H2001 Midterm 1 Flashcards
Where is all the information required to fold a protein into its tertiary structure contained?
Primary sequence
What do proteins need to include to bind oxygen?
A prosthetic group
What is a crucial role of IDPs (2)
1) binding to multiple partners
2) high-specificity / low affinity interactions
What is important to note about the hydrogen bond that stabilizes a-helices?
It STARTS from a carbonyl oxygen and GOES to the amino NH
What groups are attached to the alpha carbon in an amino acid
alpha-carboxyl and alpha-amino
Buffers
pH doesn’t change much as you add acid or base.
p53
famous tumour suppressor protein with IDP regions
What stabilizes the T state?
greater number of ionic interactions at the interfaces between subunits
What happens if there are two deep wells in the E landscape? One corresponding to the right fold, and the other the wrong fold.
Mad cows disease
What causes the twist in a coiled coil?
The two helices must twist around each other to match up their hydrophobic faces
True or False: glycine does not have to be every third residue.
False
How long are typical domains in terms of residues?
100-200 residues
Polarity
distribution of e- clouds around covalent bond
How are prions formed
PrP converted to an infectious, high B-sheet conformation called PrP^SC (scrapie); acts as a template to refold
What conditions can denature proteins? (5)
1) High temperatures
2) extreme pH
3) Organic solvents
4) chemicals like urea and guanidinium hydrochloride
5) detergents like SDS
Which point mutation listed below is least likely to wreck protein function?
Leu - Tyr
Leu - Ser
Leu - Phe
Leu - Trp
Leu - Phe
List the cellular macromolecules and their building blocks
Proteins - amino acids
Sugars - polysaccharides
Fatty acids - lipids
Nucleic acids - nucleotides
What does NOT stabilize silk fibroins?
Disfulfide bonds
What are the names of the next 6 of the monomer naming convention?
dimer, trimer, tetramer, pentamer, hexamer
Repeating unit of silk fibroin
G-S-G-A-G-A
Cavity where BPG binds is lined with positive or negative amino acids that interact with the negative groups n BPG?
Positive
Is CO2 soluble in aqueous solution?
Not very
What special bonds can cysteine form?
Disulphide bonds
Myoglobin History
binds O2; first atomic resolution protein structure ever solved with X-ray crystallography; earned nobel prize in 1962
What part of globular proteins allow them to carry out a wider range of biological functions than fibrous proteins?
Their tertiary structure
2 traditional methods to determine protein structures
1) X-Ray crystallography
2) Nuclear Magnetic Resonance (NMR)
When would a specific R group be negatively charged (general)?
pH > pKa
What do IDPs do to carry out their functions?
Fold
What side chain is likely to bind H+ in hemoglobin?
Histidine; forms ion pairs to asp that helps stabilize deoxyhemoglobin, which promotes deoxygenation by favouring transition to T state
When does enthalpy favour a process
when dH < 0
Review EDI info
At pH 7, what is the charge on this peptide:
AEGK
0
Dihedral Angles
Rotation can occur around the alpha carbons, only by two angles per residue
At neutral pH, do the charged on the C- and N- terminal groups of hemoglobin matter?
Yes, they help to form ionic interactions that stabilize deoxyhemoglobin
Review iClicker Qs in lecture 11
Apoprotein
protein without its prosthetic group
What stabilizes the structure of fibrous proteins? silk fibroin
Secondary: H bonds
Quaternary: van de waals
*Review how to explain the hydrophobic effect and hydrophobic interactions
Ionic interaction
attraction (or repulsion) of charged species (ions, dipoles, charged groups)
Allosteric activation
promotes O2 binding (CO)
Sickle-Cell Anemia is caused by mutation in B subunit of hemoglobin; glu6-val6.
a) hydrophobic residue - hydrophobic residue
b) charged residue - hydrophobic residue
c) hydrophobic - polar
B
2 major types of secondary structure
1) alpha-helices
2) beta-sheets
What are important buffer systems in biochem?
Phosphate (cytoplasm) and bicarbonate (blood plasma)
Which of the following is not a characteristic of peptide bonds?
a) Polar
b) planar
c) cis
d) formed by condensation of L amino acids
C
What is another type of secondary structure?
Beta Turns
Phi Dihedral Angle
toward N-terminus
Gibbs Free Energy Formula
dG = dH - TdS
Is myoglobin a tetramer like hemoglobin?
No, monomer
Why is the oxygen binding site buried deep in the protein?
