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
glycoproteins
saccharide + protein
N-linked or O-linked
post-translational modification
recognition cell-to-cell = integral GLYCOproteins
biggest role of carbohydrates (as ligands)
2 ways to covalent bond and describe (carbohydrates)
1) N-linked
- sugar covalently bonded to asparagine (N)
2) O-linked
- sugar covalently bonded to serine or threonine (bc OH)
Glycoprotein to enzyme-penicillin complex
1) glycoprotein
2) protein/ligand aka enzyme/substrate complex is active
3) chains cross-linked = bonding (reaction)
4) instead of enzyme being able to get chain I and cross link, penicillin blocks it and antibiotic kills bacteria
- enzyme doesn’t work
- cross linked cell wall turns into strings (noodles instead of woven mesh)
- bacteria need cell wall for protection from attack and against osmotic pressure
examples of glycoproteins
N-acetyleglucosamine
N-acetylgalactosamine
sialic acid - where flu gets stuck and enters body
Oseltamivir (tamiflu) - fights the flu
describe the entire flu process
A flu virus particle has 4 main parts
1) lipid bilayer
2) nucleoprotein-RNA complex
3) neuraminidase
4) hemagglutinin
Neuraminidase = globular protein with charges bc water soluble
- enzyme catalyses removal of sialic acid so virus can leave and infect another cell (bc it’s stuck to sialic acid)
Hemagglutinin
- allows virus to stick to target cell (sialic acid) and release DNA or RNA; it’s a protein
Sialic acid
- modified sugar with carboxylate group; N acetylated
- in nasal passages where flu enters
Oseltamivir = Tamiflu
- fights the flue because it has similar functional groups to sialic acid
- instead of flu virus binding to sialic acid and it gets stuck because neuramidase can’t remove it
lectins and selectins
- bind to carbohydrates
- help with protein sorting
- every OH group in mannose interacts with the protein: SPECIFICITY
talk about inflammation
- if you have inflammation, we need to get leukocytes to the site… but how?
- leukocytes with carbohydrates can RECOGNIZE
- things happen to express injury
- like velcro, WBC slow down and go out of capillary to help with the immune response
are lipids hydrophobic or hydrophilic
hydrophobic
What are the 2 general roles/jobs of lipids?
1) passive: fat storage, part of membrane, structural
2) active: cell signaling, chemical reactions
Do lipids have single unit? what do we pretend is the single unit?
no but we say fatty acid
fats vs oils
fats:
- solid at room temperature
- more saturated
oils:
- liquid
- unsaturated (cis double bonds)
- from plants or fish (healthier than fats)
- almost always cis with naturally occurring
What do we do with oils for human food purposes? What is a downside?
- partially hydrogenate them to make them more like butter (don’t want to pour oil on your waffles)
- add Hs
- we get some trans fat = bad
can we make omega-3s?
nope! we can only make lipids 16C long, so we rely on plants and animals(fish)
fatty acid basic structure; IMFs?
carboxyl group (deprotonated at physiological pH)
alkyl chain
- only van der waals or hydrophobic interactions
saturated vs unsaturated fatty acids
1) saturated: no double bonds in the cain
example = stearate ion
2) unsaturated: has a double bond
example = oleate ion with 1 cis double bond
how to read fatty acid abbreviations:
1) 12:0
2) 16:1c9
1) there are 12 total carbons in the chain and 0 double bonds
2) there are 16 carbons in the chain with one double bond at C9
polyunsaturated fatty acids (PUFAs)
- contain more than one double bond in their backbone
- omega-3 fatty acids
- omega-6 fatty acids
- good, healthy fats that we need but can’t make in our bodies
omega-3 fatty acids
- double bond between C3 and C4 relative to the most distant carbon (omega)
- have several unsaturated carbons
- all cis double bonds
- not conjugated (2 or more sp3 C)
omega-6 fatty acids
double bond between C6 and C7 relative to omega
triacylglycerols
- ENERGY STORAGE
- heat/insulation
- generate heat
- only lipids come together to make this bigger molecule (no other macromolecules)
- forms with condensation reactions between glycerol
- “acyl” because any R group can join
- neutral charge lets it be stored
why is storage in the form of triacylglycerols instead of single free fatty acids?
