Biochemistry Flashcards
What 3 amino acids are in the chymotrypsin active site?
What 3 amino acids does it prefer to cleave?
Active site: His, Ser, Asp (“HASp”)
Preferentially cleaves: Trp, Tyr, Phe (WYF)
3 steps to figure out whether the amino acid has the D or L configuration
- Locate the α-carbon (chiral, has amino, carboxyl, R on it)
- Determine R or S
- R = D and S = L (EXCEPT Cys = R = D)
→ all eukaryotic AAs are L = S (except Cys)
pepsin is a hydrolase that cleaves the amide of peptide bonds to produce two products:
amine (NH2) + carboxylic acid (COOH)
At physiological pH, what AAs are charged?
D, E = -1
R, K = +1
His = 0 (even though it can be positive)
Everything else = 0
What can oxidoreductases change? What do they NOT affect?
Can change # O and Hs in a molecule → can disrupt H bonds
DOES NOT affect peptide bonds
What are the 2 things that could be happening if metabolism by an enzyme happens at a CONSTANT rate?
- when Es are SATURATED
2. when S is continuously added and P is continuously removed to keep [S] at a steady level
What kind of AAs would we want in these regions?
a) inside an enzyme (active site closed off from the outside)
b) transmembrane domain
c) intracellular/extracellular domain
a) hydrophobic → interior is closed off from hydrophilic exterior
b) hydrophobic → cell membrane is hydrophobic
→ transmembrane does NOT include EC parts, just membrane!
c) hydrophilic → the inside and outside of cell are hydrophilic
What are the 8 hydrophobic AAs? What is its pI?
Val, Ala, Ile, Leu, Met, Trp, Tyr, Phe (“VAIL M’ WYF”)
pI = 6
What are the 2 AAs considered misfits? What’s special about them? What is their pI?
Gly: achiral
Pro: side chain connected to protein backbone twice, in ß turns
pI = 6
What are the 5 AAs that are hydrophilic but uncharged at physiological pH? What is their pI?
Asn, Gln, Cys, Ser, Thr (“NQ CST” = No Q (charge), CySTs are wet ion know lol)
pI = 6
What are the 2 AAs that are negatively charged in physiological pH? What is their pI?
Asp, Glu (“negative DErivative”)
-1 in physiological pH (suffix -ate means deprotonated form)
pI = 6
What are the 3 positively charged amino acids? Which ones are positive in physiological pH?
His, Arg, Lys (“HRK to only positive shit!”)
PHYSIOLOGICAL PH: Arg, Lys (“RaKe the positive things!”)
→ His is NEUTRAL in physiological pH but can be positive in other pHs
What are the pIs of the ionizable side chains of His, Arg, and Lys?
pIs (as well as their ZW) in increasing order: HKR (“Hacker”)
His (H) = 7.6 < Lys (K) = 9.9 < Arg (R) = 10.8
What is the pKa of the carboxyl group on AAs? What will be its state if pH < pKa? pH > pKa?
pKa = 2.3
pH < 2.3 → COOH (protonated)
pH > 2.3 → COO- (deprotonated)
What is the pKa of the amino group on AAs? What will be its state if pH < pKa? pH > pKa?
pKa = 9.7
pH < 9.7 → NH3+ (protonated)
pH > 9.7 → NH2 (deprotonated)
What is the difference between coenzymes and cofactors? What about prosthetic groups and metalloproteins? What is the overall relationship between all 4 of them?
Coenzymes = organic (ie. vitamin A, C) Cofactors = inorganic (ie. usually free metal ions like Fe, Zn, etc.)
Prosthetic groups = bound to Coenzymes, which they need to be functional (ie. Cys residues are the prosthetic groups on Heme C)
Metalloproteins = bound to cofactors, which they need to be functional
Coenzymes: Prosthetic groups :: Cofactors: Metalloproteins
What is a lyase? How is it different from a hydrolase?
