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Emily's M2M flashcards > Week 1 > Flashcards

Week 1 Flashcards

1
Q

What type of bond is found in Acetyl CoA?

A

C-S

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2
Q

What type of bond is found in ATP?

A

Phosphoanyhydride

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3
Q

What type of bond is found in Phosphocreatine?

A

P-N

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4
Q

What type of bond is found in Phosphoenol pyruvate?

A

C-O-P

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5
Q

What is a nucleoside?

A

A nucleotide without a phosphate

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6
Q

Which is more soluble- pyrimidine or purine?

A

Pyrimidine

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7
Q

Which is more soluble- Nucleotide or nucleoside?

A

Nucleotide

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8
Q

Which is more soluble- Nucleoside or base?

A

Nucleoside

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9
Q

What is the implication with Chargaff’s rule?

A

A-T, C-G

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10
Q

How does actinomycinD- doxorubicin act?

A

Blocks DNA replication through intercalation

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11
Q

What is the purpose of a topoisomerase?

A

Relax DNA so that it doesn’t supercoil

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12
Q

Why is RNA less stable than DNA?

A

RNA is susceptible to nucleophilic attack on the 2’OH

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13
Q

How does puromycin act?

A

It’s a nucleotide analogue that mimics the tRNA acceptor region and terminates translation

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14
Q

What are the three classes of RNA?

A

Structural, regulatory, informational

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15
Q

Transcription is __________ and ___________

A

Unidirectional and processive

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16
Q

What is the product of RNA Pol I?

A

rRNA

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17
Q

What is the product of RNA Pol II?

A

mRNA, snRNA, miRNA, lncRNA

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18
Q

What is the product of RNA Pol III?

A

tRNA, 5SRNA. . .

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19
Q

What are the three major steps in transcription?

A

Initiation, Elongation and Termination

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20
Q

What are the three major steps in initiation?

A
  1. Polymerase binds to promoter “closed complex”
  2. Pol. melts DNA and forms bubble “open complex”
  3. Pol catalyzes phosphodiester linkage of 2 rNTPs
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21
Q

During elongation, RNA polymerase travels which direction?

A

3’ -> 5’

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22
Q

What occurs during termination?

A

The Polymerase releases RNA and dissociates from DNA

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23
Q

Alpha amanitin is which type of inhibitor to RNA pol II?

A

Non-competitive

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24
Q

Alpha amanitin acts through which mechanism?

A

It blocks the RNA chain elongation by preventing translocation

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25
Q

How does Rifampicin act?

A

It binds RNA Polymerase and blocks the RNA exit channel

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26
Q

What is TFIIH important for?

A

Transcription and DNA repair

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27
Q

Mutations in TFIIH can cause

A

XP, Cockaynes syndrome and Trichothiodystr. . .

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28
Q

What are the three steps in adding the 5’ cap?

A
  1. Triphosphatase
  2. Guanylyltransferase
  3. Guanine 7 methyl transferase
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29
Q

Functions of the mRNA cap?

A
  1. Regulation of nuclear export
  2. Prevention of degradation by exonucleases
  3. Promotion of translation
  4. Promotion of 5’ proximal intron excision
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30
Q

What does over-expression of eIF4E cause?

A

Malignant transformation because it’s a cap binding protein which leads to increased translation

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31
Q

The 5’ splice site of the intron is recognized by base pairing to?

A

U1snRNA

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32
Q

The 3’ splice site of the intron is recognized by base pairing to?

A

U2snRNA

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33
Q

What are the two steps during splicing via a lariat intermediate?

A
  1. Attack by the branch point 2’OH @ the exon’s 3’ phosphate

2. Attack by the 3’OH of exon 1 on the 5’ phosphate of exon 2

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34
Q

What is the significance of Abnormal splicing of CD44?

A

It’s a signal of tumor metastasis that is useful for diagnosis and prognosis

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35
Q

What is the causal mechanism for Marfan’s syndrome?

A

Disruptive gene splicing in the fibrillin gene transcripts

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36
Q

What are the two steps in creating a PolyA Tail?

