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MCAT Bio/Biochem > Bio/Biochem > Flashcards

Bio/Biochem Flashcards

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1
Q

What is the absolute configuration of most naturally occurring amino acids?

A

Most naturally occurring amino acids are S, with the exception of cysteine

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2
Q

What determines the absolute configuration of an amino acid?

A

The spatial organization of substituents around the chiral alpha-carbon

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3
Q

What is a dipolar ion?

A

Zwitterion; an ion charged both positively and negatively

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4
Q

How is Cystine formed from Cysteine?

A

A covalent disulfide bond (bridge) is formed between the sulfur-containing R-groups on two Cysteine molecules

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5
Q

What type of bond is formed between two amino acids?

A

A peptide bond/linkage is formed between two amino acids between C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number 2) of another

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6
Q

What is a polypeptide?

A

A chain of many amino acids joined together by peptide bonds

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7
Q

How can a polypeptide be broken down into its individual amino acids?

A

Acid hydrolysis

Hydrolysis: the chemical of a compound due to a reaction with water

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8
Q

What is the role of proline in tertiary protein structure?

A

Because proline is cyclic, it is useful in accommodating tight turns in the folding of the protein

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9
Q

How are fragments from different parts of a polypeptide chain, that are sometimes located very far from each other, linked?

A

A disulfide bridge, formed between two cysteine residues, links the fragments. The cystine dimer created by the bridge, aids in the stabilization of the protein’s final confirmation.

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10
Q

What causes hydrophobic side chains to become buried within the interior of a polypeptide?

A

The hydrophobic effect brings together portions of the polypeptide to the interior, protecting them from an aqueous environment.

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11
Q

What are the four stages of protein structure?

A

Primary structure: the linear sequence of amino acids

Secondary structure: the local structure of the protein backbone; Alpha helices and beta sheets

Tertiary structure: the overall three-dimensional arrangement of the polypeptide chain in space

Quaternary structure: the association of several protein chains or subunits into a closely packed arrangement

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12
Q

What protein conformation will increase entropy when interacting with a solvation shell?

A

If the hydrophobic residues are on the interior, there is less disruption of water’s hydrogen bonding. This allows for less structure and higher entropy, which increases the protein’s conformational stability.

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13
Q

What does the 5 10 15 20 rule of pKas describe?

A

It is a mnemonic for the pKas of the four organic acid functional groups on amino acids. Carboxylic acid has a pKa of about 5, phenol has a pKa of about 10, alcohol has a pKa of about 15, and alpha hydrogen has a pKa of about 20

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14
Q

What separation techniques are used to isolate and analyze protein characteristics?

A

Isoelectric point (separation over a pH gradient) and Electrophoresis (separates based on size or charge)

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15
Q

At what pH does a protein have no net electric charge?

A

The isoelectric charge

pI = (pKa1 + pKa2)/2

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16
Q

How does a protein recognize its target for binding in non-covalent interactions?

A

Affinity and Specificity
Affinity: how readily the protein binds to its target
Specificity: the preferential binding of the target over other entities

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17
Q

What is a protein’s immune system response?

A

Proteins form antibodies which have a specific binding site that will readily bind to an antigen, so that its target is inactivated or tagged for immune response

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18
Q

By what mechanism does a motor protein perform mechanical work?

A

A motor protein can couple exergonic ATP hydrolysis to a confomational change that allows for interaction with the protein’s target substrate
ex. muscle contraction

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19
Q

How does an enzyme catalyze a biological reaction?

A

An enzyme will bind to a substrate and lower its transition state so that less activation energy is needed and the reaction proceeds faster

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20
Q

What type of reaction does the enzymes classification of oxidoreductases do?

A

Oxidation of a hydrogen (or electron) donor (loses) and reduction of the acceptor (gains)
Redox reactions OILRIG

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21
Q

What type of reaction does the enzymes classification of transferases do?

A

Moves a functional group from a donor molecule to an acceptor molecule

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22
Q

What type of reaction does the enzymes classification of hydrolases do?

A

Breaks a bond with hydrolytic clevage

chemical breakdown of a compound due to a reaction with water

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23
Q

What type of reaction does the enzymes classification of isomerases do?

A

Alter the geometry or structure of the reactant molecule (rearrangements)

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24
Q

What type of reaction does the enzymes classification of lyases do?

