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AA JW Science Review > KA Biomolecules > Flashcards

KA Biomolecules Flashcards

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Biology 101 flashcards
1
Q

Explain the Meselson–Stahl experiment.

A

E. coli were grown in a broth containing 15N (heavier than regular 14N). After several generations, the cells were transferred back to media with regular 14N. After each generation, the DNA was extracted and its density was compared to the density of DNA with pure 15N and with pure 14N.

The results showed that DNA is replicated in a semi-conservative manner.

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2
Q

Name and describe the 3 mechanisms by which a proto-oncogene may turn into an oncogene.

A
  1. Deletion or point mutation (leading to a hyperactive protein or an overexpressed protein).
  2. Gene amplification or increased mRNA stability (leading to an overexpressed protein).
  3. Chromosomal rearrangement (translocation of a gene to a nearby regulatory sequence, causing overexpression of the protein).
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3
Q

What is the 5’ cap made of?

A

The 5’ cap is made of 7-methylguanosine connected to the mRNA via a triphosphate linkage.

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4
Q

Describe the 2 steps involved in a generic enzyme-catalyzed reaction. Which step is rate-determining?

A

Step 1. E + S <–> ES

(the formation of the enzyme-substrate complex)

Step 2. ES <–> E + P

(the enzyme catalyzes the reaction, then releases the product)

Step 2 is the rate-determining step.

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5
Q

What is an operator?

A

A DNA sequence, downstream of the promoter, which serves as a binding site for a repressor protein.

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6
Q

What is special about histidine?

A

The pKa of its side chain is around 6.5, which is relatively close to physiological pH. For this reason, it is found in both the protonated and deprotonated forms in reasonable amounts. It is often found at the active site of a protein, which is useful because it can either stabilize or destabilize a substrate.

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7
Q

Explain lyase enzymes. What do they do?

A

Lyases catalyze the dissociation of a molecule. They break bonds without using water or oxidation. In order to do this, they must generate either a double bond or a ring structure in one of the products.

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8
Q

Define epigenetics, and give 2 examples of how it occurs (the mechanisms).

A

The study of heritable changes in gene activity that are not caused by changes in DNA sequence. In other words, it is when the same genotype produces multiple different phenotypes.

Examples:

  1. DNA methylation
  2. Histone modification
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9
Q

Define peptide bond, and describe its structure and geometry.

A

A peptide bond is an amide bond that forms between 2 amino acids. It is a rigid and planar bond. It is stabilized by resonance delocalization of the nitrogen’s lone pair to the carbonyl oxygen.

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10
Q

Name the 4 main “catalytic strategies” for how enzymes function.

A
  1. Acid/base catalysis - when the enzyme acts as an acid or base (helps with proton transfer).
  2. Covalent catalysis - when the enzyme forms a covalent bond with the substrate (helps with electron transfer).
  3. Electrostatic catalysis - when the enzyme helps stabilize charge (example = DNA polymerase has an Mg2+ cation to help stabilize the negatively-charged DNA).
  4. Proximity and Orientation Effects - enzymes help substrate molecules collide in the proper orientation.
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11
Q

Name the AAs that have hydrophobic alkyl side chains.

A

Glycine, alanine, valine, methionine, leucine, isoleucine, and proline.

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12
Q

What are base analogues? What do they do?

A

They are compounds that “look like” a normal base, and can get incorporated into a DNA strand, but then behave differently. Example = 5-bromouracil.

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13
Q

Name another function of telomeres, besides their “major” function.

A

They prevent chromosomes from sticking to each other.

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14
Q

What must happen before an mRNA is allowed to leave the nucleus?

A
  1. Its introns must be removed.
  2. It must receive a 5’ cap and a poly-A tail.
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15
Q

Name a few examples of tumor suppressors.

A
  1. DNA repair proteins
  2. Cell cycle repressors
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16
Q

Explain how disulfide bridges form. Explain what type of environment favors their formation.

A

They form between the thiol groups of 2 cysteine residues.

The thiol groups tend to be in their reduced form (-SH) when the protein is in reducing conditions, and in their oxidized form (-S-S-) in oxidizing conditions. Therefore, oxidizing conditions favor the formation of disulfide bridges.

