Upgrade to remove ads
Only $35.99/year

BB 490 Midterm 2 Review

Terms in this set (184)

Protein purification meaning
Separating protein of interest from other molecules
Purpose of "bucket biochemistry"
Get natural source proteins via large quantities of starting material (pre-late 1970s)
Recombinant proteins
DNA encoding protein inserted into vector, used by organism (such as E coli) to produce protein (since late 1970s)
Assay for enzymes
Enzyme activity
Western blot assay
Antibody for protein of interest is used to visualize it in a gel
Assays for proteins
Enzyme activity (for enzymes), western blot, check for band at correct position on gel
Which molecules move most slowly through a standard gel?
Largest and least negative molecules
SDS-PAGE detergent
SDS (sodium dodecyl-sulfate)
SDS-PAGE gel material
Polyacrylamide
Function of SDS
Denature protein, shape into rod, and coat with a negative charge
What determines speed of proteins in SDS-PAGE?
Size (and not charge)
Function of reducing SDS gels
Split proteins bound by disulfide bonds into two bands
Reducing agents used in SDS
BME (beta-mercaptoethanol), DTT (dithiothreitol)
Uses of mass spectrometry for protein analysis
Verify, identify, and sequence proteins
Mass spectrometry process for identifying proteins
Volatize protein of interest into vacuum, separate based on mass to charge ratio, get molecular weight information
Mass spectrometry process for sequencing proteins
Cut protein into peptides using proteases, sequence each peptide
Size exclusion (aka gel filtration) chromatography
Gel contains beads with pores that trap and slow small molecules, letting the largest molecules elute first
Ion exchange chromatography
Separates proteins based on charge using a charged column
Cation exchange chromatography
Negatively charged column only lets negatively charged proteins through
Anion exchange chromatography
Positively charged column only lets positively charged proteins through
Affinity chromatography
Receptors are attached to column to bind protein of interest until elution buffer is used
Affinity chromatogram
Nonbinding proteins are washed away first, then elution buffer is used to release protein of interest
Dominant method for purifying proteins
Affinity chromatography
Affinity tag
Sequence added to the N or C terminus of a protein to be recognized in affinity chromatography
How tags are cleaved
Protease cleavage site in vector
IMAC
Immobilized metal affinity chromatography (often used for His tags)
Ways to determine 3D structure of proteins
X-ray crystallography, NMR spectroscopy, CryoEM
X-ray crystallography process
Crystallize pure protein, get defraction pattern after applying x-rays, get electron density map, use electron density to build model of atom locations
Limits of NMR spectroscopy
Proteins must be under 40-50 kDa (400-500 amino acids)
Cryo-electron microscopy process (CryoEM)
Averages thousands of electron micrographs of proteins to get structure
Advantages of CryoEM
Works well for large proteins and complexes, proteins don't need to be crystallized
What is the major way for carbon to enter the body?
Carbohydrates (carbon incorporated into a carbohydrate during photosynthesis, becomes a major energy source)
General formula for carbohydrates
Cn(H2O)n
Sugar prefix & suffix
'Glyco' means 'sweet', 'ose' means 'full of'
Name some roles of carbohydrates
Energy storage, structural (cell walls, exoskeletons, lubricants), identification tags, modify proteins and lipids
2 Types of simple sugars
aldose- aldehyde based (HCOH)
ketose- ketone based (C=O)
Can aldoses and ketones be converted into each other?
Yes (through tautomerization)
How to differentiate between D & L sugars?
-D sugar: the furthest chiral -OH from the aldehyde or ketone is on the right side
-L sugar: the furthest chiral -OH from the aldehyde or ketone is on the left side
-To switch between D and L forms of molecules, you must invert every chiral center, not just one.
How many stereoisomers in a sugar?
2^(n), where n is the number of chiral centers in the sugar
Enantiomer
Mirror image stereoisomers (D & L sugars)
Diastereomer
Stereoisomers that are not mirror images of one another
Epimer
Stereoisomers that differ at a single chiral center
How many different names for a sugar are there?
