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MOLECULAR BIOLOGY > WEEK 10 (Central Dogma) > Flashcards

WEEK 10 (Central Dogma) Flashcards

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1
Q

What is the Central dogma of molecular biology?

A

An explanation of the flow of genetic information within a biological system

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2
Q

What is an essential part of the machinery for synthesising proteins?

A

RNA-based enzymatic catalysis

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2
Q

What is an essential part of the machinery for synthesising proteins?

A

RNA-based enzymatic catalysis

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3
Q

What is the “RNA world hypothesis” and what does it propose?

A

The ability of DNA and RNA to base pair with free nucleotides suggests a scenario in which an RNA sequence spontaneously formed that was then able to self-replicate, ultimately giving rise to many self-propagating copies of itself

This proposes that life began as RNA

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4
Q

What was the importance of Archibald Garrod?

A
  • Provided the first meaningful insight into gene function
  • Discovered the relationship between a genetic defect, a specific enzyme and a specific metabolic condition
  • One disease investigated was ALCAPTONURIA
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5
Q

Describe Alcaptonuria

A

A condition where urine becomes dark on exposure to air. Individuals with Alcaptonuria lack an enzyme in their blood that OXIDISED HOMOGENTISIC ACID (a compound formed during the breakdown of PHENYLALANINE and TYROSINE). As homogentisic acid accumulates, it is secreted in the urine and darkens in colour when oxidised by air.

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6
Q

Describe the overview of the flow of information in a eukaryotic cell

A

1) The DNA of chromosomes located within the nucleus contains the entire store of genetic information. Selected sites on the DNA are transcribed into pre-RNAs.
2) Pre-RNAs are processed into mRNAs and are transported out of the nucleus
3) In the cytoplasm, mRNAs are translated into polypeptides by ribosomes that move along the mRNA
4) Following translation, the polypeptide folds to assume its native conformation

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7
Q

What is the function of Retro viruses?

A

Retro viruses carry RNA as their genetic information. When they invade their host cell they convert their RNA into a DNA copy using REVERSE TRANSCRIPTASE.

This modifies the central dogma
DNA <-> RNA -> PROTEIN

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8
Q

What are the steps of Protein synthesis?

A
  • Transcription
  • RNA Processing (Splicing etc.)
  • Translation
  • Post-translation processing
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9
Q

What is Transcription?

A

A process in which a DNA strand provides the information for the synthesis of an RNA strand

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10
Q

What are the enzymes responsible for transcription in both prokaryotic and eukaryotic cells?

A

DNA-dependent RNA Polymerases/RNA Polymerases

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11
Q

What are the functions of RNA Polymerases?

A
  • Able to incorporate nucleotides, one at a time, into a strand of RNA whose sequence is COMPLEMENTARY to one of the DNA strands which serves as a template
  • Catalyses the highly favourable reaction in which RIBONUCLEOSIDE TRIPHOSPHATE SUBSTRATES (NTPs) are cleaved into NUCLEOSIDE MONOPHOSPHATES as they are polymerised into a covalent chain
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12
Q

What is the Promoter?

A

The site on the DNA to which an RNA Polymerase molecule binds prior to initiating transcription

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13
Q

Cellular RNA Polymerases are not capable of recognising promoters on their own but require the help of which additional proteins?

A

Transcription Factors

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14
Q

What is the function of the Promoter?

A
  • Provides a binding site for the polymerase
  • Contains the information that determines which of the two DNA strands is transcribed and the site at which transcription begins
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15
Q

Describe how RNA Polymerase works

A

RNA Polymerase moves along the template DNA strand toward its 5’ end (3’ to 5’ direction). As the Polymerase progresses, the DNA is temporarily unwound and the polymerase assembles a complementary strand of RNA that grows starting from its 5’ terminus in a 3’ direction.

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16
Q

What is a Transcription bubble?

A

A molecular structure formed during DNA transcription when a limited portion of the DNA double strand is unwound

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17
Q

What is a Transcription bubble?

A

A molecular structure formed during DNA transcription when a limited portion of the DNA double strand is unwound

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18
Q

Describe the Schematic model of elongation of a newly synthesised RNA molecule during transcription

A
  • Polymerase covers approximately 35 base pairs of DNA
  • Transcription bubble composed of single-stranded DNA contains about 15 base pairs
  • Segment present in a DNA-RNA hybrid includes about nine base pairs
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19
Q

What is the difference between RNA Polymerase I, II, III, IV & V and the RNAs they synthesise?

