Lectures 7 & 8: Amino Acids, Peptides, Proteins, and PTMs Flashcards
What does aliphatic mean?
Organic compounds in which carbon atoms form open chains, not aromatic rings.
What is the absolute configuration of naturally occuring AAs?
L
What does it mean for AAs to be zwitterionic at neutral pH?
They have both + and - charged groups
What is methionine’s special role?
First AA incorporated into a peptide chain during translation, but usually gets clipped off at the end
What are the 5 charged AAs?
Histidine Arginine Lysine Aspartic Acid Glutamic Acid
What is the direction of polypeptide synthesis?
N to C termini
Through what reaction do disulfide bonds form?
Oxidation
What happens when you add a reducing agent to a protein solution?
It will break the disulfide links
Is methionine polar?
No!
How are peptide bonds formed?
Via a condensation reaction between the amino and carboxyl groups of 2 AAs
What is the tertiary structure of proteins?
The combination of secondary structures that shield a hydrophobic core
Where can rare D isomers of proteins be found?
Bacteria cell walls so that they can escape our host defense mechanisms
What is the side chain pKa of tyrosine?
10.07
What is the side chain pKa of cysteine?
8.18
What is the side chain pKa of lysine?
10.53
What is the side chain pKa of histidine?
6.00
What is the side chain pKa of arginine?
12.48
What is the side chain pKa of aspartate?
3.65
What is the side chain pKa of glutamate?
4.25
What does the pK1 of AAs represent?
pK of carboxyl group
What does the pK2 of AAs represent?
pK of amino group
What does the pI of AAs represent?
The pH at which the AA is neutral: zwitterion
Is the basic side chain protonated if the pH is below pK2
Yes!
What AA plays an important role for buffering? Why?
His because it has a pKa near physio pH and is often found in its ionized form
In which proteins do we often find disulfide bonds? Why?
Those that are excreted in the ECM b/c the inside of the cell is a reducing environment
When do we refer to peptides as polypeptides?
When they are greater than 10 residues long
When do we refer to peptides as proteins?
When they are 50 to 100 residues long
Why are alpha helices right handed?
Because they are L
When the pH is below the pKa of an amino acid, is it deprotonated or protonated?
Protonated
What does the double bond nature of the peptide bond mean for the geometry of the bond? How many atoms does this involve? Which atoms does this involve?
Planar orientation for 6 atoms: C alpha 1, C=O, N-H, and C alpha 2
Are most peptide bonds cis or trans? What is the exception
Trans
Proline is the exception because neither configuration is more favorable because of the bulky R group
What is the phi bond (crossed through O)?
Alpha C - N
What is the psi bond (weird W)?
Alpha C - C=O
Between which 2 amino acids are H-bonds formed in an alpha helix?
N and N+4
What 2 AAs tend to destabilize alpha helices?
Proline (because its imino N cannot H bond) and glycine (because high degree of conformational entropy)
What H-bonds happens in the loops?
The i C=O group binds to the i+3 N-H group
What AAs likes to be in the loops? Why?
Glycine because it’s flexible and proline because it creates turns
How many residues in one turn of an alpha helix? How long is that?
- 6
5. 4Å
Where do the R groups face in an alpha helix?
Backward and outward (toward the amino end)
Do all residues H bond in an alpha helix?
No.
The 1st 4 NH and last 4 C=O have no H bonding partner. They may form H bonds with polar side groups of “helix capping” residues in turns preceding or
following the helix.
What is the core of an alpha helix like?
Tightly packed to optimize van der Waals interactions
Why do alpha helices have a strong additive dipole?
Because all of the carbonyls point down and all the aminos point up
What is the difference between H-bonds between parallel and anti-parallel beta sheets? Which ones are stronger?
Parallel: diagonal H-bonds
Anti-parallel: linear H-bonds (stronger)
Why is it common to see beta sheets have stretches of alternating polar and non-polar AAs?
Because the R groups extend out from the sheet alternating below and above the plane so this would allow them to have all of the polar AAs face the exterior and all the hydrophobic ones face the interior
What is the min number of AAs in a beta bend (180 turn)?
4
What is the driving force of the tertiary stucture?
The hydrophobic effect
How do we describe protein folding if neither an alpha helix nor a beta sheet?