A
  1. Cleavage

2. Polyadenylation

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37
Q

Alpha Thalassemia- how does it happen?

A

Mutation of AAUAAA consensus sequence

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38
Q

How can cancer be created by the poly A site?

A

Shortening of 3’UTR and elongating of polyA tail leads to deletion of oncogenes and continued life of the cell

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39
Q

3’ end formation is coupled with?

A

Termination of transcription by RNA Pol II

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40
Q

What are the three types of excision repair?

A
  1. Nucleotide
  2. Base
  3. Mismatch repair
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41
Q

Nucleotide excision repair is

  1. good for
  2. What happens when it goes wrong?
A
  1. Thymine dimers

2. XP, CS and TTD

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42
Q

Base excision repair requires

A

glycosylases to recognize altered bases

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43
Q

Mismatch repair proteins in bacteria vs. mammalian counterparts

A

MutS and MutL vs. MSH and MLH

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44
Q

How does the MMR machinery recognize the new strand?

A

It is not yet methylated- in eukaryotes the MMR requires DNA nicks

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45
Q

What is the overarching goal of MMR?

A

Removal of the wrongly inserted base, not its mismatching partner.

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46
Q

What happens when MMR malfunctions

A

HNPCC

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47
Q

Lesion bypass usually fixes

A

excessive thymine dimers- not super effective as it’s really mutagenic

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48
Q

DNA replication is __________ and _____________

A

bidirectional and semiconservative

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49
Q

DNA replication in Prok vs. Euk

A

Prok- one site of origin on each chromosome

Euk- multiple site of origin on each chromosome

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50
Q

When helicases unwind the double helix ________ binds to each strand of DNA to hold it in place

A

single-strand binding proteins

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51
Q

DNA synthesis proceeds in which direction?

A

5’ to 3’

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52
Q

DNA synthesis requires what?

A

RNA primers

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53
Q

Prokaryotic DNA replication is carried out by two DNA polymerases
What are their names? Which is more important? Why?

A

DNA Pol I and DNA Pol III. DNA Pol III is more important because it has a sliding clamp that keeps it attached to the DNA template over a long distance- higher processivity

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54
Q

DNA Pol I’s purpose?

A

mediate replacement of RNA primers with DNA through it’s 5’ to 3’ exonuclease activity and 5’ to 3’ DNA polymerase activity

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55
Q

Eukaryotic DNA replication requires what?

A

three polymerases

one for primare and polymerase, one for lagging strands and one for leading strands

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56
Q

What is the function of primase?

A

Catalyzing the reaction needed to form the RNA primer during replication- it’s a DNA dependent RNA polymerase

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57
Q

What are the three activities of DNA Pol I in E. coli?

A
  1. 5’ to 3’ DNA polymerase activity requiring a 3’ OH primer and a DNA template strand
  2. a 5’ to 3’ exonuclease activity for RNA primer removal
  3. a 3’ to 5’ exonuclease activity for proofreading
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58
Q

What is the function of DNA ligase?

A

an enzyme that catalyzes the formation of phosphodiester bonds between a 3’ hydroxyl group and a 5’ phosphate group of two polynucleotide chains

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59
Q

What are three types of DNA control elements?

A
  1. TATA Box/ Initiator sequence
  2. Promoter Proximal Elements
  3. Enhancers
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60
Q

What is the difference between an enhancer and a promoter?

A

Promoters are about 20 bps and are about 200 bps upstream of transcription start sites whereas enhancers are 8-20 bps but can consolidate and be 100-200 bps long. Their location can vary upstream, downstream in the last exon or within an intron.

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61
Q

How does Beta Thalassemia occur?

A

Deficient production of Beta globin protein by ethyroid cells due to mutations in the B globin promoter

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62
Q

How does alpha Thalassemia occur?

A

Deletion of locus control region of B globin gene cluster

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63
Q

What is Hemophilia B Leyden?