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17
Q

What is a conservative mutation? What is a non-conservative mutation?

A

Conservative = a mutation that codes for a different AA, but one of the same type (example = changing from glutamate to aspartate).

Non-conservative = codes for a different type of AA.

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18
Q

Which type of amino acid, D or L, is found in humans? Are there any exceptions?

A

L.

There are not really any exceptions, but glycine has no D/L configuration since it is achiral.

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19
Q

What is special about cysteine?

A

It has a thiol group in its side chain. Therefore, it can form disulfide bridges.

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20
Q

What is the Shine-Dalgarno sequence?

A

It is the site on prokaryotic mRNA that the ribosome will recognize and bind to. After binding, the ribosome will slide downstream and scan for a start codon.

The Shine-Dalgarno sequence is ONLY found in prokaryotes.

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21
Q

What are silencers? What do they do?

A

They are regions of DNA that are bound by repressor proteins in order to silence gene expression. They make it so that RNA polymerase cannot bind to the promoter.

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22
Q

What are repressors? What do they do?

A

They are proteins that bind to the operator, and block RNA polymerase.

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23
Q

What is snoRNA? What does it do?

A

snoRNA = Small nucleolar RNA. It guides covalent modifications of rRNA, tRNA, and snRNA.

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24
Q

What is p53? What does it do?

A

It is a tumor-suppressor protein. Homozygous loss of its gene can lead to cancer.

p53 activates DNA repair proteins when DNA is damaged. p53 can also arrest the cell cycle at the G1 to S regulatory checkpoint. p53 initiates apoptosis if the DNA damage is irreparable.

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25
Q

What are snRNPs? What do they do?

A

snRNP = small nuclear ribonucleic protein. One example = spliceosome.

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26
Q

How do you calculate pI for an AA that does have an ionizable side chain?

A

For an AA with an acidic side chain, take the average of the 2 pKa values for the 2 carboxylic acid groups on the molecule (The main COOH group, and the COOH group on the side chain).

For an AA with a basic side chain, take the average of the 2 pKa values for the 2 amino groups on the molecule (the amine on the alpha carbon, and the basic part of the side chain).

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27
Q

Name and describe the 3 types of enzyme inhibitors.

A
  1. Competitive - Binds to the active site.
  2. Uncompetitive - Binds to ES complex.
  3. Mixed* - Can either bind to free enzyme, OR bind to the ES complex.

* Non-competitive is a special type of mixed

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28
Q

What is glycosylation? What is one common purpose/function of it?

A

Glycosylation = adding a carbohydrate group to a protein. Typically, glycosylation is done to proteins that will be embedded in the cell membrane. Common function of this = cell-cell communication / identification.

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29
Q

Name the 2 types of protein modifications. Give a few examples of each.

A
  1. Co-translational (occur during translation)

Example: Acetylation

  1. Post-translational (occur after translation)

Examples: Glycosylation, lipidation, phosphorylation, methylation, proteolysis, and ubiquitination.

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30
Q

Explain Vmax

A

Vmax is the maximum rate at which a catalyzed reaction can proceed. The enzyme velocity curve approaches Vmax but never actually reaches it. Vmax is a constant, assuming that enzyme concentration does not change.

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31
Q

Does DNA polymerase III have proofreading and/or endonuclease and/or exonuclease ability? If so, how? Be specific.

A

It has proofreading ability, because it has 3’ to 5’ exonuclease activity.

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32
Q

What is a mispairing mutation?

A

When 2 bases are paired incorrectly. Most commonly, this would mean:

A paired with C

G paired with T

It is more rare for 2 purines or 2 pyrimidines to pair together.

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33
Q

What are spliceosomes? What do they do?

A

They are large RNA-protein complexes that remove introns from pre-mRNA strands.

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34
Q

What are intercalaters? What do they do?

A

They are chemicals that insert themselves between the two strands of a DNA molecule (intercalate), causing it to deform. Example = ethidium bromide.

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35
Q

What are the 3 sites on a ribosome? What happens at each site?

