Biochem Exam II Flashcards
disulfide bond isomerase
- you can form disulfide bonds between wrong cysteines
- proteins go and find these incorrect disulfide bonds and fix them
chaperone proteins
- function: manage the folding of other proteins in some capacity of the following
1. help proteins fold correctly
2. prevent premature folding
3. prevent polypeptides from associating with other polypeptides until they have folded properly - raise temperature enough to make proteins uncomfortable and start to denature, heat shock proteins (HSP) show up to help (GroEL is an example)
- some proteins always need help some don’t
- GroEL (slide 33)
1. unfolded protein enters
2. put lid on it (we don’t fully understand)
3. need ATP for energy (exergonic phosphate group)
4. the protein folds
5. cap comes off and protein leaves
prolyl isomerase
- what does it fix and how
- one of the most common protein folding errors is the incorrect cis trans isomerization of the amide bond adjacent to proline residues
- though proline does favor trans conformation, it’s not HUGELY favored over cis (energetically), so it happens fairly often that the cis conformation forms first and that must be fixed
- prolyl isomerase catalyzes the process of changing cis to trans
binding vs. bonding
binding =
- interactions between molecules (IMFs)
- TRANSIENT
- always equilibrium at play (we want it to the right)
bonding =
- sharing of electrons to form covalent bond
- bond formed through chemical reactions
apo proteins
a protein without its prosthetic groups
- example: protoporphyrin IX with Fe(II) = heme
- T state
holo proteins
proteins that have all of their prosthetic groups (non amino acids needed to function)
example: hemoglobin with heme
myoglobin without heme
- R state
What are the axis on a binding curve? what does a binding curve show?
y - axis = YO2 (only goes up to 1)
x - axis = enzyme concentration
binding curves show how much of an enzyme is bound at what concentration
- Kd is found when y = 0.5; when concentration of ligand = Kd
- a higher Kd = lower affinity bc it takes more ligand to bind
- a lower Kd = higher affinity bc you need less ligand to bind
Why look at a mutant on a binding curve? example?
- see how something is binding
- see what happens when you mutate it… how does it react and what does it react with
- this is important in overall protein structure
Example
aspartate (-) —-> lysine (+)
- change from - to + and see how interactions change (you won’t have ion-ion); this is important in medical applications bc many medicines are designed to block interactions because they block ligands from getting to the proteins
What is the ligand for an antibody?
antigen
myoglobin v hemoglobin
myoglobin = more localized than hemoglobin
hemoglobin = transport oxygen throughout the body (must be able to bind and release oxygen)
cooperation of O2 binding to Hgb
- hemoglobin in T state without oxygen bound to it
- R is weird to have without oxygen bound because of its conformation of molecule when O2 is bound; high affinity state
- As O2 concentration increases more of the tetramers go to R state (want to bind O2)
- at high concentration of O2, the hemoglobin approaches saturation as almost all Hb tetramers are in the higher-affinity R state (notice there are 4 binding sites)
- as 1 site on an Hb molecule binds to O2, a signal/communication is sent for all sites to bind
T state v R state in terms of conformational change
- WHOLE conformation changes when O2 binds so that it can bind O2 better
- explains cooperativity
- you can bind all 4 sites
- but you must let go eventually (thx pH)
In T state:
- heme group is sticking out (puckered) because the iron group is sticking out BECAUSE NO OXYGEN IS BOUND
- distal histidine detached from main hub
In R state:
- oxygen binds and it connects with the histidine which is connected to the rest of the molecule
- the distal histidine moves to interact with the O2
- heme completely planar
What are the 4 main factors that affect O2 binding to hemoglobin?
- pH
- O2/CO2
- CL-
- BPG
What are the parts of an antibody
2 pieces
1. heavy chain
2. light chain
ligand? antigen
factors that affect O2 binding: pH
- changes the + and - interactions
- if you lower the pH, the environment gets more acidic, so there will be more H+, and more things will get protonated (change charge)
carboxylate example:
- probably interacting with NH3+ with a salt bridge
- if the carboxylate gets protonated it won’t want to do that anymore
factors that affect O2 binding: O2/CO2
- CO2 from bicarbonate system
- the CO2 has to leave the system; most of it is dissolved in water or blood; bicarbonate changes
- some CO2 is added to the N-terminus and this changes the conformation of the protein which means the ligand cannot bind
factors that affect O2 binding: Cl-
when Cl- ion increases, it locks Hgb in its T state
- positive things interact with the Cl-
- it comes in when CO2 leaves
factors that affect O2 binding: BPG
2,3-BPG
- allosteric ligand
- it binds and it helps lock hemoglobin into specific conformations
- lots of positively charged amino acid residues because there are so many negative charges = SALT BRIDGES
allosteric ligand
any binding site anywhere else in a protein
what kind of regulations do we need in terms of getting and releasing oxygen?
SHORT AND QUICK
fetal hemoglobin
serine instead of histidine (bc it has higher affinity than the mother’s blood)
-shows that a change in one amino acid residue makes a huge difference
what macromolecule are we working with when you hear “glyco”
carbohydrate
D vs L fischer projections for carbohydrates
D = OH on the right for farthest carbon that’s not the end
L = OH on the left
How do we number carbons?
ketone needs to be priority
alpha vs beta sugars
alpha = OH is down
beta = OH is up
pyranoses
ring structure of sugar:
6 ringed sugar
furanoses
ring structure of sugar:
5 ringed sugar
glucose
- aldohexose
- right, left, right, right
ribose
- aldopentose
- right, right, right
how do alpha and beta forms arise?
when you attack the carbonyl and move the carbonyl oxygen, it can go down for alpha or up for beta
uronic acid versus onic acid
-uronic = oxidation happens at carbon 6
- onic = oxidize the first carbon
epimers
- differ by 1 stereocenter
- glucose and mannose
anomeric carbon
carbon 1 (which is what’s oxidized in -onic acids)
acetyl
simplest acyl group where R is methyl
acyl
carbonyl group with ANY R group between carbons
acetylation
adds a methyl group
how monosaccharides form rings
1) reaction of C1 of D-ribose with C4 hydroxyl forms furanose
2) reaction at C5 hydroxyl with C1 = pyranose
- Attack the carbonyl because its planar; all other OHs are locked into their original stereochemistry
- pyranose formation includes hemiacetal (between ketone and alcohol/enol)
how monosaccharides form di/poly saccharides
condensation reactions (:
- curvy bond is drawn to keep sugars in line
- endergonic (requires a lot of energy)
1) activate molecules
- we use U to activate sugars
- UTP; U = uracil
- UDP is a good leaving group
2) nucleotide gives sugar a lot more stuff to react with
3) energy, reaction happens, recognize molecules
Example: beta-D-Galactose to lactose
functions of long carbohydrates
- very repetitive
1) structure - chitin
- cellulose
2) energy storage - starch (plants)
- glycogen (animals)
sugar modification examples:
1) beta-D-glucose-1-phosphate
2) D-delta-gluconolacctone
3) beta-D-glucuronic acid and D-gluconic acid
4) beta-D-N-Acetylglucosamine
5) Muramic acid
6) N-acetylmuramic acid
N-acetyl____acid
add an acetyl group to the amide bond