(2^n)/2, where n is the number of chiral centers (divided by 2 because D and L versions of a sugar have the same name)
Furanose
5 membered ring sugar (C4 OH attacked C1)
Pyranose
6 membered ring sugar (C5 OH attacked C2)
Differentiate between an alpha and beta cyclic sugar
alpha- at C1, a new chiral center, the new -OH group is down, beta- at C1, a new chiral center, the new -OH group is up
Converting a Fischer projection to a Haworth projection
left on Fischer = up on Haworth, right on Fischer = down on Haworth
What happens when you start with the pure alpha form of a cyclic sugar in an aqueous solution?
Due to mutarotation you will end up with a mix of alpha and beta over time.
D-Ribose (Fischer)
Right, right, right
⍺-D-ribofuranose (Haworth)
D-Glucose (Fischer)
Right, right, left, right
β-D-glucopyranose (Haworth)
D-Fructose (Fischer)
Right, right, left
β-D-fructofuranose
Aldehyde oxidized to an acid
The O becomes an OH
Reducing Sugar
Monosaccharide with a hemiacetal ring
When an aldose is reduced it forms a ...
alditol- aldehyde group becomes hydroxyl group
(glucose reduced to sorbitol) (ol at the end are typically reduced sugars)
Glycoside
A sugar with something bonded to the anomeric carbon (can be either O or N)
Anomeric Carbon
The new chiral center formed in ring closure (previously the carbon containing the carbonyl in the straight-chain form)
Where can sugars be modified?
-Anomeric carbon (glycosides)
-Aminosugars- a hydroxyl group is replaced with an amine group
Oligoscaccharide
-built through glycosidic linkages
-If a hydroxyl on another sugar attacks the anomeric carbon on a sugar, you can make a glycoside. In glycosidic linkages, sugars are linked together. For example, β-D-galactose and β-D-glucose linking to make lactose
-An uphill process typically, requiring the energy of UTP
-Sometimes both anomeric carbons will be linked (for example, in sucrose)
⍺ linkage (glycosidic)
-occurs when the -OH group is below the plane
β linkage (glycosidic)
-occurs when the -OH group is above the plane
D-galactoseβ(1—>4)D-glucose
There is a β linkage between the anomeric carbon, C1, of the galactose and C4 of the glucose molecule
-Abbreviated Galβ(1—>4)Glc
Sucrose Abbreviation
Glc⍺(1—>2)Fruβ
Glycosidase
Cleaves polysaccharide. Breaks glycosidic bonds using hydrolysis. Exo (at end) or endo (in middle)
3 Functions of Polysaccharides
1. Energy storage
2. Structural support
3. Glycosaminoglycans
2 Types of energy-story polysaccharides
1. Starch, carbohydrate storage in plants
-⍺-amylose: [Glc⍺(1—>4)Glc]n
Repeating glucose units with alpha 1,4 linkages
-Amylopectin: [Glc⍺(1—>4)Glc]n with Glc⍺(1—>6) branches
2. Glycogen - basically amylopectin, but with more frequent branches
-Carbohydrate storage in animals
Why is ⍺-amylose wide and accessible?
Instead of forming stacked lines, it forms wide open helices. This is because of its ⍺ 1—>4 linkages, which are axial.
Name and describe 2 polysaccharide barriers.
Cellulose: [Glcβ(1—>4)Glc]n
Identical to ⍺-amylose, except for having β linkages.
This equatorial linkage allows for flat strips of polysaccharides. As all OH groups are equatorial, all axial groups are H. This allows for stacking through the hydrophobic effect, in a crystalline-like form
Very insoluble due to the above
We do not have glycosidases that can break the β1,4 linkage, so cellulose is indigestible by us (though some animals do).
