Exam 1

1st law of thermodynamics

energy cannot be created or destroyed, can only be converted

solar energy relation to 1st law thermodynamics

• via photosynthesis, co2 is converted to carbohydrates + oxygen which is chemical energy

• 3 types of chemical energy

  • transport work: ATP used to move molecules across a membrane

  • chemical work: work using ATP within metabolic pathways

  • mechanical work: take ATP to contract muscles for movement

2nd law of thermodynamics

spontaneous processes tend toward disorder (entropy, S)

• disorder (+ S) is favored

ice melting relation to 2nd law thermodynamics

• ice: low entropy, solid phase, little movement, ordered, lots of H bonding

• water: higher entropy, liquid phase, more movement, H bonds getting broken

• gas: highest entropy, maximal disorder and movement, no H bonds connecting molecules

living organisms require __ to maintain homeostasis

energy

• because entropy (disorder) is favored, energy input (ATP) is needed to maintain order/homeostasis

• human body is also an open system —> E input required

gibbs free energy equation

ΔG = ΔH - TΔS

ΔG’° = -RTlnK’eq

• ΔG: negative means spontaneous (no E required- high to low), positive means non-spont so E required

• ΔH: positive means E being put in, so enthalpy is unfavorable vs negative means no E input and favorable

• T: °C + 273.15 = K

• [Keq]: [product] / [reactants] equilibrium constant

  • if Keq > 1 —> more product than reactant, reaction favors moving forward, spontaneous

  • if Keq < 1 —> more reactant than product, reaction does not favor going forward, non-spont

  • if Keq = 1 —> reaction is at equilibrium

free energy, enthalpy, entropy chart

• spont at all temps : -deltaH ; + deltaS

• non spont at all temps : +deltaH ; -deltaS

• spont at high temp : +deltaH ; +deltaS

• spont at low temp : -deltaH ; -deltaS

water properties

• polar covalent bonds within molecule (bc dipole charge separation)

• bond angle (104.3) —> permanent dipole

• H bonding between molecules to solvate other molecules

H bonds

• weak- have low bond energy (E required to break bond)

• transient- constant making and breaking of bonds

• the O (-) of water interacts with the partial positive atom of another molecule and vice versa

  • this is what allows water to solvate and hydrate

hydrogen bonding and water’s solvation properties

• the O (-) of water interacts with the partial positive atom of another molecule and vice versa

  • this is what allows water to solvate and hydrate

  • dipoles

  • water is disordered —> solvates around the other ions —> hydration layer around other ions

• the O of water is the acceptor (-) and the H of water is the donor (+)

  • the other molecule will be the donor (+) to water’s acceptor or the acceptor (-) to water’s donor

water interaction with hydrophobic molecules

ex fatty acids

• do not have any dipoles (mostly C-H bonds) = not polar molecules

• the hydrophilic head can interact with water, but not the hydrophobic alkyl group

  • when h2o reacts with hydrophobic part, it becomes highly ordered. h2o molecules H bond with self but dont solvate around fatty acid —> separation

• the fatty acids aggregate together into clusters and form a shell (micelle) with hydrophilc heads on outside and fatty acid interiors not exposed to the surroudning h2o

  • h2o molecules entropy is increased as this happens

ionization of water

H2O <—> OH- + H+

acid (donates proton) ←→ CB (can accept proton)

• slight charge difference but still electrically neutral

[H+], pH, [-OH], pOH relationship

• as H+ concentration increases 10 fold, pH decreases by 1 unit

  • H+ concentration of 10^-7 —> ph 7

  • high H concentration = low pH = more acidic

• as -OH concentration increases 10 fold, pOH also decreases by 1 unit

  • high OH concentration = low pOH = more basic

pH = -log[H+]

pOH = -log[OH-]

pH + pOH = 14

pKa

the measure of the strength of an acid

• the value when the species is in 50% strong acid and 50% of its CB ion form

  • this is also the middle of the buffer region

  • pKa = -log Ka

• a higher dissociation constant means a lower pKa. SA dissociates quicker, more free H+, lower pH, more acidic