- fatty acids are charged when alone, so cramming them into a muscle cell would cause a lot of repulsion from all of the charges
- triacylglycerols have neutral charge and they are hydrophobic and happy together
explain the process of digesting fats
1) gallbladder adds biosalts to make fats more soluble (emulsify them)
2) from the small intestine, fats need to get out of the digestive tract (through the wall) to get to the rest of the body
3) we have triacylglycerols and break them down into smaller parts to get out
4) we put them back together in the body
5) make a lipoprotein to be water soluble
6) fatty acids go into muscle cell (fat burned) or fat cell (stored) in the form of triacyl glycerol
what are the 2 main issues with digesting fats that need to be addressed
1) water solubility
2) charges
lipids and pigments
lipids make pigments - especially red and yellow
- with trans and conjugated chains you get color
- more conjugation = more absorption in visible region = color
- blues are difficult
how lipids form micelles
- fatty acids are wedge-shaped and tend to form spherical micelles (bc head and one tail)
- they have a carboxylate polar head
- the close in on themselves when in water spontaneously
- this is how soap works - dirty stuff gets stuck on the inside of the circle
glycerophospholipids
- most common in membrane
- core is glycerol (diacylglycerol)
- need in membranes: structure, control of what’s in and out, permeability
- AKA PHOSPHOLIPID
- glycerol with hydrophobic tail = condensation rxn to get the phospholipid
- can be any fatty acid (1 saturated, 1 unsaturated, whatever)
phosphatidyl inositol (PI)
- carbohydrate derivatives
- not a carbohydrate bc there’s no oxygen in the ring
- but it looks similar
ceramide
R group = fatty acid
- usually sphingosine with fatty acid
- fatty acid linked via amide bond
sphingolipids
- sphingosine plus ceramide
- molecule is built around sphingosine instead of glycerol
- middle of molecule isnt glycerol
- has its own tail that isn’t a fatty acid
- example: sphingomyelin
sphingomyelin
- brain: makes up myelin sheath
glycosphingolipids
- talk about blood groups
- sugar plus ceramide
- blood groups determined by types of sugars on the head groups of glycosphingolipids
- O blood = no antigen
- A blood = A antigen
- B blood = B antigen
- O blood can only accept O blood bc the immune system will attack A and B antigens
glycolipid
- sugar plus lipid
cholesterol
- can we produce it?
- structure
- we CAN produce it (because we need it to live)
- polar head (OH) and nonpolar body
- sterol nucleus
- no fatty acid but still a lipid
Fluid Mosaic Model
- 1972
- everything in the membrane can move (proteins and lipids)
- mosaic like art = lots of stuff
- reorganizes on the fly
- constantly experiencing change as organism so we have to be able to adjust
what % by mass of membranes is protein
60%
2 types of membrane proteins
- peripheral = anchored, associated with membrane but not in it; GPI; can leave or stay for a while, whatever
- integral = integrated IN the membrane; transmembrane alpha helices
How do proteins know where to go (membrane)
- post translational modification!
- the Golgi apparatus tags proteins (covalent bond) and tells it where to go/makes it identifiable
- this tag is coded in its amino acids; enzyme knows to bind to it and catalyze the reaction to add the tag
- tags are crucial for cell to cell recognition - say what’s on the outside versus inside
How did we study how membrane proteins work
- turn protein green but change the tag
- instead of GPI, Farnesyl will exist
- you’ll see more green move to the inside
GPI
glycophophital inositol
- inosital = almost sugars
- phosphate group
- 2 acyl chains (any R group)
- protein/amino acid
- bacteria redoxin structure
- can we predict how many acids span a membrane
- alpha helices
- how many amino acids to span membrane? 1 turn of an amino acid covers a certain distance
- we can figure out how many are needed to cross a membrane
what could it mean if you see enough hydrophobic proteins in a region?
