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AP® Biology flashcards Biology 101 flashcards
1
Q

Lecture Outcomes

A

Describe the structure of RNA and the differences to DNA

  • Define the term transcription, understand how DNA is transcribed to RNA
  • List the differences in the transcription processes between eukaryotes
    and prokaryotes
  • Describe and understand the function of RNA polymerase
  • Describe the transcription initiation and termination signals in DNA
  • Describe the process of capping and polyadenylation
  • List the different classes of RNA molecules
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2
Q

The Central Dogma photo

A
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2
Q

Structure of RNA photo

A
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2
Q

The Central Dogma

A
  • Portions of DNA sequence are copied into RNA
  • Genes
    • Intergenic spaces can also be transcribed
  • Eukaryotic and Prokaryotic RNA is
    processed differently
  • Not all RNA is translated, only m(essanger)

RNA directs protein synthesis

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3
Q

Transcription: Requirements

A
  • Definition of “TRANSCRIPTION”

– “The production of RNA from a DNA template”

  • RNA - is made in a manner similar to DNA replication but only one strand is copied.
  • Enzymatic synthesis of RNA requires:
  1. The four ribonucleoside 5’ triphosphates

5’ATP 5’GTP 5’CTP 5’UTP

  1. Mg2+
  2. DNA template (no primer required)
  3. RNA polymerase (RNAP)

Mechanisms of synthesis: initiation, elongation and termination

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3
Q

RNA polymerase

A
  • Similar to DNA polymerase

– Forms phosphodiester bonds between ribonucleosides

– Uses energy stored in ribonucleoside triphosphates for polymerisation

  • Unlike DNA polymerase

– RNA synthesis starts without a primer

– Error rate higher than DNA polymerase

– Unwinding of the DNA template does not require a helicase or ATP.

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3
Q

Transcription: conventions

A
  • DNA sequences are written in the 5’ to 3’ direction
  • The “coding” or “sense” DNA strand is written in the 5’-3’ direction
  • RNA polymerase makes a complementary copy of the anti-parallel strand (template) in the
    3’ to 5’ direction from the promoter (P) to the terminator (T)
  • Transcribed mRNA is written in the 5’ to 3’ direction and is the same sequence as the coding strand in the DNA except that U is substituted for T.
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4
Q

Overall reaction photo

A

XTP represents the first nucleotide at the 5’ terminus of the RNA chain

NMP is a mononucleotide in the RNA chain,

RNA-P is RNA polymerase

PPi is the pyrophosphate released each time a nucleotide is added to the growing chain.

The Mg2+ ion is required for all nucleic acid polymerization reactions.

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5
Q

RNA polymerase photo

A
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6
Q

E. coli RNA polymerase

A
  1. E. coli RNA polymerase has 5 SUBUNITS (2 x α, β, β’ and ω). The complex of α2ββ’ ω is called the CORE ENZYME
  2. σ is responsible for promoter recognition (pyridine-rich DNA sequence of 10 or more bases). Associates with core enzyme to form the HOLOENZYME.
  3. Once correct initiation has been achieved, σ dissociates from the HOLOENZYME and the core enzyme continues elongation of the RNA chain.
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6
Q

E. coli RNA polymerase photo

A
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7
Q

Transcription in Prokaryotes photo

A
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8
Q

Transcription initiation and termination signals in DNA photo

A
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8
Q

Transcription termination signals in
E. coli

A

Can be achieved by one of two mechanisms

  1. DNA sequence dependant: an INVERTED REPEAT followed by a stretch of T bases
  2. DNA sequence dependent: bound to a protein factor (Rho)
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9
Q

Transcription Initiation signals in E. coli

A
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10
Q

Transcription signals in E. coli

A

In both cases the core enzyme associates and interacts with a free σ subunit and reforms the HOLOENZYME, which may then initiate further transcription (recycles RNA polymerase)

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11
Q

Transcription termination signals in
E. coli photo

A
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12
Q

Transcription signals in E. coli photo

A
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12
Q

Prokaryotic messenger RNA

A
  1. mRNA molecules are a copy of the coding strand of DNA sequences which determine the amino acid sequence of all proteins
  2. A DNA segment corresponding to one polypeptide chain plus the
    start and stop signals is called a CISTRON. A single mRNA
    encoding a single polypeptide is called MONOCISTRONIC mRNA
  3. In prokaryotes POLYCISTRONIC mRNAs are quite common and
    code for several different polypeptide chains
  4. mRNA’s have 5’ LEADERS, 3’ TERMINI and, in the case of
    polycistronic mRNAs, they have INTERCISTRONIC regions called
    SPACERS
  5. Prokaryotic mRNA’s have short half lives, generally a few minutes
    only
  6. Primary transcript not processed
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13
Q

Prokaryotic messenger RNA photo

A
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14
Q

Eukaryotic messenger RNA

A
  • Gene contains coding (exons) and non-coding (introns) regions
  • RNA is processed