When one O2 molecule reacts with 2 heme molecules, the result can be conversion of Fe2+ to Fe3+; burying the heme prevents this.
Carbon Monoxide poisoning
CO coordinates to heme
CO is colorless odorless, can build up in enclosed spaces, responsible for more than half of poisonings yearly.
250 fold greater affinity for hemoglobin than O2.
Bronsted Acid / Base Def
Acid: lose a proton
Base: gain a proton
What is another helix breaker and why?
Glycine; it has high conformational flexibility, making it entropically expensive to adopt the constrained a-helical structure
Intrinsically Disordered Proteins (IDPs)
lack stable tertiary and/or secondary structures under physiological conditions; exist as dynamic ensembles of interconverting structures
Endergonic
dG > 0
Will not occur spontaneously
Why do we need proteins for oxygen storage / transport?
O2 is poorly soluble in H2O; can’t be carried in tissues. Also doesn’t diffuse effectively
Hydrogen Bonding
occurs btwn an electronegative atom (O, N, F) and a H atom bonded to another electronegative atom
Are most a-helices right or left handed?
Right-handed
What stabilizes the structure of fibrous proteins? a-keratin
Secondary: H bonds
Quaternary: disulphide bonds
Enthalpy
changes are related to formation, breaking, or distortion of bonds (internal energy)
Where might proline fit well in a peptide?
In the first turn of an a-helix
Why do we use heme as opposed to free Fe as our binding group?
Free Fe is dangerous; promotes formation of highly reactive oxygen species that damage DNA (one of most common causes of death in children)
Why do cats spit up fur-balls?
a-keratin in fur is indigestible, insoluble due to S-S bonds
What range does a buffer work best for?
within +- 1 pH unit around the pKa value
Amyloids
misfolded proteins form insoluble fibrous protein aggregations formed largely of B-sheet structures
Amyloid plaques destroy nerve cells and lead to loss of thought and memory
Summary of collagen structure levels
Primary: Gly-Pro-Hyp-Gly-X-Y
Secondary: left-handed polypro helix
Tertiary: none
quaternary: right-handed triple helix, heterotrimer
Direction of collagen helix
left-handed
Summary of a-keratin structure levels
Secondary: a-helix
Tertiary: none
Quaternary: coiled coil
BPG
interacts with hemoglobin and modulates its O2 affinity
BPG binds at a site distant from O2 binding site, decreases the affinity of hemoglobin for O2
Allosteric inhibitor
Alpha-helix
secondary structure where the polypeptide chain winds tightly around; side chains stick out from the helical axis like branches
Carboxyl terminal residue
amino acid at the end with a free carboxyl group
Do we expect chunky sidechains to fit better with a-helices or b-sheets?
B-sheets
Fibrous proteins all possess structural features that give them:
a) frailty
b) delicacy
c) flimsiness
d) strength
d
What stereoisomer label is used for the only amino acids that occur in proteins?
L-amino acids (not D)
True or false: myoglobin and hemoglobin are conjugated proteins, but only myoglobin is a hemoprotein.
False; both are hemoproteins
Which amino acid sidechain is capable of participating in Hydrogen bonds?
Leucine
Tyrosine
Phenylalanine
Tyrosine
Phi values around -60 degrees and psi values around -50 degrees are in what handed helices?
Right-handed
dG vs. Keq formula
dG = - RT ln Keq
How does having small sidechains make silk fibroin strong?
close packing of B-sheets and an interlocking arrangement of R groups
Which of these point mutants (all n-p) is least likely to wreck a protein?
L - I
L - A
L - G
L - F
L - I
Tm - midpoint / inflection point
50% of protein is denatured
holoprotein
protein with its prosthetic group
True or False: H bonds are formed between two B-strands to make a B-sheet
True
Tertiary Structure
overall 3D arrangement of the atoms in a globular protein; how secondary structure pack together
Van der Waals
occur between transient partial charges / dipoles formed in e- clouds; weak
What holds helices together in coiled coils?
Hydrophobic interactions between hydrophobic residues
What orientation makes H bonding the strongest?
Linear
Thermodynamics
Tells you if a process is spontaneous or not
Tripeptide
3 amino acids, 2 peptide bonds
Review and draw / sketch a Ramachandram plot and indicate the regions for beta-sheets and right handed alpha helices
General: B-sheets above right-handed alpha-helices
What structural mechanisms are behind hemoglobin’s sensitive response to O2?