A

E site - this is where the tRNA will exit the ribosome

P site - this is where the tRNA with the growing peptide chain will be found

A site - this is where the tRNA (with only one amino acid) will attach to the ribosome

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36
Q

What is the Michaelis-Menten equation?

A

V0 = ( Vmax [S] ) / ( Km + [S] )

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37
Q

What is a translocation mutation?

A

It is when a gene on one chromosome is swapped for another gene on a different chromosome.

The two chromosomes must be non-homologous (this is what sets translocation apart from crossing over during Meiosis).

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38
Q

Describe the state of the lac operon in a cell where lactose is absent.

A

The repressor protein is sitting at the operator site, blocking RNA polymerase. Therefore, the lac operon cannot be transcribed.

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39
Q

What is proteolysis? What is one common purpose/function of it?

A

Proteolysis = cutting / splitting a protein into 2 or more pieces. Proteolysis is sometimes used to activate certain proteins. Example = insulin must be cut twice in order to be activated.

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40
Q

What do the x and y axes represent in a Lineweaver-Burk plot?

What do the slope and the y-intercept represent?

A

X axis: 1 / [S]

Y axis: 1 / V0

Slope: Km / Vmax

Y-intercept: 1 / Vmax

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41
Q

What is “suicide inhibition”?

A

It is when a substance covalently binds to an enzyme, resulting in irreversible inhibition.

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42
Q

What is miRNA? What does it do?

A

miRNA = Micro RNA. It binds to a specific mRNA, resulting in gene silencing or degradation of the mRNA.

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43
Q

What is the equation that is used to make a Lineweaver-Burke plot?

A
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44
Q

Define Kcat

A

Kcat is equal to the maximum speed of a reaction, divided by the total enzyme available. This is known as the enzyme’s turnover number. This measures how many substrates an enzyme can turn into product per second, while working at maximum speed.

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45
Q

What is a transition mutation?

A

It is when an base is replaced with another base of its type (ex: a purine is replaced with another purine).

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46
Q

What is ubiquitination? What is one common purpose/function of it?

A

Ubiquitin is a small regulatory protein that can be added to proteins (ubiquitination). When a protein has ubiquitin attached to it, it is tagged for destruction.

47
Q

What is pI?

A

pI is the isoelectric point. It is the pH at which an AA has a net zero charge.

48
Q

What is phosphorylation? What is one common purpose/function of it?

A

Phosphorylation = adding a phosphate group to a protein. Typically, phosphorylation will cause a protein to become activated / energized. Common function of this = to help regulate protein activity.

49
Q

What is a zymogen?

A

An inactive form of an enzyme, that requres covalent modification in order to become activated.

50
Q

Name the AAs that have hydrophilic, basic side chains.

A

Histidine, lysine, and arginine.

51
Q

Define mitogen.

A

A substance that promotes or triggers mitosis.

52
Q

What is lipidation? What is one common purpose/function of it?

A

Lipidation = adding a lipid to a protein. Typically, lipidation is done to proteins that will be attached to the cell membrane. Common function of this = to help attach proteins to the PM via a lipid anchor.

53
Q

Is the intracellular environment considered to be “reducing conditions” or “oxidizing conditions”? What about the extracellular environment? What effect does this have, in terms of disulfide bridge formation?

A

The intracellular environment is a reducing environment, and the extracellular environment is an oxidizing environment (there are antioxidants inside the cell).

Disulfide bridges tend to be found more in the extracellular (oxidizing) environment, but not very much in the intracellular (reducing) environment.

54
Q

What is the “Two-Hit Hypothesis”?

A

The idea that both alleles of a tumor-suppressor gene must be mutated before the effect is manifested (contrast this with proto-oncogenes, where only one allele needs to be mutated to become overactive).

55
Q

Explain how RNA polymerase knows when to stop transcription, in both prokaryotes and eukaryotes.

A

In prokaryotes, the mRNA transcript includes a transcribed “terminator sequence”. This signal causes the RNA polymerase to detach from the DNA and release the transcript.