A

ENZYME: RNA POLYMERASE I
RNAs SYNTHESISED: Larger RNAs

ENZYME: RNA POLYMERASE II
RNAs SYNTHESISED: mRNAs, small nuclear RNAs & Telomerase RNA

ENZYME: RNA POLYMERASE III
RNAs SYNTHESISED: tRNAs

ENZYME: RNA POLYMERASE IV, V (Plants only)
RNAs SYNTHESISED: siRNAs

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20
Q

What are the properties of precursor RNA?

A
  • RNAs, mRNAs and tRNAs are derived from precursor RNA
  • Considerably longer than the final RNA product
  • Initial precursor RNA is equivalent in length to the full length of the DNA transcribed
  • Initial precursor RNA is called the PRIMARY TRANSCRIPT/PRE-RNA
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21
Q

What is the Transcription unit?

A

The corresponding segment of DNA from which a primary transcript is transcribed

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22
Q

Primary transcripts do not exist within the cell as naked RNA but rather become associated with what?

A

Proteins as they are synthesised

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23
Q

Describe why Primary transcripts have a fleeting existence

A

Since they are processed into smaller, functional RNAs by a series of “cut-and-paste” reactions

24
Q

What does RNA processing require?

A

A variety of small RNAs and their associated proteins

25
Q

What are the functions of mRNA, rRNA and tRNA?

A

mRNA = provides the plan for the polypeptide chain
rRNA = provides the platform for protein synthesis
tRNA = “translates” the message on the mRNA into a polypeptide chain

26
Q

What are the key components of Transcription?

A
  • Uses an enzyme RNA Polymerase
  • Proceeds in the 5’ to 3’ direction
  • Forms a complementary strand of mRNA
  • Begins at a PROMOTOR SITE which signals the beginning of a gene
  • After the end of the gene is reached there is a terminator sequence that tells RNA polymerase to stop transcribing
27
Q

What is RNA Polymerase and what are its functions?

A

RNA Polymerase is the enzyme that controls transcription

FUNCTION:
- Search DNA for initiation site
- It unwinds a short stretch of double helical DNA to produce a single-stranded DNA template
- It selects the correct ribonucleotide and catalyses the formation of a phosphodiester bond
- Detects termination signals where transcript ends

28
Q

What are the three phases Transcription is divided into?

A

1) Initiation
2) Elongation
3) Termination

29
Q

What are the start and stop codons for eukaryotes?

A

Start = AUG (METHIONINE)
Stop = UAG, UAA, UGA

30
Q

What happens when the core enzyme is associated with the σ factor?

A

The complete enzyme (holoenzyme) is able to
- recognise and bind to the promoter regions of the DNA
- separate the strands of the DNA double helix
- initiate transcription at the proper start sites

31
Q

Describe the single type of RNA polymerase found in bacteria

A
  • Composed of five subunits
  • Tightly associated to form a core enzyme
32
Q

What happens when the core enzyme is not associated with the σ factor?

A

The core enzyme does not interact with the DNA at specific initiation sites

33
Q

Where are bacterial promoters located?

A

In the region of a DNA strand just preceding the initiation site of RNA synthesis

34
Q

Describe the nucleotides regarding RNA site synthesis

A

The nucleotide at which transcription is initiated is denoted as +1 and the preceding nucleotide as −1. Those portions of the DNA preceding the initiation site (toward the 3 ′ end of the template strand) are said to be upstream from that site. Those portions of the DNA succeeding it (toward the 5 ′ end of the template strand) are said to be downstream from that site

35
Q

What is the Open complex?

A

The complex of the polymerase, σ factor and DNA with the strands separated

36
Q

Describe Transcription in Bacteria

A

1) As the σ factor interacts with the PROMOTER, the jaws of the enzyme grip the downstream DNA duplex which resides within the channel
2) The enzyme separates the two DNA strands in the region surrounding the site
3) Once about 10 nucleotides have been successfully incorporated into a growing transcript, the enzyme undergoes a MAJOR CHANGE in conformation and is transformed into a TRANSCRIPTIONAL ELONGATION COMPLEX that can move processively along the DNA
4) Formation of an elongation complex is followed by release of the σ factor

37
Q

What are the two stretches found upstream from the initiation site?

A
  • “-35 ELEMENT” and is centred at approximately 35 bases upstream from the initiation site and occurs as TTGACA; also called a CONSENSUS SEQUENCE
  • “-10 ELEMENT/PRIBNOW BOX” and is 10 bases upstream from the initiation site and occurs as TATAAT; responsible for identifying the precise nucleotide at which transcription begins
38
Q

What happens once the σ factor recognises the Pribnow box?

