biochem1 Flashcards
what’s an oligopeptide?
very small chain of amino acids
what’s a polypeptide?
longer chain of amino acids
what is an essential amino acid?
amino acid you cannot synthesize and need to ingest
what is a non essential amino acid?
amino acid you synthesize and do not need to ingest
What does R group help determine?
chemistry such as:
1) if substrate will bind to active site; protein will fold; mechanisms in enzyme pocket.
1) 5HTT is a monoamine transport protein responsible for the reuptake of serotonin from synapses in the central nervous system. 5HTT also has a high affinity for which amino acid?
Serotonin
A) Arg B) Trp C) Val D) Glu
Solution: The stem states that 5HTT transports serotonin. It is logical to assume that it will also transport, and therefore have high affinity for, something very similar to serotonin in structure and polarity. Answer B, tryptophan, is certainly a possibility given that the aromatic portion of serotonin is nearly identical to that of Trp. Answer A, arginine, would not be a good candidate because it has a positively-charged side chain and no aromatic group. Answer C, valine, is a much smaller non-polar amino acid. Answer D also has a negatively charged side chain. This leaves Answer B as the best answer.
B
What tis the order of deprotonation?
1) Alpha- COOH group
2) -R group acidic
3) -R group, His
4) alpha- NH3+ Group
5) -R group Basic
what is a zwitterion?
dipolar version of an amino acid that has neutral ion
Are amino acids weak or strong acids?
weak
What is the isoelectric point of a neutral? acidic? basic?
pI neutral= average of pKa- amine group and pKa- carboxyl group
pI acidic= average of pKa- acidic R group and pKa carboxyl group.
pI basic= average of pKa amine group and pKa basic R group.
2) If the pH of a solution is below the pKa of the carboxylic acid of isoleucine, what will be the charge on the majority of isoleucine molecules in that solution?
A) 2+ B) 1+ C) 0 D) 1-
Isoleucine has a non-polar aliphatic side chain.
B
What reaction is forms peptide bonds? what attacks what?
- dehydration synthesis and acyl substitution
- Amine group nitrogen (nucleophile) from the NEW amino acid attacks the carbonyl carbon (electrophile) on the C terminus of the growing peptide chain.
Peptides written, read and synthesized in the direction?
N terminus –> C terminus
What has double character in the amino acid?
BOTH the C=O bond and the C-N bond in a peptide bond have DOUBLE BOND character
What does double bond character?
RIGID peptide bond with limited rotation
What happens during protein hydrolysis? where does trypsin and chymotrypsin cleave?
Trypsin and chymotrypsin cleaves proteins not the carboxyl side of specific amino acid residues;
- trypsin= arginine, lysine
- chymotrypsin= phenylalanine, tryptophan, tyrosine.
What is primary sequence?
amino acid sequence
what is alpha helix secondary protein?
- alpha helix is a polypeptide chain that is rod-shaped and coiled in a spring-like structure, held by intramolecular hydrogen bonds. A helix can be left-handed (beta) or right-handed where the alpha helix is always right-handed.
what is beta helix secondary protein?
Beta sheets is a pleated conformation of two or more fully extended peptide chains that can be parallel or antiparallel; the hydrogen bonds are flexible but not elastic and are inter-molecular. It is necessary for the carboxyl and amide moieties to line up properly in order for every residues to participate in 2 hydrogen bonds.
In a alpa helix, is the R group pointed toward, away, perpendicular or parallel from the alpha helix cylinder? What about in Beta sheet?
away in alpha cylinder
parallel in beta sheet.
What amino acid is found outside of alpha helices and why?
Proline is the first residue at the END of an alpha helix and it cannot be inside the helices a it is non polar hydrophobic and to big –> introduces kinks and turns.
what are two examples of secondary structures of amino acids found in body?
keratin and fibroin
what’s a tertiary structure?