Random coil (not actually random, just not as regular/organized)
How do large proteins tend to fold? What are 2 classes of large proteins?
Into multiple semi-independent domains of about 100-200 AAs each
IgG (immunoglobulin) and MHC (major histocompatibility complex)
How are most quarternary interactions between subunits?
Mainly occur on the surface of the subunits
What does SDS-PAGE separate proteins by?
Their linear size
What are Western blots used for?
They use specific antibodies to detect specific proteins on an SDS-PAGE and can visualize their size
What is ELISA used for and what does it stand for?
It is a rapid, specific, and quantitative method to detect and measure the presence of a specific protein in a complex sample
ELISA = enzyme-linked immunosorbent assay
What does gel filtration chromatography separate proteins by?
Globular size
What does ion exchange chromatography separate proteins by?
Charges
What does affinity chromatography separate proteins by?
By their binding affinities
What is the purpose of X-ray crystallography and NMR? What do they both require?
To gain structural information about a protein
Both require a large amount of protein
What is the purpose of mass spectrometry?
To identify and quantify proteins from a complex mixture based on their mass and the mass of their component peptides
What is the main secondary structure of myoglobin?
Alpha helices (70%)
What is myoglobin’s structure mainly stabilized by?
Hydrophobic interactions
What is the interior of myoglobin like?
Very compact, only allows for 4 molecules of water and contains the heme group
How does O2 enter myoglobin since it is so tight?
Myoglobin breathes!
What is the most abundant protein in mammals?
Collagen
Describe collagen’s quarternary structure
Right handed triple-helix composed of 3 alpha chains: coiled coil
Describe collagen’s primary structure
Repeating triplet sequence of Gly-x-y where x is often Pro and y is often 4-hydroxyproline
Describe collagen’s secondary structure
Left handed helix with 3 AAs per turn
What is another name for collagen?
Tropocollagen
What can be found in the center of collagen’s coiled coil?
Glycine residues
What are collagen fibrils?
Supramolecular assembly of individual tropocollagen molecules in which there are cross-linking covalent bonding between alpha chains and collagen molecules within the fibril
What is the role of the enzyme lysil oxidase?
It allows cross-linking of tropocollagen molecules in a fibril by modifying lysines to 5-hydroxylysines = allylysines (addition of OH)
What 3 AAs do the cross-linking between tropocollagen molecules in a collagen fibril depend on?
5-hydroxylysine = allylysine covalently binds to to:
- Other allylysines
- Lys
- His
What is the effect of aging on the cross-linking within a collagen fibril?
These increase, which causes tissues to become more rigid and have less elasticity: wrinkles and sagging
Describe collagen fibril arrangements in tendons
Parallel bundles providing strength on a 1D axis
Describe collagen fibril arrangements in skin
Layered sheets: providing 2D
strength
Describe collagen fibril arrangements in cartilage/bone
The hydroxyapatite crystals of bone nucleate at
intervals of 680Å, the periodicity of the
collagen fibril: 3D strength
Describe collagen fibril arrangements in the cornea
Planar sheets stacked crossways so as to
minimize light scatter
Describe the disease osteogenesis imperfecta
Autosomal dominant disease caused by a single AA substitution (Ala instead of Gly) that reduces the melting point of collagen to room temperature: child can experience broken bones during birth. This is often confused with child abuse.
What is another name for osteogenesis imperfecta?
Brittle bone disease
Describe Ehlers-Danlos syndrome
Group of 10 different diseases characterized w/ hyperextendability of the joints and skin (some have a lysil oxidase deficiency)
Describe (osteo)lathyrism
Disease resulting from ingestion of poisonous sweet pea seeds that inactivate lysil oxidase, which is responsible for allowing cross-linking of collagen
Describe scurvy
Deficiency is ascorbic acid (vitamin C) which is a co-factor for prolyl and lysyl hydroxylase (needed for collagen to have tensile strength)
Mild cases: fatigue, irritability, and increased risk of respiratory infections
Severe cases: blood vessel hemorrhage, tooth loss, poor wound healing, and eventually heart failure and death
What are TSEs? What are some examples? What are they caused by?
