Exam 1 Lectures 4-5 Flashcards
What is the ‘backbone’ structure of an aa?
Always:
Amine (-NH2), a carboxyl (-COOH), and (R) side chain attached to an alpha carbon
What is the pKa for carboxyl to loose H+?
Around 2
What is the pKa for amine to lose H+?
Around 9
At physiological pH, the aa is a __ and have a net __ charge
A zwitterion (pI) and have net neutral charge at physiological pH.
Chirality = chiral centers have __
2 enantiomers are possible
What is an enantiomer
Mirror images.
What configuration do we want?
L configuration (S absolute configuration)
What are the 4 aa categories Dr Ford wants us to learn?
- Polarity
- Size/shape
- Synthesis
- Proteinogenic and nonproeinogenic
What aa s sometimes polar bc of ring?
Tyrosine
What is the aa that can perform redox rxns and what is this important for?
Cysteine and for disulfide linkages
The suffix -ate eludes to
Deprotonated
Side chains pKa tells us when ___
Acidic
Cannot make ourselves or we make it but don’t make enough is an __ aa
Essential aa
We can make aa means its a __ aa
Non-essential
Tyrosine and its synthesis role as being non-essential:
Tyrosine: we can make it but making it from an essential aa phenylalanine
What does proteinogenic aa mean
Making proteins from genetic code
What does non-proteinogenic mean
Not directly decoded from genome
What is an example of non-proteinogenic aas
Aas made via translational modifications
How can we ‘expand’ the universal genetic code
By reassigning a stop codon: UAA, UAG, UGA
What is the 21 aa?
Seleocysteine (Sec, U)
What is Sec’s pka?
5.2
Sec is protonated or deprotonated at physio pH
Deprotonated
Sec is synthesized from which aa?
Serine
Sec can be process to __ in plants, algae, and yeast
Selenomethionine
Sec can be processed to __ in animals
Alanine
What stop codon Sec uses?
UGA (opal)
In mito, Sec uses UGA which is a __ codon
W
In some ciliates, Sec uses UGA which is a __ codon
C
Sec was recognized as an opal __ in 1981
Repressor
Sec is found in:
All 3 domains of life: bacteria, euks, and archea
Sec uses its own __ and __ sequence
Uses own tRNA and SECIS
Proteins that incorporate Sec are called:
Selenoproteins
Selenoproteins are important and good for health via:
Reduce oxidative stresses, for growth and coordination in cerebellum neurons, moderate inflammatory responses (ex IBD)
What happens to a selenoprotein when Sec cis not available?
Proteins end up truncated (stop codon) ie non functional selenoproteins
Selenium deficiency results in:
Myopathies: keshan disease, statin intolereance, and immune-incompetence
What is Keshan disease and how can it be treated
A cardiomyopathy and with SE suppluments
What is stain intolerance and how treated
Rhabodmyolysis (muscle death) and treated by discontinuing statin
Statins inhibit __ which causes statin intolerance
Sec-tRNA
Statins are drugs that do what
Block the formation of cholesterol in the liver
Too much selenium results in:
Hair and nail brittleness, “garlic breath”
Gastrointestinal/neurological lesions
Myopathies, renal failure, and death
What is the 22 aa
Pyrrolysine (Pyl, O)
Pyl uses what stop codon? And that codon can be an or codon in some organisms
Uses UAG (amber) can also be an L or Q codon
Pyl are found only in some proks and all are __
Methanogens
T/F: Pyl uses own tRNA
True
T/F: Several members of the human intestinal microbiome make/use Pyl including archaea and ebuacteria
True
How can nonproteinogenic aas come to exist?
Post-translational additions to proteinogenic aas (ie addition of a phosphate group, D-enantiomers, metabolism intermediates, and pre-biotic or extraterrestrial origin
Antibiotic use this to make nonproteinogenic aas:
Non-ribosomal protein synthesis (NRPS)
Statins are made by __ synthesis (nonproteinogenic)
Polyketide synthesis (PKS)
1’ structure =
Chain of aas
2’ structure =
Local folding of polypeptide chain, connected by H bonds
3’ structure=
Folding of the 2’ structure, connected by disulfide linkages
4’ structure =
Interaction of multiple peptides
Single bonds means rotation is possible, but not always preferred. This results in:
A planar chain with side chains alternating up and down (important for 2’ structure and keeps big side chains away from each other)
What are the 2 interactions that govern protein folding stability
Non-covalent interactions: easy to form easy to break
Hydrophobic interactions: escaping from H20 increases chances of hydrolyzing (breaking apart) is high thus aggregation adds stability
What are examples of non-covalent interactions
Vand der waals
Short range repulsion
Hydrogen bonds
Electrostatic forces (ion pairs and salt bridges)
How does a hydrophobic molecule in the presence and absence of H20
Non-polar groups act non favorably with H20 and favorably when they excluding themselves from H20
What is a major factor in protein folding and stability?
