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Molecular Biology Flashcards

1
Q

What is protein disulfide isomerase (PDI)?

A

Helps reduce improper disulfide bonds on proteins & correct them

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2
Q

What does peptide prolyl isomerase (PPI) do?

A

Helps catalyze transformation of proline bond from trans–>cis conformation in peptides

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3
Q

What are the protein accumulations called in Parkinson’s Disease?

A

Lewy bodies

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4
Q

What are the two classes of chaperone proteins?

A
  1. Hsp70/Hsp40

2. Chaperonin (GroEL/GroES)

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5
Q

What is the Bohr effect?

A

Blood in lung has higher pH than in metabolic tissues. At higher pH, O2 binds well; at lower pH; O2 releases well. = pH conditions encourage transfer efficiency

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6
Q

What are the major post-translational modifications of proteins that occur?

A

hydroxyproline, gamma-carboxyglutamate, glycoslylation, acetylation & methylation, reversible phosphorylation, & ubiquitination

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7
Q

What are the aromatic side chains?

A

Tyrosine, Phenylalanine, and Tryptophan

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8
Q

What are the basic side chains?

A

Histidine, Lysine, and Arginine

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9
Q

What is the role of Apolipoprotein E in Alzheimer’s Disease?

A

Apo E promotes the processing and clearance of AB42 (GOOD)

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10
Q

What is the role of presenilin in Alzheimer’s Disease?

A

Mutations in the gene can cause an increase in AB42 (BAD)

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11
Q

What does Vitamin C help with?

A

Addition of hydroxyl group to proline –> good collagen fibers

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12
Q

What disease does a Vitamin K deficiency cause?

A

Vit K helps with addition of carboxyl group to glutamate in proteins involved in clotting factors –> deficiency leads to clotting disorders

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13
Q

What are DNA control elements?

A

Local parts of the DNA sequence that control transcription of a gene. Transcription factors bind to these regions & regulate gene expression.

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14
Q

What is the TATA box?

A

Region 25-35 bps upstream of site of initiation of transcription. Directs binding of RNA polymerase II

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15
Q

What are promoter proximal elements?

A

Generally within 200 bps of initiation site. Bind transcription factors that are cell type-specific

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16
Q

What are enhancers?

A

Multiple control regions, generally 8-20 bps long. Can be tens of kilobases upstream or downstream from initiation site, last exon. Help to regulate in a cell type-specific way

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17
Q

Thalassemias

A

Variety of disorders that lead to anemia. Caused by mutations in DNA control elements, such as the promoter sequence for a beta-globin gene

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18
Q

Fragile-X Syndrome

A

1/1500 males, results in mental retardation, dysmorphic facial features, and post-pubertal macroorchidism. Overexpression of CGG repeats on FMR1 gene cause increased methylation of cytosine residues (CpG) and increased gene silencing

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19
Q

Hemophilia B Leyden

A

X-linked genetic disorder that causes clotting issues. Mutation in promoter sequence for Factor IX gene - males make 1% of normal amount. After puberty, androgen receptor binds overlapping site in promoter –> males make 60% of normal amount

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20
Q

What are transcription activators & repressors?

A

Proteins that are encoded by one gene that act on another gene to activate/repress transcription

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21
Q

What are the domains of a sequence specific DNA binding protein?

A
  1. DNA binding domain (sequence specificity)

2. Activation/repression domain (mediate protein-protein interactions, TF binding)

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22
Q

What are the two classes of activators and repressors?

A
  1. Sequence specific DNA binding proteins

2. Co-factors

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23
Q

What are the four major categories of sequence specific DNA binding proteins?

A
  1. Homeodomains
  2. Zinc finger
  3. Basic leucine zipper (Bzip)
  4. Helix-loop-helix
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24
Q

What is the difference between cofactors and general transcription factors?

A

Cofactors influence the RATE of transcription, while general transcription factors provide the pre-initiation complex needed to begin transcription

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25
Q

Combinatorial Control

A

bZIP, bHLH, & Zinc finger. All form heterodimers. Different combos = different strengths = different sites = different rates of expression

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26
Q

Waardenburg Type II Syndrome

A

Causes deafness, anomalies in pigmentation. A defect in the gene for a TF that causes the production of melanocytes.

