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Genetics & Evolutionary Biology > Transcription and Translation > Flashcards

Transcription and Translation Flashcards

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1
Q

Where does genetic information usually flow?

A
  • From DNA to DNA during its transmission from generation to generation
  • From DNA to protein during its phenotypic expression in an organism
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2
Q

What steps are involved in the transfer of genetic info from DNA to protein?

A
  • Transcription, the transfer of the genetic information from DNA to RNA
  • Translation, the transfer of information from RNA to protein
  • AKA the Central Dogma
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3
Q

Draw and label a diagram of the process of Central Dogma.

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

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4
Q

How does transcription and translation work in prokaryotes?

A
  • The primary transcript is equivalent to the mRNA molecule

- The mRNA codons on the mRNA are translated into an amino acid sequence by the ribosomes

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5
Q

How does transcription and translation work in Eukaryotes?

A
  • The primary transcript (premRNA) is a precursor to the mRNA
  • The pre-mRNA is modified at both ends, and introns are removed to produce the mRNA
  • After processing, the mRNA is exported to the cytoplasm for translation by ribosomes.
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6
Q

Study the diagrams of transcription and translation in prokaryotes and eukaryotes.

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

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7
Q

What are the general features of RNA synthesis?

A

Similar to DNA synthesis except

  • The precursors are ribonucleotide triphosphates.
  • Only one strand of DNA is used as a template.
  • RNA chains can be initiated de novo (no primer required).
  • The RNA molecule will be complementary to the DNA template strand and identical (except that uridine replaces thymidine) to the DNA nontemplate strand.
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8
Q

Which strand is the mRNA strand identical to?

A
  • The non-template strand

- the strand that runs 5’ to 3’

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9
Q

Study the process of the transcription and translation of mRNA

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

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10
Q

What is RNA polymerase?

A
  • RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription.
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11
Q

What does RNA polymerase do?

A
  • RNA synthesis is catalyzed by RNA polymerases and proceeds in the 5’ →3’ direction
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12
Q

What are some differences between RNA and DNA synthesis?

A
  • Nucleotide sugar is ribose not 2-deoxyribose

- Uridine (base = uracil) replaces thymidine (base = thymine)

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13
Q

What are promoters?

A
  • In genetics, a promoter is a region of DNA that leads to initiation of transcription of a particular gene.
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14
Q

How is RNA synthesis initiated?

A
  • RNA polymerases bind specific nucleotide sequences called promoters, and helped by transcription factors initiate RNA synthesis at transcription start sites near the promoters
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15
Q

Where does RNA synthesis occur?

A
  • RNA synthesis takes place within a locally unwound segment of DNA, sometimes called a transcription bubble, which is produced by RNA polymerase
  • This allows a few nucleotides in the template strand to base-pair with the growing end of the RNA chain
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16
Q

What was on summary slide 1?

A
  • In eukaryotes, genes are present in the nucleus, whereas polypeptides are synthesized in the cytoplasm.
  • Messenger RNA molecules function as intermediaries that carry genetic information from DNA to the ribosomes, where proteins are synthesized.
  • RNA synthesis, catalyzed by RNA polymerases, is similar to DNA synthesis in many respects.
  • RNA synthesis occurs within a localized region of strand separation, and only one strand of DNA functions as a template for RNA synthesis.
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17
Q

What are the three stages of transcription in prokaryotes?

A
  • Initiation of a new RNA chain
  • Elongation of the chain
  • Termination of transcription and release of the nascent RNA molecule
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18
Q

Study the diagram of RNA polymerase function and the diagram of Transcription in prokaryotes.

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

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19
Q

What is the difference between DNA polymerase and RNA polymerase?

A
  • DNA polymerase is in replication

- RNA polymerase is in transcription

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20
Q

Where are the transcription regions in prokaryotes?

A
  • Upstream: regions located toward the 5′end

- Downstream: regions located toward the 3′end

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21
Q

What are the numbering of transcription units?

A
  • The transcript initiation site is +1
  • Bases preceding the initiation site are given minus (–) prefixes and are referred to as upstream sequences.
  • Bases following (relative to the direction of transcription) the initiation site are given plus (+) prefixes and are referred to as downstream sequences.
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22
Q

What is a consensus sequence?

A
  • A sequence of DNA having similar structure and function in different organisms.
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23
Q

What is a recognition sequence?

A
  • A DNA sequence to which a structural motif of a DNA binding domain exhibits binding specificity
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24
Q

What are the consensus & recognition sequences in an E. coli promoter?

A
  • Consensus sequences: -10 sequence and -35 sequence

- Recognition sequence: -35 sequence

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25
Q

Why are the consensus and recognition sequences important?

A
  • These DNA sequences are recognised by the transcription apparatus and are required for transcription to take place
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26
Q

What do the consensus and recognition sequences do?