Hemoglobin has 4 myoglobin-like chains; fewer than half amino acid residues are identical, although they fold similar to myoglobin
What direction is the helical path of the supertwists
Left-handed
Separation of Oil and Water is caused by changes in what?
Entropy
Quaternary structure
spacial arrangement of a protein’s individual polypeptide chains; exhibited only by proteins which contain two or more polypeptide chains
What terminal end defines where peptides start being named?
The amino terminal, always placed at the left
Considering 3.6 residues per turn in an a-helix, which two residues in MEQALKRN would wind up on the same face of the helix?
M and A
What does the binding of O2 to one hemoglobin subunit in the T state trigger?
A change in conformation to the R state (high O2 affinity)
Chaperones
proteins present in cells that help other proteins fold
Would the presence of two Lys residues near the amino terminus stabilize or destabilize the a-helix?
Destabilize
A better view of protein folding
E landscape is funnel-shaped, so the protein is biased to fold towards the native state, with many different intermediate conformations leading to the same native state
In active tissues, there are more protons around, so the pH is _____ and hemoglobin has ____ affinity for O2 compared to in the lungs.
Lower, lower
What insect can eat wool and how?
Moths; they have high conc of mercaptans so they can reduce S-S bonds to eat wool from clothing
Entropy
Changes related to change in order or randomness of a system
At pH 1, what is the charge on this peptide:
AEGK
+2
2 major conformations of hemoglobin
“R State”: relaxed; stabilized by O2 binding (oxyhemoglobin)
“T State”: tense; more stable and dominant conformation if O2 isn’t bound (deoxyhemoglobin)
Conjugated proteins
contain permanently associated chemical components (known as the prosthetic group) in addition to amino acids
What COHb levels does a healthy person have? What about a smoker / chain smoker?
1% or less
3-8% for smokers
15% chain smokers
How is the a-helix structure stabilized?
By H bonds forming between one alpha-carbonyl and the N-H group 4 residues further along the chain
What is the structure of alpha-keratin?
Built up from a-helices in a coiled coil; 2 helices wrap around each other to give a “supertwisted” coiled coil. Helices are parallel.
Are free amino and carboxyl groups ionizable?
Yes
Try to identify phi and psi from a drawing
What amino acids can bind oxygen?
None!
Zwitterion
spatially separated positive and negative charges; overall charge is 0.
Protein that prions are made from
PrP (Prion related protein), found in healthy people and animals
Protein Data Bank
contains all experimentally determined structures
Explain how entropy causes the separation of oil and water
lipid molecules become ordered around water; however when there are clusters of molecules, the entropy is increased
True or False? Multi-domain proteins have domains with all the same function.
False
Integrated transport by hemoglobin (Bohr effect)
Lungs carry O2 to tissues, tissues send H+ and CO2 back to lungs to increase affinity for O2 binding (?)
How many amino acids
20
What is tertiary structure stabilized by?
Many noncovalent interactions
What is likely to happen if we switch a polar amino acid for a non-polar one in a protein?
It will wreck the protein
How do proteins know what tertiary structure to fold into, and who discovered this?
Christian Anfinsen: started with ribonuclease, denatured by exposure to concentrated urea – loss of all catalytic activity. He then removed urea, and ribonuclease regained its catalytic activity (refolded into native structure), all by itself (no cell components involved)
What do amino acid groups help us predict?
The consequences of mutations
Which is the strongest “weak” interaction in biomolecules?
Hydrogen bond
Secondary structure of collagen
stabilized by steric repulsion of Pro and hy-Pro rings
Not an a-helix, sometimes called the collagen helix
How many residues / turn in collagen helix
3
What stabilizes protofibril and protofilaments?
Disulfide bonds
In which direction does the dipole moment of an a-helix orient?
Large net dipole moment with - towards C-terminus, + toward N-term
Amino terminal residue
amino acid at the end with a free amino group
Globin fold
Myoglobin’s domain fold
Typically 8 a-helices
stabilized by H bonds and non-covalent interactions btwn sidechains
What catalyzes the acid dissociation of CO2 in tissues?
Carbonic anhydrase
Protein Folding
conversion of an irregular, flexible arrangement of the protein chain to a regular, relatively rigid, well defined 3D structure
What enzyme is required for hydroxylation and what symptoms could arise from a lack of this?
Vit C
Scurvy
B-strands and B-sheets
Secondary structure with a much more extended conformation
Which type of forces are NOT responsible for stabilizing tertiary structure of globular proteins?