In eukaryotes, RNA polymerase transcribes a “polyadenylation signal sequence” (AAUAAA). Then, slightly downstream from this signal, proteins cut off the pre-mRNA from the polymerase.

56
Q

Define cooperativity.

A

When substrate binding changes substrate affinity for an enzyme or protein. In other words, when the affinity of a substrate for an enzyme is affected by the presence of other substrates already bound to the enzyme.

57
Q

What are activators? What do they do?

A

They are proteins that bind to a spot adjacent to a particular promoter. They enhance the interaction between RNA polymerase and the promoter.

58
Q

In prokaryotic translation, what is the first amino acid in the peptide chain? What is one interesting fact about it?

A

N-formylmethionine.

The human body recognizes N-formylmethionine (it means that bacteria are present) and triggers an immune response.

59
Q

What are nucleosomes?

A

Repeating units found in chromatin. They are made up of a DNA strand wrapped around a core of 8 histones.

60
Q

What is “single-copy DNA”?

A

DNA that is not repetitive.

It is responsible for containing most of the important genes in an organism.

It has a low mutation rate.

61
Q

Define exonuclease activity.

A

When an enzyme can remove a nucleotide from the end of a DNA strand.

62
Q

What are inducers? What do they do?

A

They are molecules that initiate gene expression by interacting with the repressor protein, causing it to detach.

63
Q

What is special about glycine?

A

The side chain is just a hydrogen, so the alpha carbon is not chiral. The tiny side chain makes it easy for glycine to rotate, making it a very flexibile amino acid.

Because of its flexibility, glycine is known as an “alpha helix breaker” because it disrupts the shape of alpha helices.

64
Q

Explain the difference between euchromatin and heterochromatin.

A

Euchromatin = uncoiled = allows transcription.

Heterochromatin = condensed = transcription is blocked.

For heterochromatin, think “H” = “Hibernating”

65
Q

Name the 6 types of enzymes, based on the types of reactions that they catalyze.

A
  1. Transferase (A + BX –> AX + B).
  2. Ligase (A + B –> AB).
  3. Oxidoreductase (A + B: <–> A: + B)
  4. Isomerase (A –> B)
  5. Hydrolase (A + H2O –> B + C)
  6. Lyase (A –> B + C)
66
Q

Name the AAs that have hydrophobic aryl side chains.

A

Phenylalanine and tryptophan.

67
Q

Name a few examples of endogenous and exogenous causes of DNA damage.

A

Endogenous:

Reactive oxygen species (superoxide anion, and peroxides).

Exogenous:

UV rays, gamma rays, and X rays.

68
Q

Describe the state of the lac operon in a cell where lactose is present.

A

Allolactose will bind to the repressor protein, causing it to be released from the operator site. Now, RNA polymerase is able to bind to the promoter sequence. Therefore, the lac operon can be transcribed.

69
Q

Explain the nucleotide excision repair mechanism. Explain the steps that occur.

A

The nucleotide excision repair mechanism is used when there is structural damage to the DNA (e.g. pyrimidine dimers).

Step 1 - An endonuclease will remove the damaged bases.

Step 2 - A DNA polymerase will add the proper nucleotides.

Step 3 - A DNA ligase will reconnect the backbone.

70
Q

What is methylation? What is one common purpose/function of it?

A

Methylation = adding a methyl group to a protein. Typically, histones will be methylated or demethylated, in order to help regulate transcription.

71
Q

Define Km

A

The concentration of substrate at which the reaction speed (V0) is half of the Vmax.

72
Q

Name the 5 main enzymes involved in DNA replication

A
  1. Helicase
  2. Primase
  3. Polymerase
  4. Ligase
  5. Topoisomerase
73
Q

What can happen to a cell that has extensive DNA damage? Name 3 mechanisms.

A
  1. Senescence (stops dividing)
  2. Apoptosis
  3. Unregulated cell division (can cause cancer)
74
Q

What is a proto-oncogene?

A

It is a gene that codes for a protein that normally promote cell growth.

75
Q

Explain the mismatch repair mechanism. Explain the steps that occur.

A

The mismatch repair mechanism is used when there is a mismatch in the DNA strand (e.g. A is paired with G).

