1A. Structure and function of proteins and their constituent amino acids Flashcards
Most AAs are in what configuration and what enantiomer is that?
S; L
Which aa has an R configuration as an L enantiomer? WHY?
Cysteine; has an SH group that has higher priority than -COOH
Which AAs are great for phosphorylation?
Threonine, Serine, and Tyrosine
Why are T, S, and Y great for phosphorylation?
They have an -OH group!
Which aa is not chiral (its alpha carbon is not chiral) and WHY?
Glycine (Only 3 different groups due to having H as its R group)
What four components make up an aa? (not counting the alpha carbon)
Amino, Carboxyl, R, H
D enantiomers have what configuration? (HINT: clockwise)
R
L enantiomers have what configuration? (HINT: counterclockwise)
S
T/F we use D enantiomers to make proteins
False; we use L enantiomers (all in S configuration except for cysteine)
which group of an aa is protonated in a typical cell (pH about 7)? Explain in terms of pH and pka.
amino (-NH3+)
pH<pka
which group of an aa is deprotonated in a typical cell? Explain in terms of pH and pka.
carboxyl (-COO-)
pH>pka
what are zwitterions? what aa category or categories may fit under this term in a typical cell (pH=7)?
molecules with net neutral charge; polar uncharged and non-polar AAs
which aa is not optically active and why
glycine; achiral
pka>pH. Protonated or deprotonated?
Protonated
pka<pH. Protonated or deprotonated?
Deprotonated
if in a high pH environment, are most aa R groups - or +?
negative; high pH means most pkas will be less than the pH
if in a low pH environment, are most aa R groups - or +?
positive; low pH means most pkas will be more than the pH
Which basic aa is actually neutral at physiological pH and why
histidine; becomes deprotonated from NH3+ since its pka is less than pH
T/F Hydrophobic AAs are found in the cytosol or exterior surface of cells
False; Hydrophobic AAs are within cell membranes because they HATE water
what does aliphatic mean
compound with Cs and Hs
All aromatic compounds are non-polar except which two and what are they categorized as?
Histidine= basic
Tyrosine= polar, uncharged
Which AAs will never be found in alpha helix secondary structures and WHY
Proline and Glycine (THINK PG)
They destabilize and break them!
what two AAs create the phosphomimetic effect? WHY? (What even is this effect?)
Glutamic (E) and aspartic (D) acid
When R groups mimic phosphate groups. Phosphate groups are negatively charged and so are E + D, which is why they mimic them! This can cause permanent activation of an aa.
what aa creates disulfide bonds
Cysteine, it has -SH (thiol or sulfhydril)
What AAs can create salt bridges? Why are these important to form?
+ and - charged AAs; help stabilize proteins!
what are two ways to make alpha amino acids?
strecker and gabriel synthesis
T/F Strecker and gabriel synthesis both form racemic mixtures
what are racemic mixtures?
True; mixture with D and L enantiomers
ammonia, aldehyde, imine, CN, aminonitrile, HCl, and H2O are all found in which reaction?
Strecker synthesis
phthalimide salt, diethyl bromomalonate, anion, R-Br, NaOH, heat, H2O, H3O+ are all found in which reaction?
Gabriel synthesis
T/F gabriel synthesis has acid catalyzed hydrolysis.
False; it has base catalyzed hydrolysis using NaOH and heat
What type of amines does gabriel synthesis make? (HINT: found in all AAs)
primary
Disulfide bonds form under oxidation conditions which is high or low ph?
High pH; less H+, will lose electrons via H
SH + SH –>SS
Disulfide bonds break under low pH. Is this oxidation or reduction conditions?
Reduction
OiL RiG
Gaining electrons via H
SS–> SH +SH
Why is BME (beta-mercaptoethanol used in Western Blot)
to break disulfide bonds
How does a peptide bond form? what does it result in?
Nucleophilic attack
Amino attacks Carboxyl to release H2O, which means it is a condensation reaction.
Results in an amide.
what type of reaction is peptide bond formation? (two types)
condensation and endergonic
endergonic vs exergonic? which is peptide bond formation and cleavage of peptide bond?
endergonic= requires E
Exergonic= releases E
Endergonic is formation. Exergonic is cleavage.
T/F Exergonic reactions are spontaneous reactions
Yes because they do not need to wait to get E since they release energy
what is hydrolysis
addition of water to cleave a molecule
why does peptide bond hydrolysis occur very slowly? also what occurs in this process?
peptide is cleaved; high Ea and resonance (stability)
what aa creates kinks in secondary protein structures due to its rigidity?
proline; also affects tertiary since it affects folding
T/F all proteins have a quaternary structure
False! All proteins must have primary, secondary, and tertiary but not quaternary
Which protein structure is linear? How is it read?
Primary; N-terminus to C-terminus by number!
What protein structure has alpha helices and beta sheets?
Secondary
Explain what beta turns are and in what structure you would find them
Loops in the peptide chain that create beta sheets in the secondary protein structure
Which are more stable and why? Parallel or Anti parallel beta sheets.
Anti parallel because the bonds are straight, short, and strong.