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27
Q

Androgen Insensitivity Syndrome (AIS)

A

Boys are born with normal karyotype (XY) but have abnormal genitalia, do not grow 2dary sex characteristics, etc. Mutation on androgen receptor in either ligand-binding or DNA-binding domain –> androgen insensitivity

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28
Q

Craniosynostosis

A

Defect in the homeodomain of a DNA binding protein that binds to MSX2 gene –> gain of function –> premature closing of the skull in infants

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29
Q

Nucleosome

A

Fundamental repeating unit of chromatin = 147 bp of DNA wrapped around an octamer of histone proteins approximately 1.7 times

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30
Q

What are the two classes of chromatin remodeling factors?

A
  1. DNA-dependent ATPases

2. HATs & HDACs

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31
Q

What are HATs and HDACs?

A
  1. Histone acetyltransferases - transfer acetyl group onto N-terminal of lysine at end of histone = co-activators
  2. Histone deacetylase - remove acetyl group from histone = co-repressors
    = together, regulate recruitment of TFs
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32
Q

Rubinstein-Taybi Syndrome

A

Results in mental retardation, craniofacial abnormalities, etc. Results from mutation in gene coding for CBP (CREB binding protein), which is a HAT = transcriptional activator

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33
Q

Leukemia

A

Gain of function fusion proteins. Sometimes fusion of TFs with HDACs or HATs occurs –> altering of the regulators

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34
Q

What are 2 sequence specific DNA binding proteins whose entry into the nucleus is regulated?

A

NF-κB and NF-AT

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35
Q

What are 2 activators/repressors whose amount in the cell can be regulated?

A

beta-catenin & p53

36
Q

In what way can a DNA binding protein’s binding activity can be affected?

A

Id proteins – negatively regulate DNA binding by heterodimerizing with other HLH proteins through HLH domains, but prevent binding to DNA due to a lack of a basic domain

37
Q

Describe the mechanism of a phosphorylation of a DNA binding protein that affects transcription

A

Ligand binding G protein –> phosphorylation of CREB –> CREB recruits the HAT CBP (CREB binding protein) –> recruits RNA Pol II –> transcriptional activation

38
Q

Give an example of direct reversal repair of DNA

A

MGMT - methylguanine methyltransferase. Removes the methyl group from O6-methylguanine –> repairs DNA nucleotide

39
Q

What does excision repair of DNA take advantage of?

A

The double-stranded nature of DNA - uses correct strand to repair incorrect strand

40
Q

What are endonucleases?

A

They cleave the phosphodiester bonds within a polynucleotide chain

41
Q

What are exonucleases?

A

They cleave nucleotides off the end of a polynucleotide chain

42
Q

What are the 3 types of excision repair?

A

Nucleotide excision repair (NER), base excision repair (BER), and mismatch repair (MMR)

43
Q

Explain nucleotide excision repair

A

Removes damage that distorts the DNA

  1. Multi-protein complex binds to either site of the damaged DNA
  2. Helicases unwind (thru TFIIH complex)
  3. Endonucleases cut through sugar-phosphate bond; remove 30-bp oligonucleotide
  4. DNA polymerase fills in the gap; DNA ligase binds
44
Q

Explain base excision repair

A

Removes DNA damage that doesn’t distort the DNA duplex.

  1. Glycosylase hydrolyzes N-glycosidic bond, removes base = AP site.
  2. AP endonuclease (APE1) hydrolyzes sugar-phosphate bond 5’, then 3’, and the sugar-phosphate complex is removed.
  3. DNA polymerase adds correct nucleotide; DNA ligase seals.
45
Q

What is base excision repair initiated by?

A

GLYCOSYLASE - because it cuts out the base at the N-glycosidic bond, or where the N of the base bonds with the sugar. Thus, base excision repair

46
Q

What are two ways NER recognizes DNA damage?

