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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
Q

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

A

Forms a bond by ATP hydrolysis

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26
Q

What is the approximation mechanism of enzyme catalysis?

A

Simply bringing reactants together in proximity and proper orientation

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27
Q

What is the covalent catalysis mechanism of enzyme catalysis?

A

Covalent bond formation between substrate and enzyme

Covalent bond: mutual sharing of electrons

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28
Q

What is the acid-base catalysis mechanism of enzyme catalysis?

A

Enzyme assisted proton transfer

Amino acids in the active site are acids or bases

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29
Q

What is the metal ion catalysis mechanism of enzyme catalysis?

A

Assists in electrophilic or nucleophilic interactions or bindsto the substrate (increasing binding energy)

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30
Q

What two things assist enzyme activity?

A

Cofactors and coenzymes

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31
Q

Why are water-soluble enzymes a dietary requirement?

A

They are precursors to coenzymes or are coenzymes themselves (Vitamin C). Coenzymes assist an enzyme in its catalytic activity.

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32
Q

What are the 9 water-soluble vitamins?

A 
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
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33
Q

Alanine

A

Ala, A, Hydrophobic, Neutral, Non-polar

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34
Q

Cysteine

A

Cys, C, Hydrophobic, Neutral, Polar

Disulfide bridge

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35
Q

Aspartic Acid

A

Asp, D, Hydrophilic, Negative, Acidic

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36
Q

Glutamic Acid

A

Glu, E, Hydrophilic, Negative, Acidic

37
Q

Phenylalanine

A

Phe, F, Hydrophobic, Neutral, Non-polar

38
Q

Glycine

A

Gly, G, Hydrophobic, Neutral, Non-polar
Smallest AA
No optical activity because no chiral carbon

39
Q

Histidine*

A

His, H, Hydrophilic, Neutral/Positive/Negative, Electrically charged, Can act as an acid or a base at pH 7

40
Q

Isoleucine

A

Ile, I, Hydrophobic, Netural, Non-polar

41
Q

Lysine

A

Lys, K, Hydrophilic, Positive, Electrically charged, Basic

42
Q

Leucine

A

Leu, L, Hydrophobic, Neutral, Non-polar

43
Q

Methionine

A

Met, M, Hydrophobic, Neutral, Non-polar

44
Q

Asparagine

A

Asn, N, Hydrophilic, Neutral, Polar

45
Q

Proline

A

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
Q

Glutamine

A

Gln, Q, Hydrophilic, Neutral, Polar

47
Q

Arginine

A

Arg, R, Hydrophilic, Positive, Electrically charged, Basic

48
Q

Serine

A

Ser, S, Hydrophilic, Neutral, Polar

49
Q

Threonine

A

Thr, T, Hyrdophilic, Neutral, Polar

50
Q

Valine

A

Val, V, Hydrophobic, Neutral, Non-polar

51
Q

Tryptophan

A

Trp, W, Hydrophobic, Neutral, Non-polar

52
Q

Tyrosine

A

Tyr, Y, Hydrophobic, Neutral, Polar

53
Q

What is an example of cooperativity and what does that mean for this molecule?

A

Hemoglobin exhibits cooperativity

When Hb binds O2 at 1 of its mers, it becomes easier for the next O2 to bind

54
Q

How does feedback regulation work?

A

A product of the reaction binds to an allosteric site and affects the catalytic activity. This can be either positive or negative.

55
Q

How does a competitive inhibitor affect enzyme catalysis?

A

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
Q

How does a noncompetitive inhibitor affect enzyme catalysis?

A

It binds to the Enzyme or the Enzyme-substrate complex at an allosteric site
Vmax decreases and Km is unchanged

57
Q

How does a mixed inhibitor affect enzyme catalysis?

A

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
Q

How does a uncompetitive inhibitor affect enzyme catalysis?

A

It binds to the Enzyme-substrate complex at an allosteric site
Km and Vmax are decreased

59
Q

What is the main difference in structure between purines and pyrimidines?