  • SA has larger Ka, so then a lower pKa

• a weaker acid has lower dissociation constant. WA does not dissociate as much = can be a buffer

buffers

weak acids are good buffers because they do not ionize/dissociate easily, so there is a storage of protons in this species. As acids are added to an aqueous environment, the buffer will resist pH changes by being the source of protons to accept and release to the acid added to solution, rather than the protons being taken from the aqueous environment and changing the pH

• buffer region: 1 pH unit above and below the pKa (when pH = pKa)

the buffer will contiue giving and accepting H+ for/to the added acid until the acidic or basic form of the buffer is exhausted. Then the curve will shift to be more acidic or basic depedning on what the added acid or CB needed

multiple ionizable groups will also have multiple buffering regions

ex titration of aspartate

• 3 different pKa values as molecule changes through titration

pI = isoelectric point

the pH at which a molecule has an overall net charge of 0 (net neutrality)

• find the neutral species, add the pka of the one before it and the one after it and divide by 2

henderson hasselbach equation

determines ratio of protonated to deprotonated species at a given pH

pH = pKa + log [A-] / [HA]

ATP/ADP and catabolic/anabolic pathways

catabolic pathways: break down molecules and release energy used to produce ATP

anabolic pathways: form molecules by using ATP as energy to convert ATP —> ADP

• catabolism provides the ATP that anabolism uses

• 0.7-0.9 physicologal conditions, ATP favored

2 ways ATP can drive unfavorable reactions

ATP hydrolysis is favorable and can drive unfavorable reactions: here is why its favorable

1. via hydrolysis; with relief of charge separation

2. resonance stabilization with phosphate group being a good LG

chirality of amino acids + structure

• chiral: non superimposable mirror images

• 4 different groups around center carbon

• tetrahedral shape (carboxyl, amino, H are the feet, R group faces away)

• amino group

• R group is unique to each amino acid (except glycine doesnt have R group)

• there are 2 configurations (mirror images- enantiomers), but the L config is most common

nonpolar amino acids

• valine (2 ch3 on beta carbon and thats it)

• alanine (ch3 next to amino)

• methionine (long chain w sch3 at end)

• proline (n group in ring)

• glycine (h next to amino)

• isoleucine (ch3 on beta carbon, ch3 another 2 c away)

• leucine (no methyl group on beta carbon)

  • phenylalinine too

predominance of methyl groups (bc no dipole —> hydrophobic)

charged amino acids

negative:

• aspartic acid d (2 carboxyl groups, shorter chain 4c)

• glutamic acid e (2 carboxyl groups, longer chain 5c)

positive:

• histidine h (ring with 2 N groups on it)

• arginine r (n before nh3 group at end)

• lysine k (long chain with nh3 at end)

hydrophilic amino acids

• asparagine n (similar to aspartic acid but nh2 instead of o-)

• cysteine c (SH on beta carbon)

• glutamine q (similar to glutamic acid long chain but nh2 instead of o-)

• threonine t (OH on beta c, then ch3)

• serine s (OH at end of chain)

interacts with water, so each has some sort of dipole- more O and Ns than methyls

aromatic amino acids

• phenylalinine f (single ring)

  • also nonpolar

• tyrptophan w (two rings)

  • amphipathic (both hydrophobic/hydrophilic properties)

• tyrosine y (single ring with OH group)

  • amphipathic

large conjugated ring structure. large bulky residues which impacts folding

hydroxyl amino acids can be ___

phosphorylated becase they have hydroxy groups

• tyrosine (OH on ring)

• serine (OH at end of chain)

• threonine (OH on beta c)

phosphorylation is a post translational modification- occurs after protein is fully folded/complete structure/function

bonds that join amino acids

peptide bonds; creates polypeptide (chain of amino acids)

• between carboxyl group of one aa and amino group of another

• condensation- H2O producted. OH from carboxyl, H from amino

• no full free rotation bc has partial double bond character (resonance of e- on N from amino group pushing towards the carboxyl double bond)

• R groups flipped on either side of molecule

proteins made from

multiple polypeptides folded into their 3d structure

determining net charge of a polypeptide

• figure out what amino acids make it up and look at their pka values

• if the pH of the solution is higher then its more basic and amino acid is more likely to get deprotonated, and vice versa if acidic.

