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BIO 111 > EXAM 2 review > Flashcards

EXAM 2 review Flashcards

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1
Q

What evidence did the experiment w/ nutritional mutants in Neospora provide?

A

-Genes specify enzymes

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2
Q

What is the Central Dogma of molecular biology?

A
  • How info passes through the cell
  • DNA to RNA to Protein
  • RNA to DNA (reverse transcription)
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3
Q

What are the characteristics of a Codon in the genetic code?

A
  • Consists of 3 bases

- Specifies SINGLE amino acid

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4
Q

What is the difference between Eukaryotic & Prokaryotic transcription in terms of number of RNA pol?

A
  • Eukaryotes have 3 RNA pol

- Prokaryotes only have 1

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5
Q

What kind of RNA can an Anticodon be found on?

A

-On tRNA

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6
Q

What does RNA pol bind to initiate Transcription?

A

-It binds to the Promoter

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7
Q

What is the codon in mRNA read by?

A

-It is read by the anticodon in a tRNA

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8
Q

What is a special characteristic of the Splicing process?

A

-It can join multiple mRNA’s in the same transcript

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9
Q

What is the job of the Peptidyltransferase enzyme?

A

-It transfers the growing peptide from a tRNA to the next amino acid

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10
Q

In comparing gene expression in Prokaryotes vs Eukaryotes:

A
  • Eukaryotic genes can make 1 protein
  • Prokaryotic genes make more than 1 protein
  • Both produce mRNA’s that are colinear w/ the protein
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11
Q

What would happen to the CCA codon if it was mutated?

A

-It would produce a silent codon

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12
Q

What will an Inversion mutation do?

A

-Only cause a mutant phenotype if the inversion breakpoints fall within a gene

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13
Q

What is the relationship between Mutations & evolution?

A

-Mutations can create new inheritable alleles

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14
Q

What occurs in Huntington’s disease?

A

-High levels of repeats of triplet sequence of DNA that encodes glutamate

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15
Q

What is true about individuals on autism spectrum or MSSNG data?

A
  • Majority of DNA changes occur in non-protein coding regions
  • 1% of genomic changes involve epigenetics
  • 25% of those w/ autism have seizure disorder
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16
Q

What would NOT occur in Central Dogma?

A
  • Polypeptides used to create other polypeptides

- DNA directly directing production of polypeptides

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17
Q

What are Operons in Prokaryotes?

A

-They are single promotor that transcribes multiple genes

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18
Q

What does it mean that the genetic code is Redundant?

A

-1 codon can encode for multiple amino acids

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19
Q

What is the role of RNA Haloenzyme?

A
  • It is the sigma factor that attaches to form initiation complex
  • Helps w/ phosphodiester bonds & accurate initiation for transcription by recognizing promotor
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20
Q

What is the Anti-sense strand of DNA?

A

-The template for production of RNA base pairs in transcription

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21
Q

What is the Sense strand of DNA?

A

-The coding strand

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22
Q

What is unique about Prokaryotes in terms of transcription & translation?

A

-Its coupled= once 5’ end of mRNA is freed up translation for proteins begins

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23
Q

What 3 things is true about tRNA?

A
  • Transcribed w/ the assistance of RNA pol 3 in nucleus
  • It has a 3’ acceptor stem
  • May be charged w/ the help of Aminoacyl-tRNA synthase=by covalently bonding an amino acid to tRNA
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24
Q

What is the role of Peptidyl-Transferase?

A
  • RNA enzyme in large ribosomal subunit

- Helps peptide bond formation for amino acids on growing amino acid chain in P-Site

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25
Q

What is the role of Spicosomes?

A
  • They cause intronic sequences to loop into Lariat Structure
  • Contains proteins that are in the nucleus
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26
Q

What are Splicosomes made of?

A
  • Small Nuclear RNA= snRNA

- Proteins

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27
Q

What causes the correct positioning of RNA on a ribosome for initiation in Eukaryotes?

A

-The 5’ methyl cap of mRNA

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28
Q

What requires energy input?

A
  • tRNA charging (ATP)

- Translocation & Charged tRNA delivery (GTP)

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29
Q

What is a Single Nucleotide Polymorphism?

A

-It is the one base difference between individuals in a population

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30
Q

What is Linkage Disequilibrium?

A

-Non-random association between a genotype at one locus and the genotype at another locus

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31
Q

How many naturally occurring Amino acids are there?

A

20

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32
Q

How many codons are there?

A

64

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33
Q

How many codons codes for amino acids?