Chitin: [NAGβ(1—>4)NAG]n
Involved in shells of insects
Made by NAG, N-acetyl-glucosamine
This is a type of N-glucoside
Some fungi (as do insects and crustaceans themselves) make chitinases
Lisozyme
enzymes that cleave glycosidic linkages between GlcNAc and MurNAc, polymers found in bacterial cell walls
Glycosaminoglycans & give 2 examples
Highly acidic carbohydrates chains (N-glucosides)
Does not interact well with itself- stays "open" in structure
Useful for areas in the body where we need lubricants or shock absorbers
Carbohydrate groups repel each other, and act like pillows
1. proteoglycans
2. heparin
Proteoglycans
95% carbohydrate, helps build cartilage
Protein-modified carbohydrate
Blue dots on the right are proteins, all horizontal things are carbohydrates
Heparin
anticoagulant, prevent blood clots from forming
Polysaccharide with acidic groups, particularly sulfate groups
Glycoproteins
Typically a protein molecule with oligosaccharides on their surface
Saccharides can be N-linked or O-linked
N-linked saccharides are on asparagine (NH3 side chain)
O linked saccharides are on serine or threonine (OH side chain)
Typically extracellular proteins
Carbohydrate linkages help with sorting, and also serve as cell-surface recognition factors
Modulate protein properties (can protect from proteolysis)
Lectins
a protein that binds carbohydrates (many recognition proteins bind carbohydrates)
ABO blood groups.
Difference is the oligosaccharides on cell surfaces
All people have the oligosaccharides for "O group"
Some people have enzymes which add additional sugars (A or B)
Some people have both (AB)
Those who do not have the enzyme are type O
O is the universal donor, as no one will have antibodies to it
AB is the universal acceptor, as it has no antibodies toward O, A, or B
Lipids & Functions
- loosely defined term for biological fat soluble molecules
Can be fully nonpolar or amphipathic
Energy storage
Water barriers
Membranes
Signaling (steroid hormones)
Vitamins (A, D, E, K)
Fatty Acid (saturated v unsaturated)
Simple carboxylic acid with a long aliphatic (C and H only) chain
Can be fully saturated (maximum amount of hydrogens)
Can be unsaturated (having 1 or more double bonds)
Why do fatty acids form micelles?
As fatty acids have a polar head group and singular aliphatic (hydrophobic) tails, they will form micelles in water
Tail is so skinny compared to head, making is hard to make a plane and easy to make a circle
Nomenclature of fatty acids
# Carbons : # double bonds, type, position
For example, the fatty acid shown in the upper right would be 18:0, as it is 18 carbons long and also unsaturated (no double bonds)
Carbon in the COOH group is included in this
Why do unsaturated fatty acids pack less well than fatty acids?
As unsaturated fatty acids have kinks in them, they will pack less easier than saturated
So, unsaturated fatty acids will have lower melting temperatures (olive oil vs. butter)
As fatty acids get longer, they have higher melting points
Triglycerides
Fats and oils
Now, there are no carboxylic acid groups - this molecule is completely hydrophobic
R side chains are highly reduced carbons, and can store lots of energy
Can digest them to generate heat
Also work as a biological insulator
As more double bonds are added to the aliphatic R groups, the melting temperature of the triglyceride will lower (oils are liquid at room temperature and more unsaturated than fats, which are solid at room temperature)
Both fats and oils otherwise have the same triglyceride structure
Saponification
breaking ester bonds, soap was made when lye was added to fat, releasing the fatty acids which then made micelles
Hydrogenation
unsaturated fats are reduced to yield saturated fats (making oils more solid, as this increases the melting temperature by removing double bonds). This can also wind up making trans fats
Waxes
A long chain alcohol that is esterified with a fatty acid, making an ester
Overall, molecule has two "tails" - one from the original fatty acid (left), and one from the esterified long chain alcohol (right)
Length of both chains can vary based on type of wax
Very nonpolar and insoluble in water (think of coating on leaves or duck feathers)
Phosphoglycerides
(glycerophospholipids) are the main membrane-builders
Basically identical to triglycerides, except the bottom fatty acid is replaced with a phosphate group
If R3 = H (or another negative molecule) on phosphoglyceride
phosphatidic acid
If R3 = something other than H on phosphoglyceride
phosphatidyl ester
If R3 = a sugar on phosphoglyceride
glycoglycerolipid
Phospholipases
Cleaves phospholipids, named based on the groups they cleave off
Sphingolipids
Based on sphingosine instead of glycerol
Long chain hydrocarbon, attached to three carbons (top and bottom with alcohol, middle with amine bound)
Ceramide
The amino group of a sphingolipid is modified to an amide bond
Glycosphingolipid
A sphingolipid with a head group containing a sugar
Ganglioside
A sphingolipid with a head group containing an more than one sugar
BLAST
gene database for comparing DNA or amino acid similarity locally
Assay
A test for searching for specific proteins in order to separate them from other molecules (for protein purification) for example, fluorescent-tagged proteins
Natural Protein
"as is" in the cell- with no research modification
Recombinant Protein
Inserting a gene into the DNA sequence of an organism (typically some type of plasmid, like the circular DNA in bacteria) and having that organism produce the protein you want (for example, insulin)
One risk is that post-translational changes will not be included in the manufactured protein.