A
  • The -35 sequence is initially recognised and bound by sigma (σ ) subunit, used for orientation
  • The -10 (AT-rich) facilitates the unwinding of the DNA, aka the “TATAA box”
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27
Q

Why is the “TATAA box” important?

A
  • The -10 sequence is composed of T’s and A’s therefore it easiest to have a point of origin start here.
  • It is where unwinding occurs
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28
Q

Study the diagram of the E.coli promoter.

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

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29
Q

Give an example of how DNA is transcribed into mRNA using the -10 and -35 sequences

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

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30
Q

When does termination occur?

A
  • Termination of RNA chains occurs when RNA polymerase encounters a termination signal
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31
Q

What is Rho?

A
  • A type of protein
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32
Q

What are the two termination signals in E.coli?

A
  • Rho-dependent terminator —require a protein factor (ρ, or “Rho”), still being studied by scientists
  • Rho-independent terminators—do not require ρ
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33
Q

Why are we only focusing on Rho-independent terminators?

A
  • Rho-independent termination better understood due to the conserved nature of the DNA sequences
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34
Q

What is the structure of Rho-independent terminators?

A
  • GC-rich region followed by 6 AT base pairs

- RNA chains with GC-rich regions form hairpin structures that impede movement of RNA polymerase

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35
Q

Study the diagram of the termination process of RNA.

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

36
Q

What actions happen simultaneously in regard to mRNA?

A
  • Since mRNA molecules are synthesized, translated, and degraded in the 5′to 3′direction, all three processes can occur simultaneously on the same RNA molecule
37
Q

What was on summary slide 2?

A
  • RNA synthesis occurs in three stages: (1) initiation, (2) elongation, and (3) termination.
  • RNA polymerases—the enzymes that catalyze transcription—are complex multimeric proteins.
  • Promoters are DNA sequences recognised by the transcription apparatus and are required for transcription to initiate and take place
  • The covalent extension of RNA chains occurs within locally unwound segments of DNA.
  • Chain elongation stops when RNA polymerase encounters a transcription-termination signal.
38
Q

What does the codon AUG encode for?

A
  • AUG encodes for the amino acid Methionine
39
Q

What are the additional features of Eukaryotic transcription that prokaryotes don’t have?

A
  • 7-methyl guanadine cap added to the 5ʹ of the primary transcript
  • Poly(A) tail added to the 3ʹ of the primary transcript
  • Removal of intron sequences
40
Q

Study the diagram of Transcription and RNA Processing in Eukaryotes as well as the table for the three RNA polymerases

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

41
Q

How many RNA polymerases do Eukaryotes have?

A
  • RNA Polymerase I
  • RNA Polymerase II
  • RNA Polymerase III
42
Q

What does RNA polymerase I do in Eukaryotes?

A
  • RNA polymerase I: Synthesizes all but one rRNA. Located in the nucleolus (a protein structure within the nucleus)
43
Q

What does RNA polymerase II do in Eukaryotes?

A
  • RNA polymerase II: Responsible for the expression of genes that encode for long transcripts, many of which are translated into protein.
44
Q

What does RNA polymerase III do in Eukaryotes?

A
  • RNA polymerase III: Synthesizes many small RNAs such as the tRNAs, 5s rRNA and siRNA (a more recent discovery) important for gene regulation.
45
Q

What is the difference between a regulatory and a core promoter?

A
  • A core promoter is that portion of the proximal promoter that contains the transcription start sites
  • A regulatory promoter is the binding site for the basal transcriptional apparatus
46
Q

Why is the RNA polymerase II promoter important?

A
  • Locally unwound segment of DNA are required to initiate transcription
  • This involves interaction of transcription factors with specific promoter sequences
  • The promoter consists of short conserved elements upstream of the transcription start point (+1)
47
Q

What “boxes” are required for transcription? Also, study the diagram for the structure of these boxes.

A
  • TATA box: Element closest to transcription start. Plays important role in positioning the transcription startpoint and helps unwinding
  • CAAT box: Influences efficiency
  • GC & Octamer box: Often present, they influence efficiency
    https: //docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
48
Q

Why are the CAAT, GC and Octamer boxes important?

A
  • They bind transcriptional

activator proteins

49
Q

What are the three types of terminators?

A
  • UGA
  • UAG
  • UAA
50
Q

What is a 7-MG cap

A
  • AKA “7-Methyl Guanosine”
  • The cap contains a guanosine that is methylated at the position 7
  • Cap added after the chain is ~30 nucleotides long
51
Q

What is the purpose of a 7-MG cap

A

The cap has two functions:

  • Prevents degradation of the RNA transcript from RNases
  • Is recognised by the proteins that initiate translation of the RNA transcript into a protein
52
Q

What is the 3’Poly (A) tail?