A

Breaks a bond with elimination to form a double bond (or ring) or adding to a double bond

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25
What type of reaction does the enzymes classification of ligases do?
Forms a bond by ATP hydrolysis
26
What is the approximation mechanism of enzyme catalysis?
Simply bringing reactants together in proximity and proper orientation
27
What is the covalent catalysis mechanism of enzyme catalysis?
Covalent bond formation between substrate and enzyme | Covalent bond: mutual sharing of electrons
28
What is the acid-base catalysis mechanism of enzyme catalysis?
Enzyme assisted proton transfer | Amino acids in the active site are acids or bases
29
What is the metal ion catalysis mechanism of enzyme catalysis?
Assists in electrophilic or nucleophilic interactions or bindsto the substrate (increasing binding energy)
30
What two things assist enzyme activity?
Cofactors and coenzymes
31
Why are water-soluble enzymes a dietary requirement?
They are precursors to coenzymes or are coenzymes themselves (Vitamin C). Coenzymes assist an enzyme in its catalytic activity.
32
What are the 9 water-soluble vitamins?
``` Non-B complex (1): Vitamin C B complex (8): B1 Thiamine, B2 Riboflavin, B3 Niacin, B5 Pantothenic acid, B7 Biotin, B9 Folic acid, B12 Cobalamin, B6 Pyridoxine ```
33
Alanine
Ala, A, Hydrophobic, Neutral, Non-polar
34
Cysteine
Cys, C, Hydrophobic, Neutral, Polar | Disulfide bridge
35
Aspartic Acid
Asp, D, Hydrophilic, Negative, Acidic
36
Glutamic Acid
Glu, E, Hydrophilic, Negative, Acidic
37
Phenylalanine
Phe, F, Hydrophobic, Neutral, Non-polar
38
Glycine
Gly, G, Hydrophobic, Neutral, Non-polar Smallest AA No optical activity because no chiral carbon
39
Histidine*
His, H, Hydrophilic, Neutral/Positive/Negative, Electrically charged, Can act as an acid or a base at pH 7
40
Isoleucine
Ile, I, Hydrophobic, Netural, Non-polar
41
Lysine
Lys, K, Hydrophilic, Positive, Electrically charged, Basic
42
Leucine
Leu, L, Hydrophobic, Neutral, Non-polar
43
Methionine
Met, M, Hydrophobic, Neutral, Non-polar
44
Asparagine
Asn, N, Hydrophilic, Neutral, Polar
45
Proline
Pro, P, Hydrophobic, Neutral, Non-polar Proline connects back to the amide; useful in tight turns Acts as a destabilizing element in secondary structures
46
Glutamine
Gln, Q, Hydrophilic, Neutral, Polar
47
Arginine
Arg, R, Hydrophilic, Positive, Electrically charged, Basic
48
Serine
Ser, S, Hydrophilic, Neutral, Polar
49
Threonine
Thr, T, Hyrdophilic, Neutral, Polar
50
Valine
Val, V, Hydrophobic, Neutral, Non-polar
51
Tryptophan
Trp, W, Hydrophobic, Neutral, Non-polar
52
Tyrosine
Tyr, Y, Hydrophobic, Neutral, Polar
53
What is an example of cooperativity and what does that mean for this molecule?
Hemoglobin exhibits cooperativity | When Hb binds O2 at 1 of its mers, it becomes easier for the next O2 to bind
54
How does feedback regulation work?
A product of the reaction binds to an allosteric site and affects the catalytic activity. This can be either positive or negative.
55
How does a competitive inhibitor affect enzyme catalysis?
It binds to the Enzyme at the active site and blocks the substrate Km increases, Vmax is unchanged It can be overcome with more substrate
56
How does a noncompetitive inhibitor affect enzyme catalysis?
It binds to the Enzyme or the Enzyme-substrate complex at an allosteric site Vmax decreases and Km is unchanged
57
How does a mixed inhibitor affect enzyme catalysis?
It binds to the Enzyme or the Enzyme-substrate complex at an allosteric site Vmax decreases and Km either increases or decreases It can be partially overcome with more substrate
58
How does a uncompetitive inhibitor affect enzyme catalysis?
It binds to the Enzyme-substrate complex at an allosteric site Km and Vmax are decreased
59
What is the main difference in structure between purines and pyrimidines?
Purines have a double ring structure and pyrimidines have a single ring structure
60
Which bases are purines vs. pyrimidines?
Purines: adenine & guanine Pyrimidines: cytosine, thymine, & uracil
61
How does DNA reannealing occur?
After a DNA strand has been denatured by high temperatures, the strand can reform when normal conditions return
62
A polypeptide with a net positive charge at physiologic pH (~7.4) most likely contains amino acids with R groups of what type?
Basic R groups
63
All biologically produced amino acids have the same "relative configuration" of what?
L configuration R/S is "absolute configuration" D/L is "relative configuration"
64
What is the role of DNA helicase in DNA replication?
It unzips DNA at the replication fork
65
What is the role of topoisomerases in DNA replication?