  • if gets nh3 protonated then 0 —> +1 charge, if cooh gets deprotonated then either 0 —> -1

  • value can be 0 if neither group gets protonated or deprotonated.

• add up this value for each amino acid + the N and C terminals

minimal free energy state of proteins

• native folded state- fully folded protein

• as proteins go from unfolded to folded, energy decreases (lowest E state when folded) and entropy decreases

• chaperones are not always needed (folding is usually spontaneous), but they help proteins move into fully folded/native state

protein chaperones purpose + types

chaperones help partially folded proteins move to fully folded state, but are not always needed.

they push proteins over into the funnel (E)

2 types

• chambers

• clamps

chaperones CANT help when

cant help when partially folded protein states become:

• oligomers

• amorphous aggregates

  • when the protein is all tangled up and cant be separated to be pushed over edge and folded correctly

• amyloid fibrils

  • when the protein forms a super rigid structure that cant be corrected to native folded state

framework folding

• formation of alpha helices and beta strands- elements of secondary structure

• coalescence of secondary structure to folded state

hydrophobic collapse folding

• polypeptide comes tg to bury hydrophobic amino acids away from the aqueous environment

• growth of secondary structure into folded state

nucleation condensation folding

• local folding at one point of protein before the rest

  • ex secondary and tertiary folding in one area before the rest of the protein

• hierarchal assembly into native state

chamber chaperone process

• 2 chambers- cis and trans. they are separated and polypeptide goes into either one or the other. binds to hydrophobic rim?

  • top rim/edge of chamber is hydrophobic, but when proteins get folded in here they pass to the other chamber by passing through the hydrophiic interior

• substrate (unfolded protein) goes into the cis ring of the groEL chamber, a cap gets put on the cis chamber, which allows the protein to get folded. the protein binds to the hydrophobic patch on the rim of cis chamber. ADP is currently in binding site, so after protein enters, 7 ATP binds and 7 ADP + Pi leaves.

  • ATP hydrolysis takes 10 seconds, and protein gets folded in that time (gives it time to prevent sticking tg). 7 ADP and 7 Pi leaves in this time. (7ADP leaves when 7ATP enters after substrate binds, and 7pi leaves after folded protein leaves after 10s)

    • doing this cap method separates the partially unfolded proteins from other ones that might cause them to aggregate and stick tg- making it harder to get into native folded state

• once the proteins gets folded, the trans cap gets removed and the protein leaves through the trans chamber. simultaneously, cis cap gets added

  • this is assymetrical model: when cap is on cis, it initiates cap on trans to be released. folded protein leaves from trans and cap gets put on cis

GroEL and GroES

GroEL

• the large barrel chaperons that consists of the cis and trans chambers and the two rings

GroES

• the lid /cap on one GroEL ring that switches cis/trans sides to follow assymetric model

clamp chaperone process

• used while protein is still undergoing translation- so still in ribosome

• majority 70% will fold spontaneously without chaperones, while 30% will use clamps.