A

61 which includes AUG for methionine

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34
Q

How many stop codons are there?

A

3

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35
Q

What are the stop codons?

A

UAA
UAG
UGA

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36
Q

How is the genetic code read as?

A

-Units for 3 bases

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37
Q

What is an exception to the universality of the coding language?

A

-Mitochondria & Chloroplasts read the code differently (don’t read stop codons as STOP, instead they are read as amino acids)

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38
Q

What are the 4 Key characteristics in Prokaryotic Transcription?

A
  • It involves only 1 RNA pol= 2 pieces
  • Transcription & Translation are coupled
  • 2 Initiation sites
  • mRNA doesn’t need a primer
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39
Q

What are the 2 pieces of the RNA polymerase for Prokaryotic Transcription?

A
  • Core Polymerase

- Holoenzyme

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40
Q

What is the role of the Core Polymerase?

A
  • Can synthesize RNA using DNA template (won’t be accurate)
  • Has 2 alpha, 1 beta, 1 beta’ subunit
  • It binds to DNA template & ribonucleotide triphosphate precursors
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41
Q

What are the 2 sites of DNA to initiate transcription in Prokaryotes?

A
  • Promotor

- Actual Start site

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42
Q

What is the role of the Promotor in Prokaryotic Transcription?

A

-It forms recognition & binding site for RNA pol

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43
Q

Where is the Promotor for Prokaryotic Transcription located?

A
  • Located upstream of start site

- 35nt and -10nt upstream

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44
Q

What is the overview of Prokaryotic Transcription?

A
  • RNA pol binds to the promotor @ -35nt upstream

- Then the RNA unwinds the helix at -10nt upstream

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45
Q

Why is Prokaryotic Transcription coupled to Translation?

A
  • It all occurs in the same site within the cell
  • Translation starts when the 5’ end of mRNA is available
  • This way the mRNA can contain multiple genes=encodes for multiple proteins
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46
Q

How does Termination occur in Prokaryotic Transcription?

A

-Occurs at stop markers

G-C pairs followed by A-U pairs= allows the RNA to form hairpin

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47
Q

What are the 4 key characteristics of Eukaryotic Transcription?

A
  • Uses transcription factors
  • Transcription takes place in Nucleus
  • Has 3 RNA pol each w/ own promotor (RNA pol 2 is the star)
  • mRNA goes through extensive modification
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48
Q

What are the 3 different polymerases that Eukaryotic Transcription uses?

A
  • RNA Pol 1
  • RNA Pol 2
  • RNA Pol 3
49
Q

What is the role of RNA pol 1?

A

-Transcribes rRNA

50
Q

What is the role of RNA pol 2?

A
  • Transcribes mRNA & SnRNA

- Consists of CTD subunit

51
Q

What is the role of RNA pol 3?

A

-Transcribes tRNA & sRNA

52
Q

What is the promotor for RNA pol 1?

A

-It is specific for each species

53
Q

What is the promotor for RNA pol 2?

A

-It is the Core promotor w/ TATA box

54
Q

What is the promotor for RNA pol 3?

A

-It is found within the actual gene

55
Q

What is the purpose of the CTD subunit in RNA pol 2?

A
  • Carboxyl Termination Domain

- Recruits other factors w/ polymerase to make Transcription Elongation Complex (7aa repeated 52x)

56
Q

What is the role of the Transcription Factors?

A

-Interact w/ RNA pol 2 to create Initiation complex @ promotor

57
Q

What does the Initiation complex for Eukaryotic Transcription consist of?

A
  • Core promotor w/ TATA box
  • Other transcription factors
  • RNA Pol 2 comes in & binds last
58
Q

What modifications does the mRNA go through in Eukaryotic Transcription?

A

5’ Methyl G cap

3’ poly a tail

59
Q

What is the purpose of the 5’ methyl G cap on mRNA?

A
  • Important for translation
  • RNA stability
  • Further processing
60
Q

What is Polydenylation?

A
  • Occurs in Eukaryotic Transcription

- Causes a transcript to be cleaved off of 3’ end & adds the Poly-A tail

61
Q

What is Transcription in general?

A

DNA to RNA

  • Uses RNA pol= has NO proofreading abilities
  • Consists of using Coding strand & Template strand
62
Q

What is the Coding strand for Transcription?

A
  • It is the mRNA strand produced w/ complementary bases to DNA strand
  • Known as the SENSE strand bc read from 5’ to 3’= helps direct polypeptide synthesis in translation
63
Q

What is the Template strand for Transcription?