A
  • Polyadenylation is the addition of a poly tail to a mRNA. The poly tail consists of multiple A’s. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation.
53
Q

Why is the Poly(A) tail significant for transcription?

A
  • Poly(A) tail enhances stability of mRNAs and plays important role in their transport from nucleus to cytoplasm
54
Q

How is the Poly(A) Tail added?

A
  • Once the polyadenylation sequence (AAUAAA) and the GU rich sequences have been transcribed a protein complex containing an endonuclease and poly(A) polymerase binds to these sequences and cleaves 11bp downstream of the AAUAAA
  • After cleavage the polyA tail is added (up to 200 bps long) by the polyApolymerase
55
Q

Why are Intron’s taken out of the mRNA strand?

A
  • Most eukaryotic genes contain noncoding sequences called introns that interrupt the coding sequences, aka exons
  • The introns are excised from the RNA transcripts prior to their transport to the cytoplasm
56
Q

Provide a summary of introns.

A
  • Introns (or intervening sequences) are noncoding sequences located between coding sequences.
  • Introns are removed from the pre-mRNA and are not present in the mRNA.
  • Exons (both coding and noncoding sequences) are composed of the sequences that remain in the mature mRNA after splicing.
  • Introns are variable in size and may be very large.
57
Q

Which enzyme does splicing?

A
  • Endonuclease
58
Q

Why is the Excision of Intron Sequences important?

A
  • The third modification of eukaryotic RNA transcripts is the removal of introns.
  • This occurs within the nucleus and that the removal of introns allows different proteins to be synthesized by creating multiple transcripts – increasing complexity phenotypically without the need for an increase in the genotype.
59
Q

Study the diagrams for the 7-MG cap, the 3’ Poly(A) tail and the Excision of Intron sequences.

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

60
Q

What is on summary slide 3?

A
  • Three different RNA polymerases are present in eukaryotes, and each polymerase transcribes a distinct set of genes.
  • Eukaryotic gene transcripts usually undergo three major modifications:
    (1) the addition of 7-methyl guanosine caps to 5’ termini,
    (2) The addition of poly(A) tails to 3’ ends, and
    (3) The excision of noncoding intron sequences.
61
Q

What does translation involve?

A
  • Translation involves three types of RNA, all of which are transcribed from DNA templates (chromosomal genes)
  • In addition to mRNAs, three to five RNA molecules (rRNA) are present as part of the structure of each ribosome
62
Q

Why are tRNA important?

A
  • 40 to 60 small RNA molecules (tRNA) function as adaptors by mediating the incorporation of the proper amino acids into polypeptides in response to specific nucleotide sequences in mRNAs
63
Q

Where does translation occur?

A
  • Translation occurs on ribosomes, which are complex macromolecular structures located in the cytoplasm
64
Q

What is aminoacyl-tRNA

synthetases

A
  • The amino acids are attached to the correct tRNA molecules by a set of activating enzymes called aminoacyl-tRNA synthetases
65
Q

Study the diagram of the process for Translation

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

66
Q

What is rRNA?

A
  • Ribosomal RNA
  • rRNA are transcribed from a DNA template
  • rRNA gene transcript is a 30S precursor, which undergoes endonucleolytic cleavages to produce the 5S, 16S, and 23S rRNAs plus one 4S tRNA molecule
67
Q

What are prokaryotic ribosomes and how are they composed?

A
  • Ribosomes: half protein and half RNA
  • Each subunit contains large, folded RNA molecule on which the ribosomal proteins assemble
  • 30S ribosomal subunit contains a 16S RNA molecule plus 21 polypeptides. The 50S subunit contains two RNA molecules (5S and 23S) plus 31 polypeptides
68
Q

What are tRNA?

A
  • Transfer RNA
  • tRNAs are derived from larger precursor transcripts in the same way rRNA
  • tRNA molecules contain a triplet nucleotide sequence, the anticodon, which is complementary to and base pairs with the codon sequence in mRNA during translation
  • There are one to four tRNAs for each of the 20 amino acids
69
Q

Why are tRNA important?

A
  • Amino acids are attached to the tRNAs by high-energy (very reactive) bonds between the carboxyl groups of the amino acids and the 3ʹ hydroxyl termini of the tRNAs
  • The aminoacyl~tRNAs are the substrates for polypeptide synthesis on ribosomes, with each activated tRNA recognizing the correct mRNA codon and presenting the amino acid in a steric configuration (3D-structure) that facilitates peptide bond formation
70
Q

How many binding sites are there on each ribosome and what are they?