Peptide bonds
How many oxygen groups can hemoglobin bind?
4; 1 at each site
How does biochem explain changing hair from curly to straight or straight to curly?
Breaks the strong disulfide bonds with a reducing agent, put hair in the shape, then oxidize to re-form the disulfides
Which amino acid side chains are positively charged at pH 7?
Lys, Arg
Prions
proteins that can misfold and cause infectious disease.
The infectious agent is resistant to denaturation by protease, heat, and radiation.
The prions can refold abnormally into a structure which is able to convert normal molecules of the protein into a form that forms amyloid plaques.
Solution to Levinthal paradox, not supported by experimental evidence
A protein takes on specific intermediate conformations en route to the folded state
Second Law interpretation by VB
Systems tend to proceed from low entropy states to high entropy states
What is the central carbon in an amino acid called
Alpha carbon
As CO binds to one or two subunits of a hemoglobin tetrameter, the affinity for O2 is ____ , i.e. CO is an _____ of hemoglobin.
increased, allosteric activator
Would the interactions btwn neighboring D and R residues stabilize or destabilize an a-helix?
Stablize
What is protein primary structure?
Amino acid residues and peptide bonds
At pH 3, what is the charge on this peptide:
KITTEN
+1
Where does hair get its strength?
alpha-keratin
Would you expect glycines amino and carboxyl groups to be neutral or charged at pH 7?
Charged
Hair
an array of many a-keratin filaments
Protein misfolding diseases examples
Alzheimers, BSE/CJD, mad cows
True or false: subunits and domains are not the same thing.
True
Isoelectric point
pH at which a solute has no net electric charge ; pI
What happens to the pH as CO2 dissolves?
Decreases
Are most proteins globular or fibrous?
Globular
What are the approximate pKa values for the 5 main ionizable groups?
alpha carboxyl = 2
alpha amino = 9.5
asp, glu R groups = 4
lys, arg R groups = 11.5
Hist = 6 - 6.5
Residue
an amino acid unit within a protein / peptide
How to break a disulfide bond?
Use a reducing agent (such as mercaptoethanol)
Denatured state
the partially or completely unfolded form of a biological macromolecule; it is incapable of carrying out its functions
What is the fundamental units of tertiary structure?
Domains
Enzymes
protein catalysts that reduce the activation E and increase the rate of rxn
Collagen primary sequence
GXY repeats, usually with one of X or Y being Proline or hydroxyproline
No Cys, Trp, little Tyr
Post-translational modification
Chemical modification of protein after its translation
What do vdw forces depend on?
Size and shape of molecules interacting
When would a specific R group be positively charged (general)?
pH < pKa
Which of the following is false about IDP sequences?
a) IDPs have more hydrophobic amino acids than globular
b) IDPs have more polar/charged residues
c) IDPs have more glycine and proline residues
A
Protofilaments and protofibrils
Combined two-chain coiled coils in higher order structures
What does lower cysteine percentage correlate with practically?
Soft, stretchable and flexible materials; i.e. used for warmth, waterproofing
When does entropy favour a process
TdS > 0
T or F? At low pH, there is more H3O+ than OH-
T
Where might negatively charged ligands prefer to proteins (think of dipoles)?
The N-terminus
Which amino acids are prevalent in the regions of proteins that contact DNA (negatively charged)?
K, R
Do we expect long skinny sidechains to fit better with a-helices or b-sheets?
A-helices
Collagen
most abundant protein in the body (25%).
Bones, teeth, cartilage, tendons, cornea
GLue, gelatin
Insoluble, strong
30 different types
What does the sickle-cell anemia mutation cause?
Hydrophobic patch on surface of B-subunit, causes hemoglobin tetramers to polymerize long fibrils, distorting the shape of red blood cells. These don’t fit through capillaries, block and interrupt delivery of O2 to tissues
How can you learn about the oligomeric structure of multisubunit proteins?
Treat them with B-mercaptoethanol (breaks disulfides) and/or urea (disrupts non-covalent interactions)
How many hydrogen bonds can water make?
4; donor of H to 2 and acceptor of H from 2
What is the difference between the N-terminus and the N-terminal residue?
The N-terminus is the amino terminal end (just the amino group), whereas the residue is the entire amino acid group at this end of the peptide
Why do hemoglobin and myoglobin differ in structure?
Because they differ in function
What are the dihedral angles expected in B-sheets?