They relax super-coiling that results from unwinding the helix
66
What is the role of single-stranded binding proteins (SSBPs) in DNA replication?
They bind to the separated strands of DNA to keep them from reannealing (from rewinding into the helix)
67
What is the role of primase in DNA replication?
It synthesizes short RNA sequences (primers) that are temporarily attached for DNA polymerase to extend from
68
What is the role of DNA polymerase in DNA replication?
It follows the replication fork, working to add new nucleotides in 5’→3’ direction; proofreads and removes incorrect nucleotides
69
What is the role of DNA ligase in DNA replication?
It helps to anneal strands; joins Okazaki fragments
70
What is the role of telomerase in DNA replication?
It lengthens the telomeres of linear eukaryotic DNA
71
What does DNA polymerase III do in regards to mutations in the DNA strand during replication?
DNA polymerase III can exercise 3’→5’ exonuclease activity; it can proofread upstream (3’→5’ is the opposite direction of elongation) It can excise and correct the mismatched base
72
What does DNA polymerase I do in regards to mutations in the DNA strand during replication?
DNA polymerase I can provide 5’→3’ exonuclease activity to repair mismatches in the direction of elongation
73
How are mutations fixed after DNA replication has occurred?
A mismatch repair mechanism can fix mutations after replication has occurred. It is a concert of mismatch repair proteins that identify mismatched bases by way of characteristic distortion of the sugar-phosphate backbone. Once found, the incorrect match is excised (exonuclease), replaced (polymerase), and joined (ligase).
74
What would happen if a mutation in the amino acid sequence created a nonsense codon?
A nonsense codon is responsible for ending the polypeptide sequence. So this mutation would prematurely end the polypeptide.
75
At what point during normal DNA replication is genetic material lost from the telomeres?
During the joining of Okazaki fragments The RNA primer on the lagging strand during DNA replication cannot be converted to DNA by DNA polymerase and joined by DNA ligase because there is nowhere for these enzymes to bind, so it is degraded and the strand shortens
76
What constitutes the phosphodiester bonds in DNA?
Covalently linked nucleotides
77
Where does transcription occur?
Nucleus | The new RNA strand exits via nuclear pores
78
Where does translation occur?
Ribosome | Ribosomes are abundant in the cytosol and the rough ER
79
Which base pairing of nucleotides would require the most energy to break?
G:C (Guanine:Cytosine) | Guanine forms 3 hydrogen bonds with cytosine instead of 2 like A:U and A:T
80
What is the role of mRNA?
Template RNA transcript, read in codons
81
What is the role of rRNA?
Assists at the site of translation, hosts the association of tRNA
82
What is the role of tRNA?
Hold a specific amino acid and an anticodon region for binding to their matching mRNA codon
83
In what direction are new nucleotides added to a growing DNA strand?
5' to 3' direction
84
What direction is the DNA template strand read by the RNA polymerase
The 3' to 5' direction; without proofreading
85
What protects the ends of the RNA transcript from exonuclease degradation during transcription?
The addition of a 5' Cap and a Poly A Tail
86
What is the structure of a ribosome during translation?
The ribosome has a small and large subunit made of rRNA and proteins. It also has 3 active sites (E, P, & A)
87
What are the roles of each of the active sites (3) in a ribosome during translation?
E (exit) site: tRNA just released its amino acid chain, and the tRNA is free to exit the ribosome P (peptidyl) site: second binding site for tRNA Holds the tRNA during translation A (aminoacyl) site: space for tRNA with attached amino acid and anticodon to match the next codon in the mRNA sequence
88
What is the ordering of coiling within a chromosome?
DNA is wrapped around histones. Then a string of nucleosomes (eight histone complexes) is formed. Multiple nucleosomes are coiled together and these stack on top of each other to form chromatin. It is further looped and coiled to make a chromosome.
89
What is supercoiling and how can positively and negatively it affect DNA replication?
The histone-bound DNA, organized into nucleosomes, is further wrapped into coils called supercoils. Nucleosomes that are so tightly organized generally block transcription of their associated DNA. It reduces the space and allows for much more DNA to be packaged into the nucleus.

MCAT Bio/Biochem (2 decks)

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