A
  • Three tRNA binding sites on each ribosome
  • The A or aminoacyl site binds the incoming aminoacyl-tRNA, the tRNA carrying the next amino acid to be added to the growing polypeptide chain
  • The P or peptidyl site binds the tRNA to which the growing polypeptide is attached
  • The E or exit site binds the departing uncharged tRNA
71
Q

Where in the ribosome are the tRNA binding sites?

A
  • An mRNA molecule is attached to the 30S subunit → contributes specificity to the tRNA-binding sites located largely on the 50S subunit of the ribosome
72
Q

Where does the initiation of translation in E. coli occur?

A
  • Formation of the 30S subunit/mRNA complex depends, in part, on base pairing between two nucleotide sequences.
  • They include a nucleotide sequence near the 3ʹ-end of the 16S rRNA and a sequence (Shine-Dalgarno sequence) near the 5ʹ-end of the mRNA molecule
  • This is usually 7 nucleotides upstream of AUG (start codon)
73
Q

Study the diagrams for Prokaryotic Ribosome synthesis, tRNA , Translation Complex and the initiation of Translation

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

74
Q

When does polypeptide chain termination occur?

A
  • Polypeptide chain termination occurs when a chain-termination codon (stop codon) on the mRNA enters the A site of the ribosome
  • The stop codons are UAA, UAG, and UGA
75
Q

What happens during polypeptide chain termination?

A
  • When a stop codon is encountered, a release factor (RF-1) binds to the A site
  • A water molecule is added to the carboxyl terminus of the nascent polypeptide, causing termination.
76
Q

What are some properties of the genetic code?

A
  • Composed of nucleotide triplets
  • Non-overlapping
  • Comma free
  • Degenerate
  • Ordered (similar amino acids specified by related codons)
  • Contains start and stop codons
  • Nearly universal
77
Q

What does “Degenerate” mean in genetics?

A
  • Having more than one codon that may code for the same amino acid.
78
Q

How does Degenerate Genetic code work?

A
  • 20 amino acids = at least 20 different codons using four bases available in mRNA
  • Two bases per codon = only 42 or 16 possible codons (too few!)
  • Three bases per codon = 43 or 64 possible codons (too many?)
  • All amino acids except methionine and tryptophan are specified by more than one codon
79
Q

Give examples of Degenerate genetic code.

A
  • leucine, serine, and arginine—are each specified by six different codons
  • Isoleucine has three codons
  • Other amino acids each have either two or four codons
80
Q

What is Degeneracy?

A
  • The occurrence of more than one codon per amino acid is called degeneracy (not random)
81
Q

What types of degeneracy are there?

A

Degeneracy is primarily of two types:

  • Partial degeneracy: 3rd base either two pyrimidines (U or C) or two purines (A or G). Changing the third base from a purine to a pyrimidine, or vice versa, will change the amino acid specified by the codon
  • Complete degeneracy: Any of the four bases may be present at the third position in the codon, and the codon will still specify the same amino acid.
82
Q

Study the diagrams for polypeptide chain termination and degenerate genetic code

A

https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing

83
Q

How does a “wobble” occur?

A
  • Hydrogen bonding between bases in the anticodons of tRNAs and the codons of mRNAs follows strict base pairing rules only for the first two bases of the codon
  • The base-pairing involving the third base of the codon is less stringent, allowing what is called wobble at this site
84
Q

What is the significance of the wobble base?

A
  • Mutations at this site have less impact than the first two positions → decreasing the effect of mutations
85
Q

How does a wobble base decrease the effect of mutations?

A
  • Often amino acids with similar physical properties share similar codon sequences and often differ by a single base, thus if a coding mutation is created then the substituted amino acid is more likely to share similar physical properties and ultimately minimise the effect of protein sequence/ structure/function
86
Q

What is Inosine?

A
  • Several tRNAs contain the base inosine. Inosine is produced by a post-transcriptional modification of adenosine
  • Wobble hypothesis predicted that when inosine is present at the 5ʹ-end of an anticodon (the wobble position) it would base-pair with uracil, cytosine, or adenine in the codon
  • Experimental evidence: Purified alanyl-tRNA containing inosine (I) at the 5ʹ-position of the anticodon binds to ribosomes activated with GCU, GCC, or GCA trinucleotides
87
Q

What was on the last summary slide?

A
  • Each of the 20 amino acids in proteins is specified by one or more nucleotide triplets in mRNA
  • Of the 64 possible triplets, given the four bases in mRNA, 61 specify amino acids and 3 signal chain termination
  • The code is nonoverlapping, with each nucleotide part of a single codon, degenerate, with most amino acids specified by two to four codons, and ordered, with similar amino acids specified by related codons
  • The genetic code is nearly universal; with minor exceptions, the 64 triplets have the same meaning in all organisms
  • The wobble hypothesis explains how a single tRNA can respond to two or more codons

Genetics & Evolutionary Biology (16 decks)

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