Transmissible spongiform encephalopathies: mad cow disease, Creutzfeldt-Jacob, Gerstmann-Straussler-Schenker (in humans)
Caused by prions
What are TSE characterized by? What do they lead to?
By amyloid deposition in the brain which leads to ataxia, dementia, paralysis, and death
What is ataxia?
the loss of full control of bodily movements
What is the properly folded version of the prion called? What is it characterized by?
PrPc
Alpha helices and found on surface of cells
What is the misfolded version of the prion called? What is the misfolding characterized by?
PrPsc
Switch to primarily beta-sheet structures which aggregate into amyloid plaques
What is special about the amyloid plaques and the PrPsc formed because of prions?
They are resistant to proteases
Are there any treatments for prion diseases?
None!
What are chaperones?
Cellular folding accessory proteins that use energy from ATP to decrease the energy barrier associated with protein folding
How do chaperones aid prion diseases?
They help PrPsc to accelerate the change in conformation of PrPc in a propagative manner
Prion diseases are not the only ones that result in amyloid plaques (e.g. Alzheimer’s), but what is special about them?
They are transmissible!
What are the 6 types of PTMs covered by this course?
- Proteolytic processing
- Glycosylation
- Prenylation and addition of other lipids
- Ubiquitylation and addition of other proteins
- Addition of small groups like phosphorylation and methylation
- Other unique AA modifications
Can the sequence of the gene coding for a protein describe the final active form of the protein?
Not always
What 2 types of enzymes cleave proteins?
Proteases and peptidases
What are pre-peptides?
Proteins sent to the ER have a pre-peptide at the N-terminal that is cleaved co-translationally by membrane-bound signal-peptidases
What is another name for pre-peptides?
Signal-peptides
What are pro-peptides?
All other peptides that must be cleaved for the protein to be mature
What are 2 possible roles of pro-peptides?
- Inhibits the protein
2. Was necessary for appropriate folding
How do you call a protein who has a pre- and a pro-peptide?
A pre-pro-protein
What is an example of a pre-pro-protein? Explain its synthesis
Insulin
Synthesized in pancreas and stored in secretory vesicles until the blood glucose increases
What is the role of the pre-peptide on insulin?
Dictates that it will be trafficked into secretory vesicles upon synthesis
What is the pro-peptide on insulin? What is its role?
The C-peptide: it ensures that insulin forms the correct 2 disulfide bonds
What is the role of the C-peptide once removed?
Augments blood flow in skeletal muscle and skin, improved kidney and nerve function, and reduced urinary albumin excretion
Does the insulin injected in patients with Type 1 diabetes contain the C-peptide?
Nope…
How is the pre-peptide recognized for cleavage?
By the characteristics of the AAs, not their sequence
What are the roles of pro-peptides with regards to collagen?
Collagen alpha chains are synthesized with both N-terminal and C-terminal pro-peptides which form disulfide bonds that allow for rapid assemble of the quarternary coiled coil (would take several days without them)
What are dermatopraxis (cattle and sheet) and Ehler-Danlos syndrome type VII (humans) caused by? What is the result? Why has this allele not been removed from the gene pool?
Mutations in pro-collagen that inhibits removal of the N-terminal pro-peptide
Result: very fragile skin
Kept in gene pool because heterozygotes makes for tender steaks!
What are examples of zymogens that need their pro-peptide(s) to be cleaved?
Trypsinogen
Blood clotting cascade enzymes leading to the activation of thrombin which cleaves fibrinogen to fibrin which helps build a clot
What are lipid anchors?
Membrane-bound lipids that bind proteins to tie them to their site of action
What are the 2 categories of groups of lipid anchors? What are their differences?
- Fatty acyl and isoprenoid groups: anchor proteins to inner leaflet of membrane and have 1 lipid anchor
- GPI anchor proteins to outer leaflet of membrane and have 2 lipid anchors
What is an example of a permanent addition of a small chemical group to proteins?
Carboxymethylation
On what AAs does phosphorylation happen?
Ser, Thr, and Tyr
What is an example of a phosphorylation cascade?
Progression through the cell cycle is driven by a family of cyclin-dependent kinases:
- Receptor tyrosine kinases (RTKs) activate growth promoting Ras protein
- Ras protein activates mitogen activated protein kinase (MAPK) cascade
Can a protein be phosphorylated multiple times?