Wild Type
Sequence as it occurs in an organism
Mutant
Any changes in the natural sequence of the organism
What is one way to protein tag?
Putting recombinant DNA into the protein coding sequence, modifying the protein to include some type of assay, for example, green fluorescence.
SDS-PAGE
Can be used to assess the size and purity of a protein
-A type of gel-electrophoresis which incorporates
a detergent used to unfold native proteins and coat them with a negative charge
-Gel separates the proteins based on size, which is proportional to charge
What happens when SDS-PAGE contains a reducing agent?
Breaks disulfide (S-S) bonds
A quaternary protein held together with S-S bonds will yield multiple bands because there are now more free polypeptide chains
Mass Spectronomy
If genomic sequences available, separates proteins based on mass to charge ratio (not useful if two different proteins have the same molecular weight)
Protein mass can be found within 1g/mol (super accurate)
3 Kinds of Chromatography (separation tools)
1. Size Exclusion
2. Ion Exchange
3. Affinity
Size Exclusion (chromatography)
(chromatography- separation tool)
Gel with cavities in it, making big molecules go faster (because they go around) and smaller molecules go slower (because they go through), separating based on size.
Ion Exchange (chromatography)
(chromatography- separation tool)
-column is a charged particle (+/-). Cation exchange column holds on to negatively charged proteins, anion exchange column will hold on to positively charged proteins. More charged molecules will go through slower than less charged molecules. Separates based on charge.
-Elute by increasing ionic strength- add salt. Will disrupt charge-charge affinity, eluting from less charged first to more charged later.
Affinity (chromatography)
-Separates based on binding ability. Load column with something that binds to specific aspects of a protein. (for example, for an insulin receptor protein, load column with insulin so receptor sticks to it)
-very specific
-Can elute these with a better binding agent
Affinity Tag
Recombinantly include a domain in the protein that has an affinity for something in the affinity column (pe His tag 6 histidines that bind to Ni ions in the column)
3 Approaches to 3-D structure determination
1. X-Ray crystallography
2. NMR spectroscopy
3. Cryo-Electron microscopy
X-Ray Crystallography (3-D structure)
Make a crystal out of pure protein, put in front of X-ray beam, get scattering pattern, allows image of where atoms are
NMR Spectroscopy (3-D structure)
-Does not require growing crystals, though less precise
-Proteins in solution needed
-Gives a family of structures that satisfy the data (gives structures compatible with the data), only proteins up to 50 kDa)
Cryo-Electron Microscopy (3-D structure)
-Good for flexible proteins that cannot be crystalized and large proteins over 50 kDa (can't do NMR)
-Protein on grid, put in electron microscope
Levels of protein structure
Primary- sequence of residues in a chain
Secondary- regular local structure, usually involving regular H-bonding (⍺-helix, -sheet, PII, turns)
Tertiary- 3D folding of a single protein chain
Quaternary- association of chains and their arrangement with respect to each other
What 2 things contribute to stabilizing and destabilizing a protein? Why?
-Conformational entropy (disfavors protein folding): determined by the torsion angles of phi and psi and whether residues are cis or trans to one another. Trans is common, cis a rarity
-Hydrophobic effect (favors protein folding): hydrophobic residue placement in sequence will determine folding such that hydrophobic residues are away from water (primarily inside the globular protein)
Phi
Angle of N and alpha-C
Psi
Angle of alpha-C and C
Ramachandran Plot
- putting Φ and ψ angles on x and y axes.