Geometric, three-dimensional folding of the alpha helices, beta sheets, and other moieties to form a functional globular or structural protein.
What are the six interactions between amino acid that contribute to a 3* protein structure?
- Hydrogen bonding – non-covalent bond between either backbone atoms (N-H or C=O) or side chains (amine groups, carboxyl groups, alcohol groups)
- Disulfide bonds – covalent bond between the sulfurs of two cysteine residues
- Hydrophobic/hydrophilic interactions – in soluble proteins, the hydrophobic amino acids will collapse into the protein core. In membrane proteins, the hydrophilic membranes will be either outside the membrane in the cytoplasm or inside the core of the protein, away from the membrane bilayer, with hydrophobic amino acids located within the membrane bilayer.
- Ionic interactions (salt bridges) – charge-charge interactions between a positively charged amino acid and a negatively charged amino acid
- Van der Walls forces – intermolecular forces that repel atoms away from each other (steric hindrance)
- Proline turns – because of proline’s unusual cyclical shape, introducing a proline into an alpha helix or beta
sheet will cause a kink. Proline turns are also found at the end of most strands involves in beta sheets. The sharp turn helps the chain redirect in such a way that the next segment is running antiparallel to the previous segment in the sheet formation.
What does L and D- stand for in front of an amino acid? How do you distinguish them?
D – and L- amino acids are mirror images of one another, and they are not identical compounds.
By convention, if the carboxylic acid (-COOH) group in a fisher projection is placed at the top and the –R group is placed at the bottom, then L-amino acids will have the amine group on the left and D- amino acids will have the amine group on the right.
what’s quaternary structure?
multiple folded proteins into a multisubunit and two beta subunits
What’s an example of a quaternary structure in the body?
Hemoglobin- two alpha and two beta subunits.
What type of binding does hemoglobin undergo? what does it mean?
Positive cooperativity- ligand affinity increases with binding of more subsequent ligand.
what is a globule protein?
fully folded protein
what is a molten globule protein?
partially folded
what is a molten protein?
fully denatured/ unfolded
what are examples of amino acids with CHARGED side chains? (acidic, positive, negative)
ACIDIC/ NEGATIVE charged: glutamic acid (Glue, E) and aspartic acid (Asp,D)
POSITIVE/BASIC:
lysine (Lys, K), arginine (Arg, R) and histidine (His, H)
can amino acids with CHARGEd side chains be found int the interior of a protein?
No unless it is bound to a complimentary molecule/ side chain of opposite charge,w which would cancel out net charge and be in interior of globular protein.
What is true of a hydrophobic core?
hydrophobic R groups fold into the interior of a globular protein to escape water. + some smaller polar complimentary molecules to stabilize core.
What is true of hydrophilic surface? what proteins are found?
majority of R groups are either polar or charged
What are electrostatic interactions? what is the effect on globular protein interaction?
Interactions between charged- R groups, both encourage act of folding itself and stabilize protein and its folded state.
What is the effect of Hydrogen bonding on protein folding?
H bond between - R groups also encourages folding and stabilizes folded protein.
What are Disulfide bonds? what is the effect on protein interaction?
Two oxidized cysteine residues form a disulfide (R-S-S-R) bond. Strongest type of protein folding interaction.
What are salt bridges, when are they formed?
Formed when acidic and basic R groups undergo neutralization reaction resulting in salt. Maintain deoxytaunt form.
An alpha helices with proline turn can be considered as ?
disrupting 2* structure or contributing 3* structure.
What is solvation layer?
a layer of water that surrounds dissolved protein.
Why are hydrophobic proteins found in the interior when in a polar solvent or in water?
Interaction of non polar/ hydrophobic a.a with water or polar solvent requires too much energy and is not favored. Therefore polar amino acids surround the non polar, because that interaction of polar a.a and solvent (water or polar) is much me favored as it requires less enthalpy/ energy and leads to an increase in entropy.
