Exam Two Flashcards
What level structure is the amino acid sequence?
Primary
What level structure is alpha helices and beta sheets?
Secondary
What level structure is 3D folding?
Tertiary
What level structure do subunits comprise?
Quaternary
What is the structure level that is not necessarily applicable to every protein?
Quaternary
What changes electron distribution within a peptide bond?
differences in electronegativity
What makes the peptide bond so rigid that it can only rotate around C-alpha?
the resonance double bond between the C and N termini
Why do secondary structures form?
to satisfy hydrogen bonding requirement and minimize steric strain
What secondary structure is a single strand twisted?
Alpha Helix
Are right or left handed alpha helices more favorable?
right
Why are right handed alpha helices more favorable?
There is minimized steric strain between the side chains and the main chain
How many residues ahead does the carbonyl form a hydrogen bond with N-H?
approximately 4
What is the backbone of an alpha helix/what drives hydrogen bonding?
Van der Waals forces
Do the side groups on an alpha helix extend inward or outward?
outward
What secondary structure is comprised of several strands arranged to be flat?
Beta Sheet
How is the Hydrogen Bond requirement met for beta sheets?
bonding between neighboring strands
Do the side chains on a beta sheet extend on one face or on both faces?
both faces
Are fibrous proteins soluble or insoluble?
insoluble
What fibrous protein is a triple helix?
collagen
What fibrous protein is comprised of stacked beta sheets?
silk
What fibrous protein is comprised of alpha helices that are cross-linked by disulfide bonds?
alpha-keratin
What structural protein forms a coiled-coil structure?
keratin
What structural protein is the most abundant in mammals?
Collagen
What structural protein is rich in proline?
Collagen
What are the three amino acids that primarily repeat to form the collagen triple helix?
Gly-Pro-Hyp
What is the most common secondary structure? Alpha helices or beta sheets?
Alpha helices?
How much of secondary structure is irregular? i.e. not alpha helix or beta sheet?
46%
what is the driving force of secondary structure?
hydrogen bonds among peptide groups
What is a domain?
Single structural unit with several secondary structures within
Is the hydrophobic effect or hydrogen bonding more important for domain stability and tertiary folding?
hydrophobic effect
How is a protein’s 3D structure mainly formed?
tucking hydrophobic side groups in
Which shape of domain has an open middle?
beta barrel
Which shape of domain has a pretty crowded middle?
saddle
What are three other stabilizing factors in the tertiary structure of a protein?
disulfide bonds, ion pairs, zinc fingers
What kind of environment are disulfide bonds normally found in?
oxidizing (extracellular)
Where is folding information stored in a protein?
Within the protein’s primary sequence
Is structure or sequence more conserved?
structure
What are the two ways to denature proteins?
heating, adding salt or urea
What does adding salt or urea do to denature proteins?
interfere with structure of water (solvent) and disrupt the hydrogen bonds
What are proteins that prevent misfolding and aggregation of unfolded peptides?
chaperones
How many hydrophobic cores are in a tertiary structure?
One
What is the prosthetic group that contains the iron where O2 binds?
heme
What is the single peptide chain that carries O2 in muscles via diffusion?
Myoglobin
What is the tetramer that carries O2 from lungs to tissue through the bloodstream?
Hemoglobin
Why is hemoglobin so much more sophisticatd?
It knows when to grab O2 and when to release it
Oxygen binding to Mb or Hb is _________.
Transient
How do ligands bind?
Via the same noncovalent interactions that dictate protein structure
What allows Hb and Mb binding to Oxygen to be transient?
the fact that you bind with the same interactions that dictate protein structure
What are the 6 binding sites on the central Fe (II) atom of the heme group bound to?
4 Nitrogen atoms, protein at His, and O2
Why is heme not an effective oxygen carrier by itself/not bound to Hb or Mb?
By itself, Fe (II) is easily oxidized to Fe(III), which cannot bind O2.
Would a lower or higher p50 indicate better affinity for Ow?
Lower
Does myoglobin or hemoglobin have a higher p50?
Hemoglobin
Why does myoglobin bind oxygen better than hemoglobin?
the allosteric effect of quaternary structure that hemoglobin experiences
Does the T or R state have a higher affinity for Oxygen?
R = relaxed state
What does O2 binding trigger in hemoglobin?
a T to R conformational change
Does Hb bind oxygen better at lower or higher pH?
Higher pH
Is Oxygen released at low or high pH?
Low pH
Lung or tissue: CO2 rich and therefore has a low pH
Tissue
Lung or tissue: CO2 expired and therefore has a high pH
Lung
Do lungs or tissue bind oxygen better?
lungs
What kind of tissue is being described?
1. CO2 produced decreases pH (increases H+)
2. lactic acid produced by active muscle also decreases pH
3. Hb releases more O2
respiring
What does BPG do?
stabilize the deoxy form of Hb
What occurs in the absence of BPG?
too tight binding
What is the amino acid change in fetal Hb that causes a lower affinity for BPG and thus a higher affinity for O2?
His to Ser
Is BPG neutral, negatively charged, or positively charged?
negatively charged
What cells produce antibodies?
B cells
How does antibodies binding to antigens affect cellular response?
binding will mark the antigen for destruction or interfere with its function
where does an antibody bind to the antigen?
epitope of the antigen
What are antigens typically made of?
macromolecules
Is Fab made up of constant, variable, or both domains?
both
Is Fc made up of constant, variable, or both domains?
Constant
Where does the antigen bind to the antibody? Fab or Fc?