Φ = x
Ψ = y
Shows which conformations are allowed and which are not.
What are the most and least conformationally free amino acids?
Glycine (most)
Proline (least)
What drives the secondary structure of proteins?
Regularly H-bonded backbones.

⍺ helix
i + 4 → i

Distant:
Parallel β-sheet - both go from N → C,
Antiparallel β-sheet - one goes from N → C, and C → N
Little energetic difference between parallel and antiparallel
Driving force is regular hydrogen bonding from backbone
Alpha Helix (residues/turn, nm/residue, description)
-3.6 residue/turn
-0.15 nm/residue (.54 nm or 54 angstrom/turn)
-side chains point out from helix
-most stable due to Van der Waals interactions in the middle of the chain
-an amphipathic helix has nonpolar residues every 3-4 residues
Beta Sheet (residues/turn, nm/residue, description)
-Beta strand is an individual element of a beta sheet- beta sheets have at least two beta strands
-2 residue/turn
-0.34 nm/residue
-0.68 nm/turn
-have a top and a bottom side, so every other residue points in the same direction
-for an amphipathic sheet, nonpolar residues every other residue
PPII Helix (residues/turn, nm/residue, description)
-not regularly hydrogen bonded
-named after proline, but every other type of residue can also adopt this conformation
-most common structure for unfolded proteins/polypeptides
-0.3 nm/residue
-3 residues/repeat
-0.94 nm/turn
-exposes all backbone to water for H-bonding (this is why it's so good for unfolded proteins)
-turns are usually at protein surface using Glycine or Proline
Fibrous Proteins (give 3 examples)
-can be recognized by unusual amino acid composition -> will affect structure.
-⍺-ketain
-β-fibroin
-Collagen
⍺-ketain
-a fibrous protein
-2 alpha helices coiled around one another
-3.5 residues/turn
-'coiled-coil'
-hair, fingernails, horns
β-fibroin
-a fibrous protein
-every other residue is glycine, so one entire side of the sheet is glycine
-other side is either serine or alanine
-β-sheet conformation, very flexible
-silkworm silk & spider web
Collagen
-a fibrous protein
-connective tissue, esp abundant in bones & skin
-Triple PPII helix, glycine every 3rd residue (3 residues/repeat)
-glycine is the core of the 3 helices, hydrophobic pocket
-Hydroxyproline helps provide extra hydrogen bonding between strands
-If not hydroxylated, collagen is weaker (this requires vitamin C)
Tertiary Structure
Arrangement of a single polypeptide chain, usually in globular form
-main driving force is hydrophobic side chains moving to the center to be buried.
-comprised of 100-300 residue 'domains'
-some tertiary H-bonds form
-about 3000 folds exist
Intrinsically Disordered Proteins (IDP) (characteristics)
Sequence favors nonfolding (35-50% of the human genome)
Nucleolus held together with IDP's
Characteristics:
-have few aromatics, which stabilize core
-high ratio hydrophobic to hydrophilic amino acids
-have large net charge- repulsion inhibits folding
-many prolines which hinder helix & sheet formation
Quaternary Structure
-multiple polypeptide chains associating with each other
-each chain is a subunit (dimer, trimer, tetramer, ect)
-identical subunits (homo, like homodimer), if not, hetero
ΔG°' for Folded Proteins
-20 to -60 kJ/mol
ΔG°' for H-bonding
-5 to -25 kJ/mol- entire protein can be interrupted by blocking one hydrogen bond
What does it mean for a protein to have a ΔG°' of -18 kJ/mol?
For every 1000 proteins, 1 is unfolded
(uses the 6log rule, Q=10^3 ([folded]/[unfolded])
How can native protein structure be denatured?
-Heat
-pH
-detergents (SDS/chemicals like Urea weaken the hydrophobic effect)
-reducing disulphide bonds
Explain the experiment proving that sequence is enough to guide folding.