Step 1 - They recognize a mismatch by sensing that the DNA strand is distorted.

Step 2 - They will cut the DNA backbone at the mismatch.

Step 3 - An exonuclease will remove the incorrect nucleotide (exo because now it has a free end to work with, thanks to the cut made in Step 2).

Step 4 - A DNA polymerase will insert the correct nucleotide.

Step 5 - DNA ligase will reconnect the backbone.

76
Q

What are enhancers? What do they do?

A

They are sites on the DNA that are bound to by activators in order to loop the DNA in such a way as to bring a specific promoter to the initiation complex.

77
Q

For the lac operon, what is the “inducer”?

A

Allolactose (an isomer of lactose)

78
Q

What is special about proline?

A

Its nonpolar side chain wraps around and forms a bond to the amine nitrogen, forming a 5-membered ring. The term for this is that proline has a secondary alpha amino group.

Because of its interesting structure, proline is known as an “alpha helix breaker” because it introduces kinks into alpha helices.

79
Q

Name the AAs that have hydrophilic, acidic side chains.

A

Glutamate and aspartate.

80
Q

Explain “gene silencing”.

A

DNA can be methylated by methyltransferase. This is a more permanent method of downregulating gene transcription. It occurs as cells differentiate from stem cells into more specialized cell types.

81
Q

What is the steady-state assumption?

A

We are assuming that the concentration of the enzyme-substrate complex (ES) is constant.

In other words, the rate of formation of ES = the rate of loss of ES.

82
Q

Name 3 common types of post-translational modification of proteins.

A
  1. Methylation
  2. Acetylation
  3. Glycosylation (addition of a sugar)
83
Q

What is a tumor-suppressor gene?

A

A gene whose protein product either stops the cell cycle, or promotes apoptosis.

84
Q

Explain cysteine vs cystine.

A

Cysteine refers to the reduced (-SH) form.

Cystine refers to the dimer of two oxidized cysteine amino acids (-S-S-).

Pretend that the extra “e” in cysteine stands for “electrons”, so the reduced one (cysteine) has more electrons.

85
Q

Name and describe 2 ways that peptide bonds can by hydrolyzed.

A
  1. Acid hydrolysis (with heat) - with strong acids. This results in nonspecific hydrolysis.
  2. Proteolysis - Digestion by proteolytic enzymes. This results in specific hydrolysis.
86
Q

Explain coenzymes and cofactors. How are they similar, and how are they different? Name 2 examples of each.

A

They are both necessary for certain enzymes to function.

Coenzymes are organic carrier molecules. Unlike coenzymes, cofactors are directly involved in the enzyme’s catalytic mechanism.

Coenzyme examples:

NADH is an electron carrier. Acetyl CoA is an acyl carrier.

Cofactor examples:

Mg2+, Ca2+, other minerals.

87
Q

What is chromatin made of?

A

DNA, histone proteins, and non-histone proteins.

88
Q

How is translation initiated in eukaryotes?

A

The ribosome binds to the 5’ cap, then slides downstream and scans for a start codon.

89
Q

What is different about the initiation of replication for a DNA polymerase vs an RNA polymerase.

A

DNA polymerases need a primer, but RNA polymerases don’t.

90
Q

How do you calculate pI for an AA that does not have an ionizable side chain?

A

pI = ½ ( pKa1 + pKa2 )

91
Q

Explain how histones can be modified in order to turn on or turn off gene transcription. In each case, what happens to the chromatin? Name the enzymes involved.

A

Histone proteins can be acetylated (by histone acetyltransferase). This leads to uncoiling of the chromatin (more transcription).

Histone proteins can be deacetylated (by histone deacetylase). This leads to the condensation of the chromatin (less transcription).

92
Q

What is “repetitive” DNA?

A

It is DNA that has a short, repeating sequence (for example: AGTTAGTTAGTT….).

It contains no genes (therefore it is not transcribed or translated).

It has a high mutation rate.

Example = telomeres.

93
Q

How do non-competitive inhibitors affect Km and Vmax? How does this appear on a Lineweaver-Burke plot?