YES! To fine tune its activity: dimer switch
What is an example of a disease caused by the overexpression of kinases?
Overexpression of HER2 (human epidermal growth factor receptor ErbB2) can cause aggressive breast cancers
On what AAs does methylation happen? How many times can it happen on each?
Arg (up to 2) or Lys (up to 3)
Where is methylation particularly important?
On histones: histone code dictates the repression or activation of gene expression
What other PTMs does the histone code include? 4 types
- Ser phosphorylation
- Lys acetylation
- ADP-ribosylation
- Ubiquitylation
What happens to proteins that are poly-ubiquititylated?
Targeted for degradation in the 26S proteasome
On what AA does ubiquitylation happen?
Lys
How does ubiquitylation happen?
3-step cascade
How can ubiquityl moieties be removed?
Deubiquitylating enzymes (DUBS)
What role does ubiquitylation play in the histone code?
Mono-ubiquitylation It acts to trigger further histone modifications
In what organisms can ubiquitylation be found?
All eukaryotes
Describe the composition of ubiquitin
76 AA protein
What are other ubiquitin-like modifiers (UBLs)?
SUMO and NEDD8
What do you call a protein that was glycosylated?
Glycoprotein
What are the 5 roles of glycoproteins?
- Aid protein folding
- Increase protein solubility
- Increase or decrease protein stability by protecting from proteases or marking for degradation
- Signal to locate proteins/organelles in the cell
- Lubricants/shock absorbers
What are glycoforms?
Diverse forms of a protein that has been glycosylated in different ways
On what AA does N-glycosylation happen?
Asn
What type of glycosylation does collagen undergo?
O-linked on hydroxy-lysine
Where does O-linked protein glycolysation occur?
Only in Golgi
What needs to happen to the sugars before glycosylation of proteins? What is the purpose of this?
They must be charged by the addition to a nucleotide di- or mono-phosphate.
This allows the addition of the sugar to be exergonic
What does the inherited disorder Carbohydrate Deficient Glycoprotein Syndrome (GDGS) result from? What are some symptoms?
The inability to charge mannose to prepare it for glycosylation
Symptoms: cerebellar and cerebral atrophy and psychomotor retardation
Where in space are oligosaccharide constituents of glycoproteins?
They extend from the surface of the folded protein and are highly mobile
How are N-linked proteins recognized by glucosyl transferases?
Asn-X-Ser or Asn-X-Thr sequence and the carbohydrate attaches to the N of Asn (X cannot be Pro)
What is the core of N-linked glycosylation?
3 glucose, 9 mannose, and 2 N-acetylglucosamine
How does N-glycosylation occur?
- The core is first attached to dolichol phosphate one sugar at a time through a pyrophosphate linkage (1 phosphate linked to dolichol and 1 to the sugar)
- The sugar is then transferred to the protein in the ER lumen (co-translational) by binding a Asn on the peptide
- The calnexin/calreticulin chaperone system helps fold the protein
- The 3 glucoses are cleaved which signals the protein to go to the Golgi
- Glycosidases/glycosyltransferases in Golgi continue to modify the molecule
- Last modification: addition of salic acid
What are 2 PTMs that happen co-translationally?
N-glycosylation and cleavage of pre-peptide
Which Ser/Thr on the peptide are most likely to be O-linked glycosylated?
Those that are part of loops and turns and are exposed to solvent
How does O-linked glycosylation occur?
1 sugar at a time, but no core
What is the most common O-linked glycosylation?
Disaccharide core beta-Gal-alpha-NAc
What type of glycosylation does glycogenin undergo? What is its role?
O-linked on Tyr
Converts glucose to glycogen
What are proteoglycans composed of? Where do you find them?
Protein + glycosaminoglycan (usually keratan sulfate or chondroiten sulfate) + O and N linked carbs
Constitutes much of the ECM
What do proteoglycans form?
The basement membrane or ECM
What is aggrecan?
The main proteoglycan of cartilage
Describe the structure of aggrecan
- Hyaluronic acid backbone
- Link proteins attached to backbone with non-covalent bonds
- Link proteins attach aggrecan to backbone
- N-linked carbs on aggrecan (N-terminal region)
- Keratan sulfate attached to O-linked carbs (central region)
- C-terminal region rich in chondroitin sulfate linked to Serines connected to Glycines
How does aggrecan provide resiliency to cartilage?