Phi around -135 and psi around 135
True or False: there is no pH at which the alpha-amino and alpha-carboxyl groups of a free amino acid in an aqueous solution are both un-ionized.
True
Protein
Polymer of L-amino acids; capable of completing a variety of biological tasks
Protein Folding Energetics
difference in free E between folded and unfolded states is only about 10kcal/mol; proteins only barely fold
If you have a protein made up of D-amino acids instead of L, what do you think will happen if you treat it with a protease?
Nothing!
This is one strategy for stabilizing small protein drugs
Two types of common structural patterns in proteins (list ex of each)
1) Motifs: small; B-a-B loop
2) Domain folds: bigger; a/B Barrel
First Law Interpretation by VB
Energy can’t be created or destroyed, but it can change form
What is the backbone of a peptide?
N-C-C-N-C-C-N-C-C
New Protein structure identification method
Cryoelectron microscopy and artificial intelligence (AlphaFold)
What is a second determinant to check if a point mutation will wreck a protien?
Size; if the size is very different it’s more likely to wreck the protein
Does a-keratin have tertiary structure?
Not really; secondary structure is helix and quaternary structure is coiled coil
Native conformation (protein)
biologically relevant, folded protein conformation; denoted N
Shape of hemoglobin binding curve vs. myoglobin
Myoglobin: hyperbolic
Hemoglobin: sigmoidal (S shaped) because it permits a more sensitive response to ligand concentration
Energy landscapes
visual representations of E of protein conformations; the folded conformation is the minimum of E, the deep well
What happens to CO2?
some is carried away by hemoglobin, but most is hydrated to form bicarbonate
Which force is responsible for the slight spontaneity of protein folding, considering ionic, vdw, and hbond have dG values around 0?
Hydrophobic
Why is wool stretchier than silk?
Silk is stabilized by weak and numerous non-covalent interactions, whereas a-keratin is stabilized by strong but few covalent interactions (disulfide bonds), meaning silk cannot stretch, although it is flexible
Three major types of proteins
1) Globular
2) Fibrous
3) Integral membrane
What amino acid is the only case where the alpha carbon is not a chiral centre?
Glycine
Heme binds to Fe in what state? How many coordination bonds are possible?
Fe2+
6 coord bonds; 4 to N atoms in porphyrin ring and 2 perpendicular to porphyrin ring (one to N atom of the protein, other to O molecule)
What is the only interactions that favours folding
Hydrophobic
The overall 3D arrangement of secondary structure elements that characterizes a single domain is called a what?
Fold
True or False? there is a specific 3-base genetic code for the amino acid hydroxyproline so that it is incorporated into the protein during translation of mRNA
False
Peptide prefixes above tri
Tetra, penta, hexa, hepta, octa, nona, deca, oligo, poly
What prosthetic groups are good at binding oxygen?
Transition metals, including Fe and Cu
Why does binding of O2 make the affinity for O2 greater?
Causes the heme group to become planar, leading to a change in conformation of the whole protein
What type of reaction forms a protein?
Condensation reaction; endergonic
This means water is eliminated in formation
Allosteric protein
Conformation is changed when it binds a ligand; the new conformation changes the protein’s ability to react to a second molecule
Where do peptide bonds form?
Between the amino group of one amino acid and the carboxyl group of another (both alpha)
Psi dihedral angle
toward C-terminus
Are van der Waals ever repulsive?
No, they always induce the opposite charge
Where does H bonding happen in quat structure of collagen?
from NH of Gly to carbonyl O of adjacent strand; no H bond for pro
Which of the following is true about protein domains?
a) a protein must have more than one domain to be functional.
b) protein domains lose their 3D structure when separated from the polypeptide chain.
c) protein domains lose their function when separated from the polypeptide chain.
d) protein domains often fold into stable globular units.
d
Henderson-Hasselbalch Equation
pH = pKa + log [conjugate base] / [conjugate acid]
What is protein secondary structure?
The local conformation of some part of the polypeptide
The protein folding problem / Levinthal paradox
many different conformations for proteins with many amino acids. A topic of active research.
List the 4 non-covalent, weak interactions
Ionic
Van der Waals
Hydrogen bonds
Hydrophobic
Dipeptide
2 amino acids, 1 peptide bond
Take some time to review the amino acids
Which amino acid can form disulfide bonds?
Cysteine
What are the 2 possible directions of B-sheets?