A

They do not affect Km, but they decrease apparent Vmax. The lines on the plot will appear like this: high [I] will yield a greater slope AND a greater y-intercept. (all the lines will have the same x-intercept).

94
Q

Define homotropic and heterotropic.

A

A homotropic allosteric regulator is both a substrate and a regulator of its target enzyme.

A heterotropic allosteric regulator is not a substrate of the enzyme.

95
Q

What is a promoter?

A

A specific DNA sequence (includes the TATA box in eukaryotes) that serves as a binding site for RNA polymerase.

96
Q

What is a transversion mutation?

A

It is when an base is replaced with another base of the opposite type (ex: a purine is replaced with a pyrimidine or vice versa).

97
Q

What is the equation for catalytic efficiency?

A

Catalytic efficiency = Kcat / Km

98
Q

Name the AAs that have hydrophilic, neutral side chains.

A

Serine, threonine, asparagine, glutamine, cysteine, and tyrosine.

99
Q

What is the main difference between prokaryotes and eukaryotes, in terms of transcription initiation?

A

Unlike prokaryotes, eukaryotes require transcription factors.

100
Q

Does DNA polymerase I have proofreading and/or endonuclease and/or exonuclease ability? If so, how? Be specific.

A

It has proofreading ability.

It also has 5’ to 3’ exonuclease activity. It will remove the RNA primer at the end of replication.

101
Q

How are alpha helices stabilized? Be specific.

A

They are stabilized by hydrogen bonds.

Specifically, the carbonyl oxygen of the nth amino acid is the H-bond acceptor, and the hydrogen from the N-H amide group of the (n+4)th amino acid is the H-bond donor.

102
Q

How do uncompetitive inhibitors affect Km and Vmax? How does this appear on a Lineweaver-Burke plot?

A

They decrease apparent Km, and they decrease apparent Vmax. The lines on the plot will all have the same slope, but high [I] will have a greater y-intercept.

103
Q

What is another symbol that can be used to represent activation energy, besides Ea?

A

ΔG‡

(Delta)G(double dagger)

104
Q

How do competitive inhibitors affect Km and Vmax? How does this appear on a Lineweaver-Burke plot?

A

They increase apparent Km, but do not affect Vmax. The lines on the plot will all have the same y-intercept, but high [I] will have a greater slope.

105
Q

Describe the specificity of trypsin. In other words, where does it cut?

A

Trypsin cleaves peptide bonds on the carboxyl side of arginine and lysine residues, except when either is followed by proline.

106
Q

Name and describe all the genes in the lac operon.

A
  1. Lac Z - Codes for beta-galactosidase.
  2. Lac Y - Codes for lactose permease.
  3. Lac A - Codes for an enzyme that helps in lactose metabolism.
107
Q

Explain what happens when lysine gets acetylated.

A

The free -NH3+ at the end gets an acetyl group (-COCH3) added to it. This turns the amine into an amide, meaning it can no longer carry a positive charge.

108
Q

Picture the graph of an enzyme-catalyzed reaction. At what point during catalysis is the binding between enzyme and substrate the strongest? Why?

A

The transition state (the top of the “peak” in the graph). This is because the enzyme and substrate have “molded” together (induced fit).

109
Q

Where do reactive oxygen species come from?

A

They are a normal byproduct of the electron transport chain.

110
Q

Where do transcription factors bind to?

A

The operator sequence.

111
Q

What is snRNA? What does it do?

A

snRNA = small nuclear RNA. They help to process pre-mRNA in the nucleus. They can sometimes be associated with specific proteins, and form a complex called a snRNP.

112
Q

What is chromosomal inversion? What is the major effect of this?

A

It is when two genes on the same chromosome switch places.

This tends to affect how the genes are regulated.

113
Q

Name 3 violations of the central dogma.

A
  1. Reverse transcription - Retroviruses (information flows “backward” from RNA to DNA).
  2. RNA viruses - They can use RNA as a template to make a new RNA strand. Also, they don’t use DNA at all.
  3. ncRNA (Non-coding RNA) - tRNA and rRNA (these are not translated, so violate the central dogma).

AA JW Science Review (6 decks)

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