Lyase = split molecules WITHOUT water hydrolase = split molecules WITH water
Enzymes catalyze reactions through all means EXCEPT:
a) bringing substrates together
b) ↓ activation energy
c) facilitating bond cleavage and formation
d) ↑ stability of rxn pdts
D
E does NOT alter energetics or stabilities of rxnts or pdts!
Western blot measures the quantity of what biological molecule? From top to bottom of the ladder, does size increase/decrease? What does a band represent?
proteins
decrease (smaller proteins travel farther)
1 band = 1 unique protein
What do reducing agents do and what happens as a result? What do they break? What do they not break?
They reduce another rxnt; they get OXIDIZED!
They break disulfide bonds
They do NOT break peptide bonds
What bonds are involved in each protein structure level? Which level REQUIRES covalent bonds to form?
1° = peptide bonds (COVALENT BONDS REQUIRED)
2° = hydrogen bonds
3° and 4° = electrostatic interactions, hydrogen bonds, disulfide bridges
What are α-amino acids? What is an α-carbon?
α-amino acid: has amino group and R group attached to Cα
α-carbon (Cα): carbon adjacent to the carbonyl carbon
What is the biggest AA? Smallest AA? How do you decrease steric hindrance?
Biggest: tryptophan (W)
Smallest: Glycine (G)
Decrease steric hindrance by replacing large AAs with smaller ones
What does a competitive inhibitor do? How are the Km and Vmax affected? What do the M-M and L-B plots look like?
competes with substrate for active site (can overcome this inhibition by adding way more substrate)
Km ↑ (need more substrate to overcome inhibition)
Vmax not changed
M-M: Two hyperbolic curves with the same start and finish, but inhibitor present is lower curve than inhibitor absent
L-B: inhibitor present has the SAME Y-INT but STEEPER slope than inhibitor absent
What does a non-competitive inhibitor do? How are the Km and Vmax affected? What do the M-M and L-B plots look like?
Binds to another allosteric site, rendering the active site nonfunctional (substrate usually can’t bind anymore, but can)
Km not changed (NCI binds to an allosteric site on E which is accessible when E OR ES → equal affinity to E and ES)
Vmax ↓
M-M: two hyperbolic curves with the same start but the inhibitor present has a way lower finish than inhibitor absent (but same-shaped curve, which can show Km not changed)
L-B: inhibitor present has the SAME X-INT but STEEPER slope than inhibitor absent
What does an uncompetitive inhibitor do? How are the Km and Vmax affected? What do the M-M and L-B plots look like?
only binds to ES complex and prevents substrate dissociation
Km ↓
Vmax ↓
M-M: inhibitor present hyperbolic curve would kink way sooner and is way lower than the inhibitor absent hyperbolic curve
L-B: inhibitor present line is shifted LEFT of inhibitor absent line (both have SAME SLOPES though)
What does a mixed competitive inhibitor do? How are the Km and Vmax affected? What do the M-M and L-B plots look like?
Like non-competitive inhibitor, but they do NOT have an equal affinity to the E and ES (one maybe higher than the other)
Km ↑ (usually) but can also ↓
Vmax ↓ (usually)
M-M: inhibitor present hyperbolic curve would kink way sooner and is way lower than the inhibitor absent hyperbolic curve but both curves INTERSECT
L-B: intersects in some random non-axial point, slope of inhibition present > slope of inhibition absent (Km increased)
T/F: ATP hydrolysis is about -30.5 kJ/mol, which is similar to GTP hydrolysis
TRUE
If a question provides you with delta G data and asks you what reaction can support what reaction, how do you approach that problem?
- Look at the numbers and rank the smallest to largest
- Choose the answer that says something along the lines of a reaction with the HIGHER negative delta G can support the one with a LOWER negative (or even lower positive) delta G
what is the difference between a transferase and a kinase?
transferase: catalyzes the transfer of any group to a specific molecule (amine, phosphate, carboxyl, etc.)
kinase: transfer of SPECIFICALLY PHOSPHATE groups from ATP to a specific molecule (essentially a SUBSET of transferase)
What is a nonsense mutation? What happens to the protein as a result?
single bp SUB that changes AA → stop codon
truncated, nonfunctional protein
What is a missense mutation? What happens to the protein as a result? What is a real-life example of this?
single bp SUB that changes AA → another AA
can affect SHAPE + FXN of the protein
sickle cell anemia
What is a frameshift mutation?
involves deletion or insertion of bp in numbers NOT in multiples of 3!