A

Purines have a double ring structure and pyrimidines have a single ring structure

60
Q

Which bases are purines vs. pyrimidines?

A

Purines: adenine & guanine
Pyrimidines: cytosine, thymine, & uracil

61
Q

How does DNA reannealing occur?

A

After a DNA strand has been denatured by high temperatures, the strand can reform when normal conditions return

62
Q

A polypeptide with a net positive charge at physiologic pH (~7.4) most likely contains amino acids with R groups of what type?

A

Basic R groups

63
Q

All biologically produced amino acids have the same “relative configuration” of what?

A

L configuration
R/S is “absolute configuration”
D/L is “relative configuration”

64
Q

What is the role of DNA helicase in DNA replication?

A

It unzips DNA at the replication fork

65
Q

What is the role of topoisomerases in DNA replication?

A

They relax super-coiling that results from unwinding the helix

66
Q

What is the role of single-stranded binding proteins (SSBPs) in DNA replication?

A

They bind to the separated strands of DNA to keep them from reannealing (from rewinding into the helix)

67
Q

What is the role of primase in DNA replication?

A

It synthesizes short RNA sequences (primers) that are temporarily attached for DNA polymerase to extend from

68
Q

What is the role of DNA polymerase in DNA replication?

A

It follows the replication fork, working to add new nucleotides in 5’→3’ direction; proofreads and removes incorrect nucleotides

69
Q

What is the role of DNA ligase in DNA replication?

A

It helps to anneal strands; joins Okazaki fragments

70
Q

What is the role of telomerase in DNA replication?

A

It lengthens the telomeres of linear eukaryotic DNA

71
Q

What does DNA polymerase III do in regards to mutations in the DNA strand during replication?

A

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
Q

What does DNA polymerase I do in regards to mutations in the DNA strand during replication?

A

DNA polymerase I can provide 5’→3’ exonuclease activity to repair mismatches in the direction of elongation

73
Q

How are mutations fixed after DNA replication has occurred?

A

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
Q

What would happen if a mutation in the amino acid sequence created a nonsense codon?

A

A nonsense codon is responsible for ending the polypeptide sequence. So this mutation would prematurely end the polypeptide.

75
Q

At what point during normal DNA replication is genetic material lost from the telomeres?

A

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
Q

What constitutes the phosphodiester bonds in DNA?

A

Covalently linked nucleotides

77
Q

Where does transcription occur?

A

Nucleus

The new RNA strand exits via nuclear pores

78
Q

Where does translation occur?

A

Ribosome

Ribosomes are abundant in the cytosol and the rough ER

79
Q

Which base pairing of nucleotides would require the most energy to break?

A

G:C (Guanine:Cytosine)

Guanine forms 3 hydrogen bonds with cytosine instead of 2 like A:U and A:T

80
Q

What is the role of mRNA?

A

Template RNA transcript, read in codons

81
Q

What is the role of rRNA?

A

Assists at the site of translation, hosts the association of tRNA

82
Q

What is the role of tRNA?

A

Hold a specific amino acid and an anticodon region for binding to their matching mRNA codon

83
Q

In what direction are new nucleotides added to a growing DNA strand?

A

5’ to 3’ direction

84
Q

What direction is the DNA template strand read by the RNA polymerase

A

The 3’ to 5’ direction; without proofreading

85
Q

What protects the ends of the RNA transcript from exonuclease degradation during transcription?

A

The addition of a 5’ Cap and a Poly A Tail

86
Q

What is the structure of a ribosome during translation?

A

The ribosome has a small and large subunit made of rRNA and proteins. It also has 3 active sites (E, P, & A)

87
Q

What are the roles of each of the active sites (3) in a ribosome during translation?

A

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
Q

What is the ordering of coiling within a chromosome?

A

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
Q

What is supercoiling and how can positively and negatively it affect DNA replication?

A

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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