Parallel are at an angle, long, and weaker.
Why are alpha helices important in secondary structure of proteins?
Contain DNA binding sequences and transmembrane sequences to anchor down proteins to the membrane!
i+4 bonding sequence is seen in what protein structure? Be specific.
Alpha helices of secondary structure
What is the primary stabilizing force in secondary structure of proteins
Hydrogen bonding between O of carboxyl and H of amino
What is the term for the energetically favored folding state for a tertiary protein? Why is it favored?
Native state; maximizes entropy and minimizes intrinsic Energy
Disulfide linkages, ionic bonds (salt bridges), h bonding, dipole dipole and London dispersion forces are seen and are important in which structure of protein? Explain where you would see each type of bond.
Tertiary!
Disulfide= between cysteines
Ionic Bonds= between charges amino acids
H bonding= between O and H of amino acids
Dipole dipole= between polar atoms
London= between non polar atoms
What is the only covalent bond that affects tertiary structure? This is formed between what?
Remember that tertiary structure is 3D
Disulfide bridges; between two cysteines
What happens when protein is unfolded
Loses or has an altered function
What would you call a chain with 3 of the same type of peptides?
Homotrimer
What would you call a chain with 2 different peptides?
Heterodimer
What are prosthetic groups and why are they important in proteins? List a few organic and inorganic ones.
Non-protein molecules that help with function!
Organic= carbs, lipids, vitamins
Inorganic= metal ions
Define an apoprotein. Is it functional?
Protein without prosthetic group. Not functional!
T/F a holoprotein is a protein that is non-functional
False; a holoprotein has a prosthetic group which means it is functional since prosthetic groups help with functionality!
Proteins will spontaneously fold to a high or low energy state? Why?
Low energy state because it is more stable
Explain what molten globules are and how they can be bad.
Protein state with tertiary folding but not in its native state—> not functional!
Can lead to protein aggregates.
What type of proteins can help achieve a high energy state to get out of molten globule state into the native state?
(Opposite to peptide bond formation/cleavage since we need Energy in to break and not to form!)
Chaperone proteins
How does high salinity affect protein folding?
Disrupts ionic bonding—> no folding so no function
Protein folding is like a trial and error process. What shape does this represent?
Jagged funnel!
What is the term for when a protein unfolds after it has reached native state? Changes in what can lead to this?
Denature; pH, salinity, temperature
T/F once a protein is denatured, that’s it. It will no longer be functional ever again.
False! Denaturing only causes unfolding so the primary structure (peptide bonds) are still intact. Once it is in optimal conditions, it will fold right back up! (Remember that proteins want to be in low Energy states which is when it is folded)
Define entropy!
Disorder and randomness! This is what the universe wants!
Hydrophobic residues move toward the inner part of the protein. Why are they important?
They help stabilize the protein!
Which has high entropy? Folded or unfolded proteins?
Unfolded proteins because they are more disordered.
If folded proteins have low entropy, why is folding energetically favored?
Folding of a protein causes the solvation layer (water molecules around protein) to become more disordered.
More water molecules will be free floating since hydrophobic residues will be inside. Leads to high disorder—> high entropy!!
What is the isoelectric point (pI) and what is this similar to?
pH at which charge is 0
Similar to zwitterions!
Alkaline pH means solution is what?
Basic
pH> pI
Alkaline
Negative or positive?
Negative
Think of it like the pka!!! Lower pka, more deprotonation
pH<pI
Acidic
Positive or negative?
Positive
similar to when pka is greater since more protonation would occur
More acidic groups in a solution would do what to the pI?
Lower the pI due to low pka
Lead to more negative charge
More basic groups added to a solution would do what to a pI
Increase it due to high pka
More positive charge
What charges is an anion and a cation? Charges for anode and cathode? Explain charge differences.
Anion is -
Cation is +
Anode is + because it attracts anions -
Cathode is - because it attracts cations+
What is the technique used to figure out pI (isoelectric point) of a protein? Explain technique.
Isoelectric focusing
pH gradient on a membrane with a cathode and an anode. Once protein stops moving, it has a net charge of 0 and you have found the pI!!
What type of electrophoresis separates proteins by size and charge? Explain it. Where would you find the smaller proteins?
Native PAGE
Separates tertiary structures of proteins. Proteins go from anode to cathode(+). Smaller proteins migrate faster so they will be furthest to the bottom! Standards are used to know actual molecular weight.
What type of protein separation technique only separates by size and NOT charge?
SDS-page
What makes SDS-PAGE unique? What other compound is used to help separate proteins with this technique?
It’s a negative compound that binds to both hydrophilic and hydrophobic (amphipathic). Creates a uniform negative charge.
Completely denatures tertiary structure down to primary structure by breaking all non covalent bonds which leads to same mass to charge ratio!
BME (beta mercaptoethanol) breaks the covalent bonds (disulfide bridges).