A

X-linked clotting disorder due to inherited mutation in the DNA control element in the promoter of the Factor IX gene- alleviated during puberty due to active androgen receptor

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64
Q

What is Fragile X Syndrome?

A

CGG repeat in the 5’ region of the FMR 1 gene which facilitates methylation of the cytosine residues in CpG islands and transcriptional inactivation of the FMR1 gene

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65
Q

What are the two classes of Activators and repressors?

A
  1. Sequence specific DNA binding proteins

2. Co-factors

66
Q

Where do SSBP’s act?

A

They bind to promoter or enhancer elements to regulate transcription. They insert their alpha helices into the major groove of DNA

67
Q

Where do co-factors act?

A

They do not bind directly to DNA, but bind sequence-specific DNA binding proteins and affect transcription through the contact

68
Q

Sequence specific DNA binding proteins are modular, containing two major domains:

A
  1. DNA binding domain

2. Activation or repression domain

69
Q

What are the four families of DNA binding proteins?

A
  1. Homeodomain proteins
  2. Zinc-finger proteins
  3. Basic leucine zipper proteins
  4. Basic helix-loop-helix motif
70
Q

Homeodomain Protein examples

A

Hox family, Pit1, Msx

71
Q

Zinc-finger protein examples

A

estrogen receptor, androgen receptor, retinoic acid

72
Q

Basic leucine zipper protein examples

A

c-fos and c-jun

73
Q

bHLH examples

A

MyoD, myogenin, Myf5

74
Q

What causes craniosynostosis?

A

mutation in the homeodomain protein MSX2 which is required for proper craniofacial development

75
Q

What causes androgen insensitivity syndrome?

A

Mutations in the DNA binding domain or ligand binding domain of the androgen receptor (zinc finger DNA binding protein)

76
Q

What causes Waardenburg Syndrome type II?

A

Mutations in microphthalmia-associated transcription factor gene which encodes a bHLH DNA binding protein- it’s a transcription factor that plays a major role in the development of melanocytes

77
Q

How do transcriptional activators or repressors stimulate transcription?

A
  1. Regulate assembly of initiation complexes and rate of initiation of transcription
  2. Regulate changes in chromatin structure influencing the ability of general transcription factors to bind promoters
78
Q

What are the two classes or chromatin remodelling factors?

A
  1. DNA-dependent ATPases (SWI/SNF) which disrupt histone octamers and DNA
  2. Factors that reversibly modify histone through aceylation (HATs and HDACs)
79
Q

The N-termini of histones are rich in _______ residues

A

lysine

80
Q

How do HATS work?

A

They are co-activators which originally were thought to neutralize the positively charged ends and eliminate electrostatic interactions with DNA phosphates, but now we believe that it allows for the binding of specific transcription factors

81
Q

How do HDACs work?

A

The are co-repressors which were originally believed to help histones retain positive charge at N-terminal ends.

82
Q

How does Rubinstein-Taybi Syndrome occur?

A

results from mutations in one copy of the CREB binding protein gene (CBP). CBP is a transcriptional coactivator and is a HAT. Results in widespread transcriptional changes

83
Q

How does Leukemia occur?

A

Result of chromosomal translocations leading to gain of function fusion proteins- some of which involved fusions of transcriptional regulators with HATs or HDACs

84
Q

What are the two ways that transcriptional activators/repressors work?

A
  1. Interact with TFs/Pol II associated proteins to influence initiation of elongation of the primary transcript
  2. Interact with chromatin to regulate accessibility of DNA to Pol II transcriptional apparatus
85
Q

What are five ways that sequence-specific DNA binding proteins are regulated?

A
  1. The conformation of the DNA-binding protein can be altered by ligand binding
  2. Entry into the nucleus can be regulated
  3. The amount of transcription factor in the cell can be regulated
  4. DNA binding can be regulated
  5. Phosphorylation of the DNA-binding protein can alter various properties including protein degradation, recruitment of co-activators, and DNA binding.
86
Q

What are examples of ligand binding effects?