(-) charged glycosaminoglycans cause the molecule to be heavily hydrated: when the aggrecan is compressed the water is squeezed out, the charges then repel each other, which springs back the molecule to its original shape
What happens to proteoglycans with age? What is a consequence of this?
They shrink: joints don’t absorb shock as well
What is the difference between ELISA and mass spectrometry?
ELISA uses antibodies to detect the presence of a specific protein vs mass spectrometry identifies proteins based on their mass
Difference between α helix and ß sheet?
Unlike the α helix, the ß sheet is formed by hydrogen bonds between protein strands, rather than within a strand.
What is a perturbed pKa?
The pKa of AAs when they are closely packed in proteins
Are N-linked sugars branched? O-linked?
- N-linked: branched
- O-linked: linear or branched
Is protein folding exer or endergonic?
Exergonic
On what AAs can ADP-ribosylation happen?
Arg, Glu, Asp, or modified His (dipthamide)
Is ADP-ribosylation reversible?
Yes
What are 3 examples of ADP-ribosylation?
- On histones in response to DNA damage
- Cholera: on G proteins to cause life threatening diarrhea
- Diphteria: on an eukaryotic elongation factor essential for protein translation, shutting down protein synthesis
On what AAs does iodination happen?
Tyr (-OH)
What is the main example of iodination?
To produce thyroid hormones T3 and T4
What type of PTM is iodination?
Halogenation (most common type)
What PTMs happen during synthesis of thyroid hormones?
- Iodination
- Proteolysis
- Covalent modifications
On what AA does gamma-carboxyylation happen?
Glu near N-terminus
What does gamma-carboxylation form?
gamma-carboxy-glutamate (Gla)
What does gamma-carboxylation require?
Vitamin K
What is gamma-carboxylation required for?
The blood clotting cascade
Is W found on the surface or interior of proteins?
Both!
How to determine # of peptide bonds in a peptide?
of peptide bonds = # of AAs -1
Can the alpha helix shield R chains from the solvent?
NOPE
Can the beta sheet shield R chains from the solvent?
NOPE
What is a ribbon diagram good for depicting?
Polypeptide backbone
What are mesh diagrams and surface contour maps good for depicting?
Protein surface
What is a ribbon with ball and stick diagram good for depicting?
Polypeptide backbone + hydrophobic/hydrophilic residues
What is a space filling diagram good for depicting?
Hydrophobic/hydrophilic residues
What is the motif of the pre-peptide, which allows for recognition?
Lys/Arg/His-Stretch of hydrophobic AAs-N-terminus
When does the cleavage of the pre-peptide occur?
While translation is still happening
When are the pro-peptides of collagen removed? By what? WHY??
After it has been secreted by extracellular peptidases to prevent the formation of collagen fibrils inside the cell
When is the pro-peptide of insulin removed?
Before secretion
Which PTM is the most common?
Glycosylation!
On what AA does O-linked glycosylation happen?
Ser/Thr exposed on the FINAL CONFORMATION or any AA that has -OH (tyr)
What is the last sugar to be added in N-linked glycosylation?
Sialic acid
What is the difference between glycoprotein and proteoglycan?
Glycoprotein: more protein than sugar by weight
Proteoglycan: more sugar than protein by weight
Why are keratin sulfates and chondroitin sulfates sticking out horizontally on the aggrecans?
Because they are both - charged and repel each other
Where are prions found attached to? By kind of attachement?
Neural cells by GPI anchors
What is the disease kuru?
A TSE where amyloid plaques form on the cerebellum so pts have difficulty walking
What happens during mad cow disease?
Amyloid plaques in the brain stem where breathing and heart are controlled
What is fatal familial insomnia caused by? Where do the amyloid plaques form?
Rare mutation in prion protein sequence makes spontaneous acquisition of the prion disease more likely
Thalamus
What happens during Creutzfeld-Jacob disease (CJD)?
Mutation in prion protein sequence leading to amyloid plaques in the cortex: dementia (similar to Alzheimer’s), lacunae in brain tissue