T/F beta mercaptoethanol is an oxidizing reagent
False, it is a reducing reagent. It adds electrons or hydrogens to the sulfides to break the bonds!!
what is western blot used for? what is needed for this?
visualize proteins; need to transfer onto a membrane and use radioactive antibodies to actually see proteins!!
define an independent variable. choose an example:
a.) mutation
b.) rate of mutation
something that researchers can change or alter
a.) mutation
define a dependent variable. Choose an example:
a.) mutation
b.) rate of mutation
something that researchers can use to measure change
b.)rate of mutation
Explain what this means: G27V
AA mutation.
at position 27, a glycine is mutated to be a valine
why are beta sheets zig zagged in the secondary prtoein structure?
planar geometry of C-C and C-N bonds (No H bonding with R groups, only back bone!!)
what would happen if a protein would be placed in an organic solvent?
the hydrophobic residues would be exterior and the hydrophilic would be interior!
what are some reducing agents (like BME) found in our body?
NADPH, NADH, FADH2
reducing–>gaining electrons
these agents will donate electrons (Hs)
how much does an amino acid weigh? (in Da)
110 Da
when looking at a western blot (SDS+BME), what does each line represent?
one peptide or monomer (subunit) present
Define specificity of enzymes. What allows for this or why is it specific?
Enzymes have specific, unique active sites. These active sites have unique aa residues that provide the specific chemical environment for a substrate to bind to.
B cells have antigen receptors. What do they do once bounded to an antigen?
Secrete antibodies because an antigen is a pathogen.
What do antibodies do?
They will coat and neutralize antigens before they are able to enter and infect a cell.
Where do neutralized antigens go to?
Go to spleen to be filtered and then excreted as urine.
What is a glycoprotein? What is an example of one? Hint: immune system
A carbohydrate and a polypeptide.
Antibody or immunoglobulins
What does cytotoxic T cell mediated do?
Kill cells that have antigen on them (infected cells)
How are motor proteins able to provide movement?
Get energy from ATP hydrolysis. Add water to break ATP to ADP.
Phosphate bond has high energy so breaking it releases the energy so it can be used. (EXERGONIC)
Myosin, actin, kinesin, and Dunedin are examples of what?
Motor proteins
Kinesin (motor protein) moves what towards the outside of a well?
Chromosomes and vesicles
Dynein (motor protein) moves what toward the nucleus?
Cilia and flagella
How do enzymes act as catalysts by increasing reaction rate?
They decrease activation energy and energy of transition state
Explain effect of high temperature on a reaction rate. What would happen if temperate was very high/low?
High temperature increases reaction rate.
Extreme temperatures can denature protein and lead to a non functional enzyme.
What complex lowers the activation energy?
The enzyme substrate complex (ES)
Describe the optimal pH of an active site. What would happen if pH was not in this range?
Slightly acidic or non polar.
Extreme pH can denature protein leading to a non functional enzyme
Enzymes end in what
-ase
What are the 6 classes of enzymes?
LIL HOT
Ligase
Isomerase
Phase
Hydrolases
Oxidoreductase
Transferase
Class of enzyme?
A+B—> AB
Ligase
Class of enzyme?
A—>B
Isomerase
Create an isomer
T/F isomers have same formula and same bond configuration
False
Isomers have same formula but they have different arrangement of atoms
Class of enzymes?
A—> B+C
No H2O or redox agent used
Lyase
Class of enzyme?
A + water —> B+C
Hydrolases
Hydrolysis reaction!
Class of enzymes?
A: + B —> A + B:
Oxidoreductase
Redox!
Class of enzyme?
A + BX —> AX + B
Transferase
Phosphorylase vs kinase?
They both add phosphates but phosphorylase uses a phosphate from inorganic phosphate (Pi) and kinase uses a phosphate from ATP
T/ F enzymes decrease activation energy but they do not alter the free energy (difference between substrates and products)
True!!
Only affect activating energy!
What is the induced fit model and why is this better than lock and key model?
Induced fit model has two steps. Weak initial bonding and then a conformational change within enzyme to increase stability by strengthening binding.
Lock and key model only has one step and represents a jigsaw puzzle. Not correct!
Name the mechanism of catalysis.
When two substrates are brought in close proximity
Approximation
Name the mechanism of catalysis
Enzyme forms a temporary covalent bond with substrate
Covalent catalysis
Name the mechanism of catalysis
Enzyme acts as a base or acid
Acid base catalysis
Name the mechanism of catalysis
Enzymes assist in nucleophilic and electrophilic interactions
Metal ion catalysis
Name 3 non-enzymatic functions of proteins
Binding, immune system, motor (movement)
Difference between cofactors and coenzymes. Name some examples of both.
Cofactors are Inorganic ions
-magnesium
-iron
-zinc
coenzymes are organic ions.
-vitamins
Cofactors are magnesium, zinc, etc. what is the most commonly found charge and what is it called?
+2
Divalent
Divalent cofactors are common. What is an example in which zinc +2 is required ?
DNA polymerase needs this to make dna molecules
What are some water soluble vitamins? What are these categorized as?
Vitamin B + C (dietary requirement)
Coenzymes
Vitamin C is important for collagen (connective tissue)!
Dehydrogenase is an example of what class of enzymes? What does it do?
Oxidoreductase
Reduces
NAD+, NADP+
-both accept electrons (Hs)