Bovine Ribonuclease:
1) disulphide bonds reduced using BME, protein denatured using urea.
2)oxidized (disulphide bonds reform)
3) removed urea, molecule renatured
4) renatured molecule 100% perfect as it was!!
BUT if you first remove urea (renaturing molecule), then oxidize (reform disulphide bonds), less than 1% molecules perfect :(
All-or-none folding
There is a very narrow temperature range for proteins to go from folded to unfolded.
The protein folding problem
How do we determine the folded structure of the protein based on just the sequence? (de novo prediction)
-Rosetta program can predict the domain within 0.2 nm, but that is still not close enough.
Protein aggregation
-promotes misfolding
-A protein in clear solution can fold up correctly
-in cells, there are other proteins in solution which can affect the ability of a protein to fold correctly
Amyloid Fibril
a beta sheet plaque
an amorphous aggregate
can occur in cells
aggregation is in competition with proper folding
Inclusion Body
insoluble aggregates of a protein, usually consists of viral capsid proteins
solution: fewer copies of the gene, lower temperatures, take misfolded protein, unfold it, put it in a clean solution to refold
Chaperone
Helps proteins fold properly by keeping them from getting too close to other proteins in the cell
-shields nonpolar regions of folding proteins to prevent aggregation
-HSP, Heat Shock Proteins, are expressed in response to high temps (like a fever), and as proteins become unstable and start to unfold, HSP's are chaperones that provide a more stable environment
-GroEL-GroES: chaperone of E. coli, physically fits folding protein inside it
Prion
An infectious, misfolded protein which promotes the misfolding of other proteins as well.
Seven principles of protein structure-function relations
1. All functions flow from structure.
2. For ordered proteins, proper folding is their first function.
3. Large size provides stable framework placing key residues in precise places for function (pe active sites, binding sites).
4. Capable of highly specific molecular recognition.
5. Details matter-- even small movements can be important.
6. Proteins may have multiple functions.
7. Protein sequences have been selected over evolutionary timescales for effective functioning.
8. Single mutations can have no impact or cause major problems or bring advantages.
Lungs oxygen partial pressure, Relative CO2 content, pH
100 torr O2, low CO2, pH = 7.6
Blood oxygen partial pressure, Relative CO2 content, pH
30 torr, lots of CO2, pH = 7.2
Myoglobin & Hemoglobin similarities
Both bind a heme prosthetic group
First two protein structures ever solved
Mb
Composed of 8 alpha-helices
Binds a heme prosthetic group between F8 (binds iron) and E7 (H-bonds to O2 on heme)
Hb
Composed of 2 alpha and 2 beta chains (tetramer), each monomer looks like Mb
Prosthetic group
a group tightly bound to a protein which is generally a part of it (a ligand is only sometimes tightly bound)
Holoprotein
Protein with its prosthetic group
Apoprotein
Protein without its prosthetic group
Heme
Fe(II) group atom with a porphyrin group which is roughly planar. Has 6 coordination sites, 4 of which are taken up by nitrogen on the porophyrin. The remaining two coordination sites are open (above and below)
-one binds to a histidine residue
-one binds to O2 or H2O
Why aren't we dying of CO poisoning at atmospheric levels?
In free heme, CO binding is favored 6000:1 over O2 binding, however, prosthetic heme reduced this ratio to 200:1 due to sterics and hydrogen bonding
Why do sterics interfere with CO binding to heme?
CO (sp hybridized) wants to bind linearly, but E7 histidine prevents this from happening, so CO must bond at an angle, which is less favorable. O2 is sp2 hybridized, and is not affected by this.
-A distal histidine can also make a hydrogen bond with O2, increasing O2 favorability over CO
Mb Oxygen binding curve (Kd equation, dissociation equation, equation for Y)
MbO2 ⇌ Mb + O2 (disassociation of oxygen to myoglobin)
Kd = [Mb][O2]/[MbO2]
Y-axis is the fraction of bound myoglobin [MbO2] / ([Mb] + [MbO2])
Universal hyperbolic binding curve
Y = [L] / (Kd + [L]), where [L] is the concentration of ligand, and Kd is the dissociation constant outlined above. When Kd = [L], Y will be 0.5, meaning half of the protein is bound.