A
  • It is 2nd strand of DNA

- Known as ANTI-SENSE strand bc read from 3’ to 5’

64
Q

What is Translation in general?

A

RNA to Proteins

  • takes place on ribosomes
  • tRNA is the star here
65
Q

What are the 6 types of RNA?

A
  • tRNA
  • rRNA
  • mRNA
  • Small RNA
  • srpRNA
  • snRNA
66
Q

What is the role of tRNA?

A
  • Used in translation bc used as intermediary between mRNA and amino acids
  • Helps position Amino acids on Ribosome
67
Q

What is the role of rRNA?

A
  • Critical to the function of Ribosomes

- found on both small & large ribosomal subunits

68
Q

What is the role of mRNA?

A

-Used in transcription

69
Q

What is the role of Small RNA?

A
  • Consists of siRNA and miRNA

- Both control gene expression

70
Q

What is the role of srpRNA?

A
  • Signal Recognition Particle for protein synthesis on RER=drags the proteins to RER for further modification
  • srpRNA consists of RNA & proteins
71
Q

What is Pre-mRNA splicing ?

A
  • Removal of introns (non-coding sequences)

- Then joining the Exons together (coding-sequences) to make mature mRNA

72
Q

What are the 4 steps for pre-mRNA splicing?

A

1) snRNA forms base pairs w/ 5’ end of intron & branch side (3’ end)
2) snRNPS associate to make a spliceosome
3) 5’ end of intron is removed & forms bond @ branching site and 5’ attaches to the 2’ OH to form lariat
4) Exons are joined & spliceosomes disassemble

73
Q

How does the Splicesome recognize the introns for removal?

A

-The introns begins w/ same 2 base sequence and ends w/ another 2 base sequence= tags them for removal

74
Q

When does pre-mRNA splicing occur?

A

-in the nucleus BEFORE export to the cytoplasm

75
Q

What is Alternative Splicing?

A
  • Primary transcript can be spliced into different mRNA by including different sets of exons
  • 1 gene can produce 25 distinct mRNA’s
76
Q

What is the Proteasome?

A

-Proteins produced from a genome

77
Q

What is Transcriptome?

A

-When RNA is produced from genome

78
Q

What are Introns?

A
  • Non-coding sequences= makes gene non-colinear w/ protein product which is why it needs to be removed
  • Makeup 24% of human genome
79
Q

What are Exons?

A

-Coding sequences that are expressed

80
Q

What are the 4 key characteristics of Ribosomes?

A
  • Key organelle in translation=can only ensure correct codon & anticodon pairing
  • Has 3 tRNA binding sites
  • It moves horizontally during translation
  • Has decoding & enzymatic funtions
81
Q

What are the 3 tRNA binding sites?

A

Read like 5’ E, P, A 3’

  • E site is where the uncharged tRNA exits
  • P site=Peptidyl site= Where the polypeptide chain grows
  • A site=Amincoacyl site= where the tRNA enters
82
Q

What are the 3 key characteristics of tRNA?

A
  • It can be folded into Leaf clover shape=has 2 functional ends
  • tRNA is charged when it carries an amino acid
  • Needs Aminoacyl-tRNA synthase to bind to amino acids
83
Q

What is the tRNA leaf clover shape?

A
  • Anticodon Loop

- Acceptor stem

84
Q

What is the role of the Anticodon loop of the tRNA leave clover shape?

A
  • It is located at the bottom of the leaf

- It base-pairs w/ codons in mRNA

85
Q

What is the role of the Acceptor stem?

A
  • It is located at the 3’ end
  • Is joined w/ the carboxyl terminus of an amino acid
  • Always read as 5’ CCA 3’
86
Q

What is tRNA charging reaction?

A
  • It joins the acceptor stem w/ the carboxyl terminus of an amino acid
  • Product= amino acid + charged tRNA
87
Q

What does a ribosome do with is decoding function?

A

-It decodes at a small subunit of the ribosome

88
Q

What does a ribosome do with its enzymatic function?

A

-Uses peptidyl transferase for peptide bond formation in the LARGE subunit

89
Q

What is the overview of Translation?

A

1) mRNA is threaded through ribosome
2) tRNA carrying the amino acid bind to ribosome
3) Ribosome & tRNA position amino acid= allows for peptide bond formation between new amino acid & growing peptide chain

90
Q

How does translation begin?

A

-The ribosome uses the first AUG it encounters in mRNA to signal intiation

91
Q

What is Translation like in Prokaryotes?