A
  • Amino acid residues within the protein interact with each of the six nucleotides of the TATAAT sequence of the contemplate strand
  • Two nucleotides are flipped out of the nucleotide stack and into the core of the protein
    [this initiates MELTING of the ADJOINING REGION of promoter DNA and formation of the transcription bubble]
39
Q

The initiation site marks the boundary of what?

A

The boundary between the + and - sides of the gene

40
Q

Describe how Transcription in Eukaryotes differs from Prokaryotes

A
  • Occurs within the nucleus
  • Requirement for a large variety of accessory proteins/transcription factors
  • Initiation requires the compact chromatin fiber
  • Initiation and regulation of transcription entail a more extensive interaction between cis-acting DNA sequences and trans-acting protein factors involved in stimulating and initiating transcription
  • Alteration of the primary RNA transcript to produce mature eukaryotic mRNA involved many complex stages called “processing”
41
Q

Describe the synthesis of mRNA

A

1) In the nucleus, transcription of RNA begins when RNA polymerase II binds to the DNA at a region called the PROMOTER to form a PREINITIATION COMPLEX
[process is facilitated by TRANSCRIPTION FACTORS & Large hnRNAs are primarily precursors to the smaller cytoplasmic mRNAs]
2) mRNAs move out into the cytoplasm via the nuclear pore

42
Q

What are the properties of hnRNAs?

A
  • Large molecular weights
  • Represented by RNAs of diverse (heterogenous) nucleotide sequence
  • Found only in the nucleus
43
Q

What are Transcription factors?

A

Proteins that bind to DNA near the start of transcription of a gene. They either inhibit or assist RNA polymerase in initiation and maintenance of transcription.

44
Q

What are the two broad categories of transcription factors?

A
  • The general transcription factors (GTFs)
  • The transcriptional activators and repressors
45
Q

What are the properties of mRNAs?

A
  • Contain a continuous sequence of nucleotides encoding a specific polypeptide
  • Found in the cytoplasm
  • Attached to ribosomes when they are translated
  • Contain a significant noncoding segment
  • Eukaryotic mRNAs have special modifications at their 5’ and 3’ ends
    [3’ has a string of 50 to 250 ADENOSINE RESIDUES that form a poly(A) tail, 5’ has a METHYLATED GUANOSINE CAP]
46
Q

Describe the steps from RNA processing (pre-mRNA to mRNA)

A

1) Capping
2) Addition of Poly A tail
3) Splicing

47
Q

What is the importance of Alternative splicing?

A
  • Very common in higher eukaryotes
  • A way to get more than one protein product out of the same gene
  • A way to control gene expression in cells
48
Q

What makes transcription of Mitochondrial genome different?

A
  • Circular
  • One heavy strand and one light strand
  • Most of the coding nucleotides are found on the heavy strand
  • Two promoters therefore both strands of mitochondrial DNA are used for transcription
49
Q

Prokaryotes also have a monocistronic transcription unit (TRUE/FALSE)

A

FALSE

50
Q

What ensures stable binding of RNA polymerase at the promoter site?

A

σ factor

Explanation: σ factor decreases the binding of the core enzyme to non-specific DNA sequences and increases binding to the promoter

51
Q

How many base pairs of DNA is transcribed by RNA polymerase in one go?

A

7-8

52
Q

What enzyme involved in ribosomal protein synthesis is a ribozyme?

A

Peptide Transferase

53
Q

The major differences between the prokaryotic and eukaryotic protein synthesis mechanisms are in which part of the process?

A

The initiation of synthesis

54
Q

The termination of synthesis depends on which termination factor?

A

Rho (r)

Rho is a large hexametric protein that physically interacts with the growing RNA transcript, facilitating termination of transcription

55
Q

What is Gene expression?

A

The activation of a gene which results in a protein

56
Q

What is RNA Polymerase and what are its functions?

A

RNA Polymerase is the enzyme that controls transcription

FUNCTION:
- Search DNA for initiation site
- It unwinds a short stretch of double helical DNA to produce a single-stranded DNA template
- It selects the correct ribonucleotide and catalyses the formation of a phosphodiester bond
- Detects termination signals where transcript ends

57
Q

Why does transcription in eukaryotic cells have many “processing steps” whereas prokaryotes do not?

A
  • Prokaryotic cells do not contain introns
  • Transcription and translation of prokaryotic cells happens at the same place (cytosol) whereas in eukaryotic cells the mRNA has to move out the nucleus, through the nuclear pore and into the cytoplasm
58
Q

Describe Mitochondrial DNA

A
  • Circular
  • One heavy strand and one light strand
  • Most of the coding nucleotides are found on the heavy strand
  • Two promoters therefore both strands of mitochondrial DNA are used for transcription

MOLECULAR BIOLOGY (11 decks)

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