coupled: rxn going Lo to Hi (endergonic) paired with rxn going Hi to Lo (exergonic)

- no hole

- move IONS AGAINST gradient

- using energy from ATP hydrolysis