  • usually bc larger proteins, those with hydrophobic patches, etc

• 2 clamps: DnaJ and DnaK, bind to hydrophobic patches of protein to prevent them from falling/collapsing/folding on each other before having the info from the whole polypeptide (mid translation)

• when the whole peptide is finished translating, the clamps are removed to release polypeptide since it now has all the information to fold correctly

• from here, 20% will fold with no extra help and 10% will move into chamber chaperone to help as well

secondary structures

• alpha helices

• beta pleated sheets

alpha helix properties

• optimal confirmation for a polypeptide is a spontaneous twisted structure to allow H-bonding between residue n and n+4 (4 amino acids away from each other)

  • -O from carboxyl group in n=1 with +HN group in n=4

• after that, H bonds spontaneously form between available Os and Hs

  • strength comes from all H bonds tg

• R groups all on same side, but then from the twist, all R groups end up facing outwards to allow interaction with other species

• 1 turn/coil has 3.6 residues (amino acids) 5.4 A distance away from each other

• sidedness: R groups form a hydrophobic and hydrophilic (charged side) which allows this twisted structure to form and stay tg

• dipoles: +N terminus —> -C terminus

  • due to resonance: lone pair on the N gets pulled towards the double bond, making the slight dipole

  • indivisual small dipoles from each peptide bond come together and form an overall helix dipole

  • the more AAs in a protein (max 50, min 5) the stronger the dipole bc more accumulation

  • in enzymes, the + side of polypeptides faces towards the - ATP binding site

beta strands/pleated sheets

• the region doesnt form helices but extends to form sheets (which are all joined together bc all one polypeptide)

• R groups can alternate sides now, bc not in a twisted configuration. Causes sidedness too

• beta strands come together to form pleated sheets and there is still flexibility

• H bonding not as common as in alpha helices

antiparallel and parallel beta sheets

beta strands come tg to form beta sheets:

antiparallel

• N —> C

• C ←- N

• gives optimal form for H bonding, makes it a mroe stale structure than parallel and occurs more often

• H bonding between atoms that make up backbone (C=O with H-N) NOT w R groups

parallel

• N —> C

• N —> C

• makes beta turns (the things connecting the sheets tg) less likely and more difficult to form

• geometry is not optimal- there is still H bonding (just less structured), but it is less than antiparallel

beta turns

connects two beta strands to form antiparallel beta sheet

• each turn has 4 residues and H bond forms between residue 1 and 4

• the AAs (3 and 4) from the hinge portion of the beta turn are usually glycine and proline.

  • these are not involved in H bonding

  • glycine because it has no R group so more flexibility to fold in hinge region

  • proline has a rigid ring structure which is good for making sharp turns

tertiary structure

• alpha helices and beta sheets come together via R group interactions to form a folded 3d shape for function

• hydrophobic amino acids cluster in the interior (core) of the protein to minimize interaction with water

• hydrophilic AAs are more exterior and interact with water/shield the hydrophobic AAs

hydrophobic effect

• to minimize hydrophobic AA interaction with water, the hydrophobic R groups from multiple AAs will come together to minimize amount of surface area interaction with water/reduce size of hydration layer

• this is a spontaneous reaction

  • hyddrophobic AAs have an equal sharing of electrons, they don’t have dipoles to interact with water.

stabilizing tertiary structure (3 ways)

• van der waals interactions

• disulfide bonds

• salt bridges

  • eletrostatic interactions

  • H bonding

van der waals interactions

• interactions/attractions between electrically neutral molecules, forming a temporary dipole

• very weak, non-covalent, and distance-dependent

• when atoms are too close, there is strong repulsion

• when atoms are too far, there is weak attraction

  • so need to find optimal distance for interaction to occur

disulfide bonds

• very strong covalent bonds between the SH groups of cysteine

• occurs via oxidation of the 2 cysteines

  • 2 H+ and 2e- released

salt bridges

• consists of both electrostatic interactions and hydrogen bonding

• are not covalent bonds, but occur in tertiary structure of protein

quartenary structure + types

• the result of interaction between multiple polypeptides

• some proteins are done at tertiary structure, but some large ones have multuple polypeptides come tg to form a protein in quartenary

heterotetramer

• dimer or dimers- 2 alpha subunits and 2 beta subunits (2 diff types of polypeptides)

homotetramer

• 4 of the same subunits- 4 alpha or 4 beta sheets subunits

  • both are stabilized by the salt bridges, disulfide bonds, van der waals