NOT A SUB!
How to calculate # of AA residues that will be present in a protein when given the # of bp on all the exons?
- count up all the bp and divide by 3
2. SUBTRACT that number by 1 b/c the final codon = stop codon, which DOES NOT code for an AA!
T/F: mRNA is synthesized and translated in the ribosome in 3’ → 5’ direction
FALSE → 5’ → 3’ for BOTH mRNA synthesis and translation
What kind of enzyme is an rRNA? What is its function?
ribozyme (enzyme made of RNA) [NOT a polymerase!]
catalyzes the formation of peptide bonds
What is a Kozak sequence? Where is it found? Is it in pro and euk?
DEF: protein translation initiation site in most eukaryotic mRNA (5’ cap is initially the ribosome binding site but then that helps mRNA bind to Kozak seq to initiate translation)
5’ UTR
EUK ONLY!!
What is a Shine-Dalgarno sequence? Where is it found? Is it in pro and euk?
DEF: ribosomal binding site (equiv to euk Kozac sequence) that is recognized by the pre-initiation complex in a prokaryotic cell system
5’ UTR
PRO ONLY!!
What is a cell lysate? If I’m studying ribosomes and I had my cell lysate, what would it contain?
DEF: fluid containing contents of lysed cells
ASSEMBLED ribosomes AND ribosomal SUBUNITS!!
Prokaryotic vs Eukaryotic ribosomes in terms of small subunit + large subunit, as well as the assembled ribosome
Pro: 30S + 50S = 70S
Euk: 40S + 60S = 80S
(“Euk is bigger than Pro between 30-80”)
DNA polymerase can be: I. isolated in lab II. synthesize in vivo and in vitro III. be mass-produced IV. used in PCR
I, II, III
NOT used in PCR b/c it denatures in high temp (instead uses Taq polymerase which is much more tolerable in higher temps)
In gel electrophoresis (a type of electrolytic cell), where will the DNA migrate towards, the anode or cathode?
DNA = negative → will migrate towards ANODE (+)
If the question gives you a picture of base pairs, how will you recognize the CORRECT form of the A-T pair?
A-T has 2 H bonds
A: NH and N (has 2 N as H bond sites)
T: O and NH (has 1 O and 1 N as H bond sites)
(“ANNTON!”)
If the question gives you a picture of base pairs, how will you recognize the CORRECT form of the G-C pair?
G-C has 3 H bonds
G: O and NH and NH (has 2 N donors)
C: NH and N and O (has 1 N acceptor and 1 N donor)
“GONHNHerhea has many H’s” → so the one with more H = more hydrogen donors, which means that has to be G
The phosphodiester bond is a result of a condensation rxn between _____ of first nucleotide and ____ on 5’ carbon of 2nd nucleotide. It releases ____ as a byproduct.
3’ OH
OH in phosphoryl group
H2O
snRNAs and snRNPs participate in what process and how?
small nuclear RNAs and small nuclear ribonucleoproteins participate in spliceosome assembly
By recognizing 5’ and 3’ splice sites of introns and then catalyzing their removal
What is an isoform? How can it be made?
any 2 or more functionally similar proteins that have similar but NOT IDENTICAL AA sequence
can be made by translating RNA transcripts from same gene which have had different exons cut out via alternative splicing
restriction endonuclease cleaves what and where?
dsDNA
in the MIDDLE of DNA chain at or near specific sites
exonuclease cleaves what and where?
DNA
5’ or 3’ end, but NOT THE MIDDLE of DNA chain!
ribonuclease cleaves what and where? What does this result in?
RNA (DOES NOT CLEAVE dsDNA!!!)
phosphodiester bonds, degrading RNA into smaller components
deoxyribonuclease cleaves what and where? What does this result in?
DNA
phosphodiester bonds, degrading DNA into smaller components