1) Antiparallel: N-term of one aligned with C-term of next
2) Parallel: N-terms of adjacent peptides aligned
How many residues are in each turn in an alpha-helix?
3.6
What does higher cysteine percentage correlate with practically?
Harder, rigid, and inflexible materials; i.e. used for protection and defense
What is the primary sequence of a-keratin?
A repeat of 7 residues (abcdefg) with hydrophobic residues at positions a and d, on the same face
Fetal Hemoglobin
a fetus must extract O2 from its mothers blood, so fetal hemoglobin must have higher affinity for O2 than the mother does.
The amino acid composition of spider silk (more flexible) and silk from cocoons (less flexible) is different. Which combo belongs to spiders?
A) 45% G
30% A
12% S
no C
B) 37% G
21% A
4.5% S
no C
B
What amino acid is called a helix-breaker and why?
Proline, because it has no backbone NH to participate in H bonds
Domain Fold
the particular topographical arrangement of secondary structure elements that characterizes a single domain
Allosteric inhibition
inhibits O2 binding (H+ and CO2)
What type of mer is hemoglobin?
Heterotetramer
Standard Conditions in Biochemistry
[H+] = 10^-7M (pH 7)
How strong are disulfide bonds?
About 100 times stronger than H bonds
Unfolded conformation (protein)
denoted U
Polypeptide
2 or more amino acids joined by peptide bonds
Silk fibroin
Protein produced by spiders and insects; very strong and waterproof
What determines a protein’s function?
Its structure!
Hydrophobic Effect
The only of the forces due to entropy.
Cooperative binding
A little bit of binding initially leads to a lot more binding; gives sigmoidal shaped binding curves
Summary of fibroin structure levels
Secondary: antiparallel B-strands
Tertiary: none
Quaternary: stacked B-strands
Do parallel or anti-parallel B-sheets have stronger H bonds?
Antiparallel, because the bonds are linear
At low pH, things will tend to be more or less protonated than at high pH?
More
Metamorphic proteins
2 conformations in equilibrium with different activity for each conformation
What are Beta turns?
found in regions where polypeptide chain reverses direction, within a span of 4 residues, stabilized by H bonds between first and fourth resiudes
General rule for globular protein organization
Most hydrophobic residues are on the inside, most hydrophilic residues are on the outside
What differences in amino acid composition make IDPs less structured than globular proteins?
Less hydrophobic core
Are the CO and NH groups that connect one amino acid to the next ionizable in a peptide?
No
What is fetal hemoglobin composed of?
Gamma subunits (not as many K/R residues) instead of B subunits; this has a lower affinity for BPG = higher affinity for O2
What is dG at eq
0
Exergonic
dG < 0
Occurs Spontaneously
Domain
a compact unit of protein structure that is usually capable of folding stably as an independent entity in solution
How does oxygen get to the buried binding site?
Dynamics; the proteins are always rearranging and are only marginally stable. This opens cavities that momentarily open / close, big enough to hold O2
What holds the quaternary structure of hemoglobin together?
Hydrophobic and ionic interactions
Ramachandran plot
plot of psi vs. phi; blue areas show ‘allowed’ options
What is responsible for biological function of a protein?
Folded structure
What does BPG play an important role in?
Physiological adaptation to high altitude and the reduced O2 available there
BPG conc in blood rises, leading to more O2 being released into tissues
Monomor / subunit
one polypeptide chain in a protein with more than 1 chain
Can hemoglobin bind to H+?
Yes, but at a different site from O2 binding site
What is the function of fibrous proteins?
Structural support
Myoglobin and hemoglobin
related proteins that store and transport oxygen
What is the secondary structure of silk fibroin?
Antiparallel B-pleated sheet, stabilized by H bonding. Sheets stack with glycines facing each other, and ala/ser facing each other, stabilized by noncovalent interactions
3 characteristics of the peptide bond
1) Planar
2) Polar
3) Trans
How do disulfides form properly in tertiary structure?
Non-covalent interactions ensure that cysteines are positioned to form disulfide bonds correctly
Which of the 20 amino acids have ionizable sidechains? (5)
R, K, E, D, H
Collagen quaternary structure
heterotrimer, right-handed triple helix, glycine residues in the centre, R groups face out, sided gelix
Coupled Process
an unfavourable process can be coupled with a highly favourable one to drive the overall process
What is one of the biggest things to remember when finding pH of peptides?
Don’t forget to account for the charge of the terminal groups