A

-They use an Initiation Complex= initiator charged w/ chemically modified methionine + small ribosomal subunit & mRNA strand

92
Q

How is the small ribosomal subunit positioned on mRNA for Prokaryotic translation?

A
  • Ribosomal Binding Sequence (RBS)

- Located on 5’ end & complementary to the 3’ end of small subunit rRNA

93
Q

What happens after the complex of mRNA, initiator tRNA and small ribosomal subunit are added in Prokaryotic Translation?

A

-The large ribosomal subunit is added

94
Q

What is translation like in Eukaryotes?

A
  • Similar to prokaryotes EXCEPT
  • their initiation amino acid is methionine
  • their mRNA’s lack RBS
  • Small subunit binds to mRNA by binding to it’s 5’ cap
  • more complex than prokaryotes
95
Q

What results from the fact that there are fewer tRNA’s than Codons?

A

-Wobble Pairing= tRNA’S wobbly on mRNA so that it can be read by more than one codon

96
Q

What does Termination of translation require?

A
  • STOP codons move into A site & recognized by released factors
  • Then proteins may be sent to RER w/ the help of SRP
97
Q

What is the structure of the growing peptide during Translation?

A 
Top= Amino Terminus (N terminus)
Middle= all amino acids bonded to eachother
Bottom= Carboxyl End (C terminus) which is bound to tRNA
98
Q

What happens in the Transcription bubble in both Prokaryotes & Eukaryotes?

A

-RNA nucleotides match up w/ their complementary bases on temporary DNA strand

99
Q

What is unusual about initiator tRNA?

A

-Carries modified amino acid fMET & only binds to ribosome on P site

100
Q

Why is Ubiquitin associated w/ toxic damage?

A

-Damaged proteins are tagged w/ ubiquitin for degeneration

101
Q

What are the 6 different points where Eukaryotes can regulate gene expression?

A
  • Initiation of Transcription
  • RNA splicing
  • Passage through nuclear membrane
  • Protein synthesis
  • RNA inference
  • Post-translational modification
102
Q

What is the difference between the mature mRNA in Prokaryotes & Eukaryotes?

A
  • Prokaryotes can specify for more than one protein

- Eukaryotes can only specify for one

103
Q

How could drug developers use RNA inference ina medical application?

A

-They could stop the production of a defective protein

104
Q

What are the 3 important functions of Gene Splicing?

A
  • They allow one coding sequence to be expressed differently according to each cell type
  • They change all gene types randomly
  • Add another layer to gene regulation
105
Q

What supresses Transcription?

A
  • They methylation of DNA at cytosines followed by guanines

- Treating histones w/ histone deacetylase

106
Q

What are the 3 characteristics of Epigentic changes?

A
  • They’re heritable
  • May alter patterns in DNA methylation
  • May alter gene expression
107
Q

What are the characteristics of Histamines?

A
  • It would effect nearby cells by initiating a signal transduction pathway
  • It is also a ligand
108
Q

What is the correct positioning of RNA on a ribosome in initiation aided by?

A

-the 5’ Methyl cap in eukaryotes

109
Q

What would happen to the cells that use chaperone proteins if the chaperone proteins are damaged?

A

-It would be unable to restore its tertiary structure

110
Q

How do you make histones positively charged?

A

-You would add Histone Deacetylase which decreases the rate of gene expression

111
Q

What are characteristics of Estrogen & Progesterone?

A
  • They have intracellular receptors

- Function to affect gene expression directly

112
Q

Why do Prader-Willi syndrome & Angelman syndrome have different phenotypes?

A

-Individuals affected by either syndrome have a deletion in chromosome 15 but have different imprint on homologue

113
Q

The receptor for Insulin-Like growth factor is a receptor tyrosine kinase. what happens when the factor binds to the receptor?

A
  • They autophosphorylate

- Initiate a signal transduction cascade

114
Q

What is true about Denaturation?

A

-It may be caused by an increase in salt concentration= causes protein to lose its tertiary structure

115
Q

If only one of your autosomal genes is only paternally imprinted, which allele do you express?

A

-Maternal allele

116
Q

What is Paracrine Signaling?

A

-It is the response that Histamine does that causes your finger to swell when you prick it

117
Q

Who received a nobel prize after their death?

A

-Ralph Steinman

118
Q

Who receive a nobel prize for identifying the alpha helix?

A

-Linus Pauling

119
Q

How many deaths were drug over dose deaths in 2016 in indiana?

A

1500

BIO 111 (20 decks)

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