Hydrophobic interactions
Via Van der Waals, molecules interact and nullify by
Their charge and how far they are away from one another
Short range repulsions can be explained by molecules that are too far have __ attraction, too close __, and therefore require __distance
Too far have no attraction
Too close molecules diffuse together and repulse. Not viable and high energy
Require optimal distance that is LOW ENERGY and just the right amount of distance away from one another
what are possible H bonds
N-H
O-H
F-H
Ie halogens in H bonds
T/F: H bonds are much stronger that covalent bonds
False. WEAKER
T/F: H bonds are longer than covalent bonds
True
What is the energy range for H bonds
1-5 kcal/mol
T/F: H bonds are flexible and easily formed
True
What is the pro of a electrostatic forces
Electrostatic (+ and -) easy to from and easy to break down
Effect of high levels of salt
Break up proteins, technique used for isolating proteins
What is the hydrophobic effect
Non-polar molecules escaping from H20 and fuse together
What are the determinant of folding
Secondary structure equals efficient packing
Hierarchical folding = certain groups fold
Hydrophobic effect, in primary sequence, aggregate in the central of the structure (core of protein) escaping from aqueous environment
Context dependent =folding differently and functioning differently
Characteristics of 2’ structure
Flexible
Rich in H bonds (what gives the flexible structure)
Contains:
Alpha-helical structure is space saving
Beta-sheet less flexible but provides stability (a parallel structure)
How are alpha-helices stabilized
By intrachain H bonds (disulfide bonds in same sequence) btwn N-H and C=O groups
Intrachain H bond in alpha-helix is a H bond that forms __ ahead in sequence
4 aas
In alpha-helix, each aa residue is related to the next one by:
A rise of 1.5 A along the helix axis
A 100 degree rotation
3.6 aa residue per turn of helix
T/F: alpha-helix can be either left or right handed screw sense? Which one is more energetically favorable?
True. Almost always right bc energetically more favorable
How are beta-sheets stabilized?
H bonding btwn polypeptide strands
beta-sheet formed?
Composed of 2 or more polypeptide chains called beta-strands via H bonds
Beta-sheets are fully extended?
Yes
Distance btwn adjacent aas along a beta-strand
3.5 A
B-sheet can run:
In parallel or anti-parallel direction
Reversal directions provide __ for polypeptide chain
Compact and globular shapes
What are the types of turns and what do they all provide?
Reverse turn, beta-turn, and hairpin turn. All provide flexibility
In many reverse turns, _ and _ groups form H bonds for __ which is useful because proteins are social structures
C=O and N-H groups; for stability
Type of loop?
Omega loop
Loops do not have regular periodic structure but instead:
Are well defined and rigid, positioned on the surface of the protein, and participates in protein-protein interactions and interactions with other molecules
Super helix, alpha-helical coiled coil folding provides:
Proteins long fibers that are useful in structural role (alpha-keratin, collagen, cell cytoskeleton, muscle proteins) and involved in biological functions (regulate gene expression, oncoproteins)
Super helix, alpha-helical coiled coil 2 helices like in a-keratin associate via:
Weak interactions like van der waals and ionic interactions
Super helix, alpha-helical coiled coil characterized by a __ region of 300 aas that contain __ repeats which provide?
Central region that contain heptad repeats. Provides 2 alpha-helices to interact with one another and observed in intermediate filament proteins
adding B-mercaptoethanol allows what to happen?
breaks incorrect sulfate bridges to allow to form properly
Why are repeating motifs important?
proteins have regions that have an affinity for X but will not bind without motif
what is the repeating motif in cadmodulin?
ca2+ binding site
why is context dependent important?
a sequence can adopt an alternative conformation in different proteins. ex VDLLKN has alpha helix in one protein and a beta strand in another
what is the molten globule state?
intermediate transient state btwn native and fully unfolded globular protein
why is the radius of the molten globule larger than the native state?
so the hydrophobic region can be exposed and aqueous environment interacts with center to form new H bonds’; provides flexibility for peptide bonds to properly fold
why does the unfolded state have high energy?
number of possible conformations are numerous
why does the folded state have low entrophy?
bc only 1 conformation
the native structure is the _
lowest free energy structure
the denatured structure is _
a high conformational entropy unstructured state
percentage of native contacts increase in protein folding because
they are stabilizing