Fab
Is Fab made up of heavy, light, or both chains?
Both
Is Fc made up of heavy, light, or both chains?
Heavy
How do antigens bind?
induced fit
What does antibody specificity detect?
a protein/antigen of interest
What does ELISA detect?
the presence/amount of antibodies
What does Western blot/immunoblot detect?
a specific protein within a mixture
What is the covid antibody test?
ELISA
what is the covid antigen test?
rapid test
What does a catalyst do?
accelerates the reaction rate by lowering the energy of activation
What kind of enzyme catalyzes the transfer of electrons?
oxidoreductase
What kind of enzyme catalyzes group transfer reactions
transferases
What kind of enzyme catalyzes hydrolysis reactions
hydrolases
What kind of enzyme catalyzes cleavage of C-C, C-O, or C-N by elimination, leaving double bonds or rings?
Lyases
What kind of enzyme catalyzes transfer of groups within molecules to yield isomeric forms?
Isomerases
What kind of enzyme catalyzes formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP?
Ligases
Where is the active site usually found?
At the interface of 2 domains
What is the equation of S to P with the presence of an enzyme?
E+S —> ES —> EP —> E+P
How does an enzyme lower the activation energy?
by forming the ES complex
What are transition state analogs?
transition state lookalikes that bind to the enzyme better than the substrate
What are non-protein substances that turn on inactive enzymes?
Cofactors
How is acid base catalysis pH dependent?
if pH of the enzyme < pKa then enzyme will act as an acid
if pH of the enzyme > pKa then enzyme will act as a base
What are the amino acids commonly used in general acid-base catalysis?
Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr
What are the stages of covalent catalysis?
- nucleophilic enzyme attacks electrophilic substrate
- temporary covalent bond formed between the nucleophile and electrophile
- rearrangement of electrons
- removal of enzyme: rearrangement of electrons into the product
What is a sure sign of covalent catalysis?
Schiff base formation
What amino acids would form a Schiff base?
Asn, Gln, Lys, Arg, His
What are some of the metals that are not catalytic and therefore would not participate in metal catalysis?
Na+, K+, Ca2+
What is the most common way that metal catalysis works?
metals facilitate ionization of water to help form a nucleophilic OH
Where does chymotrypsin cleave?
after Phe, Trp, and Tyr residues
What kind of catalysis does chymotrypsin participate in?
Acid/Base AND covalent
What is the catalytic triad of serine proteases?
3 important amino acid residues in its catalytic site
What is the catalytic triad made up of in all serine proteases?
His 57, Asp 102, Ser 195
How can chymotrypsin’s catalytic triad be so far away from each other on their chain and still interact?
They are close in the 3D structure
What kind of molecule does chymotrypsin accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?
bulky, aromatic molecules so the pocket has lots of space
What kind of molecule does trypsin accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?
positively charged molecules so the pocket has a negatively charged molecule
What kind of molecule does elastase accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?
small, non-charged molecules so the pocket is crowded and non-charged
What are the 2 important mechanisms for transition state stabilization in chymotrypsin?
Oxyanion hole and low barrier hydrogen bonds between Asp 102 and His 57
What kind of catalysis does RNAse participate in?
Acid/Base
Why does RNAse have two different His residues with DIFFERENT pKas?
One works as an acid, one works as a base
Why doesn’t RNAse work on DNA?
the OH in the mechanism that is found only on RNA and not DNA is very important
What enzyme breaks up bacterial cell wall’s polysaccharides (peptidoglycan)
lysozyme
What does the binding of peptidoglycan to lysozyme do to the structure?
Changes the conformation of the D ring so the bond to be cut will align
is NAG or NAM recognized in the peptidoglycan
NAM
What is an inhibitor of transpeptidase
penicillin
What breaks open the beta-lactam ring of penicillin and thus inactivates it?
beta-lactamase
What is an inhibitor of beta-lactamase
clavulanic acid (augmentin)
How is chymotrypsin activated?
By removal of 2 dipeptides
How does activation affect the catalytic activity of an enzyme?
There isn’t that much change, but it does open up the specificity pocket so that it is more accessible to the substrate and open up the oxyanion hole
What do protease inhibitors do?
Act as a safety backup; inhibit proteases in the case of premature activation
How do protease inhibitors work?
Once they are bound, the complex is too tight so that the leaving group can’t leave and water can’t enter
What is an example of a REVERSIBLE covalent modification?
phosphorylation
What enzyme adds phosphate groups onto a substrate?
kinase
What enzyme removes phosphate groups from a substrate?
Phosphatase
What is an example of a noncovalent modification?
allosteric regulators
How does modulator binding affect the enzyme?
It changes the conformation of the entire enzyme so that the substrate can bind better
Does the modulator bind to the catalytic subunit or the regulatory subunit?
regulatory
Which amino acids do kinases transfer phosphates to?
Ser, Thr, and Tyr
What does a curved arrow in a reaction represent?
the movement of an electron pair
How many oxygen atoms can Hb bind at once?
4
How many oxygen atoms can Mb bind at once?
1
What is the shape of the hemoglobin-oxygen binding curve?
sigmoidal
Which test has proteins in their native state?
ELISA
Which test has proteins with no higher order structure?
western blotting
Which test are proteins transferred to a membrane or a sheet?
western blotting
What fragments of an antibody crystallize readily?
Fc
What fragments of an antibody are recognized by macrophage surface receptors?
Fc
What fragments of an antibody often undergo conformational changes?
Fab
What fragments of an antibody contain the immunoglobulin fold?
Both Fab and Fc