What is the effect of a higher Kd value on the universal hyperbolic binding curve? (Mb)
The midpoint of the curve will shift further to the right. A smaller Kd value will shift the midpoint to the left.
Asymptote of hyperbolic Mb oxygen binding curve
Asymptote is at 1 (100% of protein bound) - at 30 torr (10x the value of Kd), myoglobin is 90% saturated
Hb Oxygen binding curve
(sigmoidal because has multiple binding sites)
Hb(O2)4 ⇌ Hb + 4O2
Positive cooperativity
When starting, things don't bind very well, but the binding of one thing makes the binding of something else easier. Allosteric effect- binding one place leads to changes at another place.
Hill coefficient
Describes how cooperative a protein is, how many ligands are effectively binding at once. This ranges from 1 (none) to n (# of sites). For hemoglobin, this is between 2.5 and 3.
MWC model for cooperativity (Monod-Wyman-Changeux model)
all or nothing
All allosteric proteins can be thought of using this model.
MWC model T-State
Tense conformation, weak binding
More energetically stable without ligand
MWC model R-State
Relaxed conformation, strong binding
More energetically stable with ligand
As you add more ligand, you drag the equillibrium toward the R-state; binding improves
Allosteric effector
molecules that will bind to either T or R state, stabilizing it
Allosteric activator
Molecules that preferentially bind to the R-state, activating a protein
Allosteric inhibitor
Molecules that preferentially bind to a T-state, inhibiting the protein
What does the sigmoidal curve look like when the allosteric activator is present?
Shift to the left- more time in high affinity (R) state
What does the sigmoidal curve look like when the allosteric inhibitor is present?
Shift to the right- more time in the low affinity (T) state
What is the physical mechanism for oxygen cooperativity in hemoglobin?
T to R transition for every protein has 3 steps:
1. Local changes in whatever tertiary subunit is binding
2. Those local tertiary changes impact interactions of subunits, causing quaternary changes
3. Quaternary change causes other subunits to have a local tertiary structure change- distant tertiary change
Allosteric inhibitors of Hb
Preferentially bind to the T-state
BPG (2,3 biphosphoglycerate)
H+
CO2
BPG
2,3 biphosphoglycerate
a fundamental setpoint maker
Adding it makes more T-state for longer
Has 5 negative charges
-Sits in gap between β subunits while Hb is in T state. --Will not fit in the gap if Hb is in R state, so preferentially binds to T state.
Increasing ionic strength will weaken this interaction - sigmoidal curve will shift back toward left.
H+
Allostatic inhibitor- the Bohr effect
As you increase the concentration of H+, the binding curve will shift further to the right (as it becomes harder to leave T state).
-Proton binds to histidine
CO2
covalently binds to the alpha amino group of the chain, stabilizing the T-state
Are the conditions of the lungs and tissues (PO2 / pH) steady state homeostasis, or equilibrium?
-Always new O2 coming in
-New CO2 is always flowing out
-Breathing requires energy (lungs, heart)
Most important evolutionary changes in DNA
Missense-change in an amino acid residue
Insertion-add an amino acid
Deletion-delete an amino acid
Gene duplication-2 copies of a gene
Homolog
has a common ancestor
Ortholog
derived from the same gene in different organisms (pe myoglobin in horses vs. humans vs. chimpanzees) -subset of homolog
Paralog
derived via gene duplication (hemoglobin vs. myoglobin)
-subset of homolog
What causes branching in the evolutionary tree?
gene duplication (a common ancestor)
What causes phenotypic variation populations?
proteins
What causes sickle cell anemia?
Caused from a glutamate switching to a valine on beta chain residue 6 of hemoglobin ("Hemoglobin S")
Why might a Glu to Val change lead to protein aggregation?
Val is hydrophobic, so will lead to more hydrophobic interactions between proteins, causing aggregation
Anomers
Epimers that differ at the anomeric carbon (alpha and beta forms of ring form sugars)
Other sets by this creator