A

The nuclear receptor family of Zinc finger transcription factors work by binding to steroid hormones which can affect dimerization of receptor, recruitment of coactivators/repressor and translocation into the nucleus i.e. esotrogen receptor activation and glucocorticoid receptor activation

87
Q

How does estrogen induce transcriptional activity?

A

by causing ER dimerization

88
Q

How does Tamoxifen work?

A

it binds to ER and prevents the recruitment of HAT co-factors

89
Q

What is an example of regulation of nuclear entry?

A

NF-kB is usually held in the cytoplasm by IkB. if IkB gets phosphorylated, it gets degraded. Then NK-kB is released and moves into the nucleus where it turns on genes involved in inflammation.

90
Q

How does aspirin work?

A

Aspirin inhibits phosphorylation and degradation of IkB which prevents the translocation of NFkB to the nucleus which inhibits transcription of genes involved in the inflammatory response.

91
Q

What is an example of regulation of nuclear entry by NF-AT?

A

High intracellular calcium activates calcineurin’s phosphatase activity which dephos’s cytoplasmic NF-AT. This exposes the nuclear localization sequence, allowing NF-AT to enter the nucleus where it affects transcription of genes involve in immune response and in heart function.

92
Q

Who to the immunosuppressants cyclosporin and FK506 work?

A

They inhibit calcineurin thereby inhibiting NF-AT action

93
Q

What are examples of regulating amount of TF in cell?

A

Beta Catenin which in the absence of Wnt signaling is targeted for degradation through the ubiquitin-proteasome pathway via phosphorylation.

94
Q

What happens in the presence of Wnt signaling?

A

The Axin-APC-GSK3 complex is destabililzed, preventing phsophorylation of B-catenin and leading to an increase in the cytoplasmic pool of the protein. This allows some of the B-catenin to move into the nucleus where it interacts with the TCF family of transcription factors and promotes the expression of Wnt responsive genes.

95
Q

What’s an example of regulating TF in the cell using p53?

A

p53 is downregulated by binding to the MDM2 protein which masks its activation domain and targets is for destruction by the ubiquitin- proteasome pathway

96
Q

Example of regulating DNA binding

A

Id proteins- the Id family members negatively regulate DNA binding by heterodimerizing with other HLH proteins through their HLH domains, but preventing DNA binding due to their lack of a basic domain

97
Q

Example of how phosphorylation affects activity of trans-acting factors

A

CREB- a series of events initiated by the binding of a ligand to a guanine nucleotide binding protein coupled receptor induces the phosphorylation of the CREB protein which, while present on the DNA, is inactive to promote transcription unless phosphorylated. Once phosphorylated, the CREB protein recruits the histone acetyl transferas CREB which has intrinsic HAT activity and recruits RNA Pol II- leading to transcriptional activation of the gene.

98
Q

What is the mRNA start codon?

A

AUG

99
Q

How do the mRNAs and tRNAs interact?

A

the tRNAs base-pair directly to the codons in the mRNA through the tRNA’s anticodon loop

100
Q

What is the function of the Aminoacyl tRNA synthetases?

A

they are protein enzymes that put the right amino acid on the right tRNA. They are important because each identifies the right tRNA and puts on the correct amino acid. Each AA/tRNA has its own synthetase associated with it.

101
Q

What are the sizes of the ribosome subunits in bacteria and eukaryotic cells?

A

30S and 50S vs. 40S and 60S

102
Q

What are initiation factors?

A

proteins that bring the ribosome to the message and assist in getting the machinery assembled. 3 in bacteria and over a dozen in eukaryotes.

103
Q

What are elongation factors?

A

Proteins that deliver tRNAs and move the ribosome down the message.

104
Q

What needs to come together for successful translation?

A

mRNA, tRNA, aminoacyl tRNA synthetases, ribosomes, initiation factors, elongation factors and partners and termination/recycling factors

105
Q

What are termination/recycling factors?

A

proteins that end the process at a stop codon and dissociate the subunits so that they can be used again.

106
Q

What are the four steps in translation?