- maybe transmembrane protein
- hydrophobic goes IN the membrane because of the lipid tails
- tryptophan, valine, leucine = hydrophobic
- glutamate, serine = hydrophilic
how do integral proteins know where to go
cotranslation
- ribosomes in rough ER let protein go straight to membrane and avoid hydrophobic issues
raft platform
- form larger structures
- proteins can interact with rafts
- can change and adapt based on environment
valinomycin
- a drug molecule
- hold K+ ion and lets go on the other side of the membrane
- has hydrophobic parts
- COULD be a protein or not
- fits K+ perfectly: Na+ would be too small to fit and bigger ions wouldn’t fit
- the oxygens of valinomycin merge into the K+ for ion-ion interaction/salt bridges
permeases
- like transporters
- very specific
- always integral proteins
- GLUT1 = lots of glucose transporters
GLUT 1
- why have multiple proteins with the same function?
- GLUT 1 = glucose transporter
- bc they can be expressed in different cells in different ways to REGULATE them
- have some glucose transporters on all the time because we always have glucose in the blood
- we activate more transporters when glucose spikes (exercise, eat)
lactose permease and xylulose/H+
1) lactose permease: inside open (lactose exits on inside of cell)
2) xylulose: lactose exits on the outside of the cell
CONFORMATIONAL CHANGE
P-glycoprotein
moves drugs; takes foreign things out of the cell
multidrug transporters and cancer cells
need multidrug transporters because cancer cells adapt and get used to them so you need new ones
uniport
do one thing
symport v s antiport
symport = send BOTH THINGS IN THE SAME DIRECTION
- both in or both out
antiport = equalizing/keeping something maintained; 1 in and 1 out
example: bicarbonate out and chloride in
beta barrels as membrane proteins
- not empty in the middle (side chains)
- less specific
why hydrophilic pore in membrane?
membrane is mostly hydrophobic so it needs help transporting hydrophilic things
aquaporin
- helps water get through membrane
- 4 domains (tetramer)
- alpha helices
- asparagine, histidine, and arginine = all have an N that can help H bond with water so it can pass through
why would a water leave the network its in to go to a pore? why do we need more water in our out of a cell?
- energetically more favorable
- polar
- have to replace the IMFs (bc they keep low energy)
- replace with new H bonds - something with amino acids?
2)
- maybe storage (plants)
- maintain concentration gradients and osmotic pressures
selectivity filter/mechanism of the K+ channel
- need to open channels selectively depending on what is needed; sometimes against the concentration gradient
1) large water-filled vestibule allows hydration of K+; allows water to float around it
2) the alpha helix has a dipole (polar) and generates magnetism with its big negative charge sucking in the K+
3) K+ enters the channel - needs to replace interactions it’s having with water with carbonyl oxygens
4) backbone carbonyl oxygens form a cage that fits the K+ perfectly - replace the waters
5) the K+ comes out on the other side
closed conformation and open conformation
closed = alpha helix towards each other; seals the channel
open = alpha helices move towards extracellular side of bilayer (away)
pumps in membranes
- require energy
- Na+-K+ ATPase
- different domains for different functions
- hydrolysis of phosphate bond (energy from ATP)
sodium potassium pump explained
- cycle to keep moving Na+ out and K+ in
1) 3 sodium in the channel; it is open to the extracellular side because the phosphate is on the amino acid residue
- this keeps a specific conformation bc of the large - charge
2) the sodium leaves into the extracellular
3) 2 potassium enter the pump
- need a conformational change to close the pump
- the phosphate leaves the amino acid residue
4) ATP binds to the amino acid residue and K+ enters the cell
- this is another conformational change
5) 3 Na+ go back into the pump from the inside of the cell
6) the ADP leaves and the amino acid goes back to phosphorylated stage (with phosphate group attached to amino acid residue)
lumen of small intestine
lumen = inside of intestine where the food is
intestine job = get nutrition
- bring things in and kick things out on the other side
voltage gated channel
at resting potential, the channel is closed
when membrane is depolarized, the channel opens through conformational change
- depolarization = EPSP = influx of Na+
- hyperpolarization = IPSP = influx of Cl-
ligand gated channel
open and close in response to a chemical message coming to the cell
example: nicotinic acetylcholine receptor
- closed
- 2 acetylcholine molecules bind which twist the helices
- helices now have polar, smaller residues lining the channel and it opens