A

Global genome NER (repairs whole genome; defects = XP) and transcription-coupled NER (repairs transcribed regions; defects = Cockayne Syndrome)

47
Q

What are human diseases caused by defects in NER?

A

Xeroderma pigmentosum, Trichothiodystrophy, and Cockayne Syndrome

48
Q

What does mismatch repair (MMR) do?

A

Repairs errors made by DNA polymerase during replication

49
Q

What are the protein complexes that initiate MMR?

A

E. coli: MutL & MutS

Humans: MLH & MSH

50
Q

How does MMR know which strand is new in bacteria and eukaryotes?

A

Bacteria: the parent strand is heavily methylated - so the non-methylated strand is new
Eukaryotes: there are more nicks in the new strand

51
Q

How does MMR work?

A

MutL/MutS or MLH/MSH complex run along newly synthesized DNA, find error. Helicases unwind DNA, endonucleases chew out fragment, DNA polymerase refills, DNA ligase seals.

52
Q

What disease is caused by mutations in the MMR machinery?

A

Hereditary non-polyposis colorectal cancer (HNPCC)

53
Q

What is the major enzyme for DNA replication, and why?

A

DNA polymerase III, because it has a sliding clamp that keeps it attached to DNA over long distances

54
Q

What does DNA polymerase I do?

A
  1. Performs clean up functions during DNA replication & repair
  2. REMOVES RNA PRIMERS from burgeoning DNA strand - has 5’-3’ exonuclease and 5’-3’ polymerase activity
  3. Also has 3’-5’ exonuclease activity, along with DNA pol III
55
Q

What is XPB?

A

An ATP-dependent DNA helicase, that’s part of the TFIIH transcription factor complex.

Plays a role in normal basal transcription and NER.

56
Q

What are gout and Lesch-Nyhan Disease caused by?

A

Buildup of purines in our tissues. Purines are the least soluble nucleic acid compound –> cause gross defects in tissues

57
Q

What is the difference between a nucleotide and a nucleoside?

A 
Nucleotide = has a phosphate, base, & sugar
Nucleoside = no phosphate. Only has base & sugar
58
Q

How does doxorubicin (actinomycin) work?

A

It’s an intercalating agent - it inserts a 3-ring structure into the DNA, causing dramatic structural effects –> changes in transcription & replication.
Interferes with topoisomerases = anti-cancer drug

59
Q

What does cisplatin do?

A

It’s a base alkylating agent –> forms large covalent adducts to DNA that are not easily repaired. Chemotherapeutic drug.

60
Q

What are some examples of structural RNAs?

A

tRNA, rRNA, snoRNA, snRNA

61
Q

What are some examples of information-containing RNAs?

A

mRNA

62
Q

What are some examples of regulatory RNAs?

A

miRNA, siRNA

63
Q

What does puromycin do?

A

It’s an antibiotic. Mimics the 3’ acceptor end of a tRNA that has an amino acid. It binds in a ribosome as the ribosome is translating & covalently attaches to a growing polypeptide chain –> terminates chain, prevents completion of translation.

64
Q

What do ATM & ATR do?

A

They are essential protein kinases used during DNA damage checkpoints, which stop the cell cycle when DNA is damaged in order to allow for DNA repair. They signal to p53, which can regulate division or apoptosis if necessary

65
Q

Name the 4 main RNAs and their functions

A

Pol I: rRNA
Pol II: mRNA (has CTD domain - unique)
Pol III: tRNA
E. coli RNA pol: all E. coli RNA

66
Q

How does α-amanitin work?

A

It’s a toxin found in mushrooms. Binds to RNA pol II at the site of the bridge helix. Prevents translocation, elongation of the growing mRNA chain –> kills you

67
Q

How does rifampicin work?

A

It prevents transcription in bacteria by binding to bacterial RNA polymerase and blocking the RNA exit channel

68
Q

What does TFIIH do?

A
  1. Basal transcription factor
  2. Participates in NER
  3. XPD acts as helicase
  4. CDK 7 phosphorylates CTD on RNA pol II during promoter clearance

Mutations cause XP, Cockayne’s Syndrome, & Trichothiodystrophy

69
Q

What are the 3 major ways in which most mRNAs are processed?