A
  1. initiation
  2. Elongation
  3. Termination
  4. Ribosome recycling
107
Q

What is the difference between translational initiation in bacteria and eukaryotes?

A

In bacteria the ribosome binds essentially right at the start codon due to the Shine-Dalgarno sequence and three initiation factors work to assemble the full ribosome. In eukaryotes, initiation factor eIF4E is required to bind to the 7-methyl guanosine cap on the 5’ end of the mRNA which leads to the binding of many other eIF’s. Then the ribosome scans down the message to find the AUG start codon. The large subunit joins the small the factors are released and the goal of initiation has been achieved.

108
Q

What is the goal of initiation of translation?

A

The goal is to assemble a ribosome with the start codon AUG and initiator methionine tRNA in the P-site ready to receive the next aa-tRNA in the A-site

109
Q

In addition to cap-dependent processes, there is a cap-independent process. What is it called and how does it work?

A

There are IRESs (internal ribosome entry sites) which are used by viruses to initiate translation after they shut down host cell cap-dependent synthesis.

110
Q

At which step in the translation process does the most regulation occur?

A

Initiation

111
Q

How does the peptide bond form?

A

The peptide bond forms when the protein chain moves from the P-site tRNA onto the A-site tRNA. Now the action of an elongation factor catalyzes the translocation.

112
Q

What molecule deliver the aa-tRNA to the A-site?

A

EF1A in eukaryotes and EF-Tu in bacteria

113
Q

What signals the start of termination?

A

The stop codon is detected by a recycling factor in the A-site

114
Q

How do recycling factors work?

A

They fit into the same space as a tRNA, but when they do, they trigger the termination of the peptide chain

115
Q

What is a missense mutation?

A

The codon is changed so it encodes a different amino acid

116
Q

What is a silent mutation?

A

The codon is changed, but the same amino acid is encoded

117
Q

What is a frame-shift mutation?

A

An addition or deletion of a nucleotide shifts the reading frame

118
Q

What is a nonsense mutation?

A

A mutation resulting in a premature stop codon

119
Q

What is a sense mutation?

A

The opposite of a nonsense mutation- now the stop codon is removed and the ribosome keeps going

120
Q

What are examples of DNA frameshift mutations that manifest as disease?

A

Hemoglobin Wayne and Hemoglobin Constant spring from a frame-shift and sense mutation respectively. Both lead to proteins with longer C-terminal tails and are associated with chronic anemia

121
Q

How can translation be regulated or altered?

A
  1. Regulation by varying the mRNA structure and sequence
  2. Regulation by altering the function of initiation factors
  3. Regulation by protein binding to the mRNA
122
Q

if pH < pKA, the ___________ form dominates

A

protonated

123
Q

If pH > pKA, the ____________ form dominates

A

deprotonated

124
Q

amino acids with non-polar aliphatic R groups

A

Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine

125
Q

amino acids with aromatic R groups

A

Tyrosine, Tryptophan, Phenylalanine

126
Q

amino acids with polar, uncharged R groups

A

Threonine, Serine, Cysteine, Proline, Asparagine, Glutamine

127
Q

amino acids with polar, positively charge R groups

A

Histidine, Lysine, Arginine

128
Q

amino acids with Polar and negatively charged R groups

A

Aspartate, Glutamate

129
Q

If you have hydroxyproline, you have what disease?

A

scurvy

130
Q

If you add an extra carbonyl to glutamate, you have

A

carboxyglutamate which results in vitamin K deficiency and trouble clotting

131
Q

N linked glycosylation?

A

sugars added to asparagine

132
Q

O linked glycosylation?

A

Sugars added to ser or thr

133
Q

How does Gleevec work?

A

competitively inhibits by binding to bcr-abl’s active site which means that the substrate can’t bind and the tumor cell can’t proliferate

134
Q

What is Bortezomib?

A

It’s a proteasome inhibitor used to treat multiple myeloma

135
Q

Which bond is the phi bond?

A

The amide- alpha carbon bond

136
Q

Which bond is the psi bond?

A

The carbonyl carbon- alpha carbon bond

137
Q

What are the functions of a peptide?