–> MAJOR CONTRIBUTION TO OVERALL CONFORMATIONAL STABILITY OF FOLDED PROTEIN
What are the 4 protein denaturing agents?
1) acid
2) heat
3) urea
4) mercaptoethanol
Is it possible to get a denatured protein to re-fold? How
Most likely not.
Only possible the proteins as slowly denatured with detergent and Disulfide bond aren’t broken- it can reform secondary structure.
What is Electorphoresis?
separating protein based on fixe. the smallest protein will go the furthest.
Which amino acid will go further (furthest toward positive charge) on electrophoresis gel; Phenylalanine or glycine?
glycine- smallest amino acid
what is isoelectric focusing? How does it work?
Separating proteins based on pI.
A protein in a region of the gel with a pH lower than its isoelectric point will be positively charged (because it will be fully protonated) and so will move toward the negative cathode. A protein in a region with a pH higher than its isoelectric point will be negatively charged (because it will be fully unprotonated) and so will move toward the positive anode. As the protein moves through increasing pH in the gel, the protein’s charge will decrease until it reaches the pH of its pI, at which point it will become neutral.
In Isoelectric focusing with pH gradient which amino acid will go to the positive and which amino acid will go to negative side;
serine; histidine; aspartic acid; leucine; cysteine
serine pI acidic= (9+2)/2= 5.5
3.5 –> toward positive side of gradient
histidine pIbasic= (9+6.04)/2= 7.5
1.5–> toward middle of gradient
Asp pIacidic= (3.71+1.95)/2= 2.83
–> toward positive side of gradient
leucine pI= (9.58+2.32)/2= 5.95 –> toward middle of gradient sie
cysteine pI= (10.28+8.14)= 9.21
toward negative side of gradient
What are four types of non enzymatic proteins? give examples for each
Binding proteins= hemoglobin, calmudolin, histones, TF, troponin, tropomyosin,
Immune system =ntibodies and antigens
Structural proteins= actin, tubular, keratin
motor proteins= dyneins and kynesins (+)
What is the difference between
Both catalysts and enzymes increase the rate of a reaction by lowering the activation energy. Enzymes, however, are organic molecules, while catalysts can be inorganic molecules (like metal ions).
How do enzymes affect a) reaction rate? b)energy of activation c) equilibrium d) Keq e) yield f) percent yield?
a) increase reaction rate
b) lower activation energy
c) DO NOT affect equilibrium
d) DO NOT affect Keq
e) DO NOT affect yield
f) DO NOT affect percent yield.
How do each affect reaction rate:
a) pH
b) temp
c) substrate concentration
d) enzyme concentration
a) enzymes work best at optimal pH and change in pH leads to decrease in reaction rate.
b) optimal temperature. too low temps = decreased reaction rate, too high= denature enzyme and low reaction rate. mild temperature increase can increase reaction rate.
c) At low substrate concentrations, the reaction rate will increase rapidly until reach saturation- decrease/ and stabilize.
d) similar saturation curve than for substrate- if concentration is low, adding enzymes will increase reaction rate but it too much enzyme it will decrease and stabilize.
What are the different enzyme reaction type? what’s the mnemonic?
OverTheHILL
Oxidoreductases= REDOX
Transferases= Transfer functional group
Hydrolases= Hydrolysis
Isomerases= rearrangements
Lyases - cleavage / synthesis
Ligases= addition or synthesis of LARGE molecules, usually ATP dependent.
Two theories of enzyme specificity are: and & . Which of these two theories has been largely dismissed by scientists? Why has it been dismissed?
induced fit and lock and key.
Lock and key has been dismissed because it owed mean a rigid inflexible active site.
What’s a cofactor?
A general term for any species required by an enzyme to function; coenzymes and
prosthetic groups are both examples of cofactors.
what’s a coenzyme?
Non-protein species NOT permanently attached to the enzyme but required by the enzyme to function.