A
  1. Capping (Adding a 5’ cap)
  2. Splicing (Removal of introns)
  3. Cleavage/polyadenylation (Addition of poly-A tail to 3’ end)
70
Q

What is the spliceosome composed of?

A

pre-mRNA, over 100 proteins, and 5 snRNAs

71
Q

What are the functions of the 3 different U snRNA proteins?

A

U1 snRNA = recognizes 5’ site (GU) of intron to be spliced out
U2 snRNA = recognizes branch point (A) of intron (branch point is before AG 3’ end sequence)
U2AF snRNA = recognizes AG end point at 3’ end of intron

72
Q

What are aminoacyl tRNA synthetases?

A

Protein enzymes that put the right amino acid on the right tRNA

73
Q

What is the peptidyl transferase center?

A

Catalyzes peptide bond formation within the ribosome

74
Q

What does eIF4E do?

A

It’s the 5’ cap-binding protein that initiates translation of an mRNA sequence.
Also recruits eIF4G

75
Q

How does rapamycin work?

A

mTOR induces phosphorylation of eIF4E binding proteins –> the 4E-BPs then do not bind eIF4E –> eIF4E can then bind to 5’ cap, initiate translation

Under stress conditions, 4E-BPs will be dephosphorylated –> prevent binding of eIF4E –> prevent translation. Rapamycin also induces dephosphorylation of 4E-BPs

76
Q

How does interferon work?

A

Broad strokes: interferon is produced by a cell under stress, sent to neighboring cells, that mount antiviral defense systems.

Cellular: eIF2-alpha is critical to binding of initiator tRNA to ribosome. Interferon phosphorylates eIF2-alpha. When eIF2-alpha is phosphorylated, process does not occur –> translation & viral protein synthesis shuts down.

77
Q

What is a holoenzyme?

A

An enzyme complexed together with its cofactors/coenzymes

78
Q

In enzyme kinetics, what is Km?

A

the substrate concentration when enzyme is at half velocity

79
Q

In enzyme kinetics, what is Kcat?

A

“turnover rate” = number of substrate molecules turned into product, per enzyme molecule, per second

80
Q

What does NF-κB do?

A

It’s a DNA binding protein that normally is located in the cytoplasm. Stays in cytoplasm through being bound by IκB. Phosphorylation of IκB degrades it, which allows NF-κB to move into nucleus & transcribe a series of inflammatory response genes. Aspirin works to prevent phosphorylation of IκB.

81
Q

How is NF-AT regulated?

A

High intracellular calcium activates calcineurin’s phosphatase activity, which dephosphorylates NF-AT. NF-AT is then free to move into the nucleus and transcribes genes involved in heart function, immune response

82
Q

What effect does cyclosporin have?

A

Cyclosporin inhibits calcineurin, which thus cannot dephosphorylate NF-AT –> inhibit NF-AT action

83
Q

What are 5 sources of DNA double-stranded breaks?

A
  1. Endogenous
    a. immune system rearrangements
    b. DNA replication (single-strand breaks)
    c. Successful meiosis
  2. Exogenous
    a. Ionizing radiation [cosmic rays and soils]
    b. Medical imaging and treatments
84
Q

Explain non-homologous end joining (NHEJ) double-stranded break repair

A
  1. Initiates with recognition of the DS break by Ku
  2. Ku recruits DNA-PKcs
  3. Nuclease removes damaged DNA if there is damage (Artemis complex)
  4. Polymerase fills gaps
  5. Repair with ligase: LIG-4
85
Q

Explaing homologous end repair in a DS break

A
  • perfect repair
  • limited to S and G2 of cell cycle
  • requires sister chromatid (sister homologue)
    o uses the sister chromatid in mitotic cells; uses homologue in meiotic cells
  • KEY STEP: exonuclease degrades 5’ end
  • 3’ end of strand invades the sister chromatid
  • now has template for synthesis, can keep going until it gets past the break
86
Q

What protein catalyzes homologous DS break repair during meiosis?

A

Spo11

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