A

Hormones and pheromones (i.e. insulin and oxytocin)
Neuropeptides (i.e. substance P)
Antibiotics (polymyxin B for Gram plus and bacitracin for Gram minus)
Protection (i.e. amanitin in mushrooms, conotoxin in snails and chlorotoxin in scorpions)

138
Q

What are two examples of medically important peptides?

A

Vasopressin and Angiotensin II

139
Q

Features of the alpha helix?

A

Right handed screw- H bonds between CO of the n residue and the NH of the n+4 residue- residues 1 and 8 are on top of each other and all of the side chains are on the outside

140
Q

Who wants to help form an alpha helix?

A

small hydrophobic residues like leucine and alanine

141
Q

Who wants to break an alpha helix?

A

Proline and glycine

142
Q

What is an example of an alpha helix that’s important for life?

A

hemoglobin- mutations here cause thalassemia

143
Q

What is an example of a left-handed alpha helix?

A

Collagen- it’s important for collagen function- three left-handed helices intertwine into a right handed helix

144
Q

What are the two types of Beta sheets?

A

Parallel and anti-parallel

145
Q

Examples of alpha helices?

A

Structurally fibrous- keratin, myosin, toppomyosin, fibrinogen
Globular- hemoglobin and myoglobin

146
Q

How are beta sheets formed?

A

hydrogen bonds between the backbone of neighboring strands

147
Q

Examples of proteins composed mainly of beta pleated sheets?

A

Fibrous- spider silk and silk

Globular- Immunoglobulin, Firbroblast growth, pepsin, HIV Protease

148
Q

What is Circular Dichroism analysis?

A

CD measures the absorption difference of left and right circularly polarized light

149
Q

What are the features of the B turn?

A

180 degree turn accomplished over four amino acids and is stabilized by a hydrogen bond to the carbonyl oxygen of the first amino acid to the amide proton of the 4th amino acid proline (position 2) and glycine (position 3) are common

150
Q

What are the two major classes of proteins?

A

Fibrous and Globular

151
Q

What are the characteristics of a fibrous protein?

A

Typically insoluble and made from a single secondary structure

152
Q

What are the characteristics of a globular protein?

A

Water or lipid soluble

153
Q

What is X Ray Crystallography?

A

It’s a way to determine protein structure using electron density and diffraction data. The pro is that there are no size limits, the con is that crystallization is the rate limiting step

154
Q

What is Biomolecular NMR?

A

A method for determining protein structure using NMR. Pros are that you don’t need to crystallize the protein for the con is that we need very concentrated proteins and that it’s difficult for large proteins

155
Q

What are three examples of antibodies being used as drugs to inhibit protein-protein interactions and which diseases do they treat?

A

Bevacizumab (Avastin) Anti-VEGF for treatment of tumors
Infliximab (Remicade) Anti TNFalpha treatment of rheumatoid arthritis
Rituximab Anti-CD20 for B cell lymphoma

156
Q

What are Hsp70 and Hsp40 (DNAK and DNAJ in prokaryotes)?

A

They are chaperones which bind to the hydrophobic region to prevent aggregation- induced at high temps- they help transport proteins in their unfolded states

157
Q

What are GroES and GroEL?

A

chaperonin which uses ATP to fold proteins

158
Q

Why is peptide prolyl cis-trans isomerase important?

A

It activates calcineurin. Cyclosporin inhibits cyclophilin which is a PPI and serves as an immunosuppressant

159
Q

How is cystic fibrosis related to protein mis-folding?

A

The most common mutation is the deletion of F508 which leads to protein mis-folding

160
Q

What are the three major protein purification approaches?

A

Gel-filtration based on size
Ion-exchange based on charge differences
Affinity based on ability to bind to specific ligands

161
Q

What can you determine using Edman degradation?

A

The N-terminal sequence

162
Q

What’s the difference between a cofactor and a coenzyme?

A

Coenzymes have chemical groups that are used up- cofactors are not

Emily's M2M flashcards (1 decks)

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