– RNA capping (G with methyl group added to 5’ end)

– Polyadenylation (series of “A” added to 3’ end)

– Identifies RNA molecule as an mRNA

  • Introns removed by a splicesome which recognises the boundaries between introns and exons
  • Exons stitched back together and translated
  • mRNA molecules eventually degraded
14
Q

Eukaryotic messenger RNA photo

A
15
Q

Classes of RNA molecules

A
16
Q

Lecture Outcomes

A
  • Describe the major classes of RNA molecules
  • Describe the differences between prokaryotic and eukaryotic mRNA
  • Describe the structure and function of tRNA and function of aminoacyl-tRNA synthetases
  • Describe differences between prokaryotic and eukaryotic ribosomes
  • Understand the roles of ribosome binding sites in translation of mRNA to protein
  • Learn the definitions of polycistronic mRNA, polyribosome, mRNA cap, poly-A tail, codon, anticodon, amino acyl tRNA
17
Q

There are many steps between DNA
and Protein

A

The production of a protein by a
eukaryotic cell.

The final level of each protein in a cell depends on the efficiency of each step.

18
Q

There are many steps between DNA
and Protein photo

A
19
Q

Three major classes of RNA molecules

A
  1. Messenger RNA (mRNA):
  • copy of DNA which codes for the protein
  1. Transfer RNA (tRNA):
  • tRNA’s are small adaptor molecules which align specific amino acids opposite their triplet CODON in the mRNA molecule during the translation of mRNA into protein
  1. Ribosomal RNA (rRNA):
  • rRNA is an integral part of ribosomal structures and is an important part of the protein synthesising machinery

These 3 interact to enable translation of the mRNA to protein

20
Q

Eukaryotic and Prokaryotic cells handle
their RNA transcripts differently

A

Eukaryotes

  • Transcription/translation
    occur separately
  • In different compartments
  • Enables greater control

Prokaryotes

  • Transcription/translation
    are coupled
  • Occur simultaneously
21
Q

Eukaryotic and Prokaryotic cells handle
their RNA transcripts differently

A
21
Q

Unlike bacterial mRNAs, eukaryotic mRNAs are
modified by capping and polyadenylation

A
  • Cap = 7-methylguanosine
  • Poly-A tail = long string of adenosines linked to 3’-end of mRNA:
  • Not incorporated in the DNA sequence
  • Binding site for several proteins
  • Roles of 5’ end cap and 3’ end polyadenylation:
  • Assist the export of mRNA molecules from the nucleus
  • Protect the mRNA from degradation in the cytoplasm and increase its half life
  • Enable the binding of ribosomes, promote translation
22
Q

mRNA sequence is decoded in sets of 3 nucleotides called codons photo

A
23
Q

Transfer RNAs

A
  • Amino acid cannot directly recognise the mRNA codon, needs
    adaptor.
  • tRNAs are small adaptor molecules ~ 80 nucleotides long:
  • align specific amino acids opposite their triplet codon in the mRNA molecule during translation
  • Bases other than A, G, C and U are present in tRNA as a result of
    post-transcriptional modification e.g. inosine (a modified adenine), pseudouridine, dihydrouridine
23
Q

tRNA Structure photo

A
23
Q

Genetic code is translated by two
adaptors

A

Acts 1st : Aminoacyl-tRNA synthetase couples a particular amino acid to its corresponding tRNA

Acts 2nd : tRNA whose anticodon forms base pairs with codon of mRNA

24
Q

tRNA Structure

A
  • Internal complementary base pairing of RNA gives cloverleaf structure
  • Anticodon sequence of 3 bases determines mRNA codon binding
  • Amino acid attachment site is at 3’ end of tRNA
  • Modified bases
  • D = dihydrouracil
  • Ψ = pseudouridine
  • 3D shape determines attachment of correct amino acid (matching the codon/anticodon pair) by aminoacyl-tRNA synthetases
25
Q

tRNA Structure photo

A
26
Q

Genetic code is translated by two
adaptors photo

A
27
Q

Aminoacyl-tRNA Synthetases

A
  • For every amino acid one aminoacyl-tRNA synthetase exists:

i.e. links a particular amino acid to several tRNAs

  • These enzymes are responsible for the attachment of the correct amino acid to the tRNA:

i.e. the amino acid specified by the anticodon of the tRNA and the amino acid attachment sequence on the 3’ end

Terminology:

  • leucyl-tRNA synthetase attaches leucine (aa) to tRNALeu
  • alanyl-tRNA synthetase attaches alanine to tRNAAla, and etc.
  • When the correct amino acid has been attached to its tRNA, the tRNA is said to be CHARGED or ACYLATED
  • Termed an amino acyl tRNA
  • ATP hydrolysis required
  • mischarging means an incorrect amino acid attachment
28
Q

Aminoacyl-tRNA Synthetases photo

A
29
Q

Prokaryotic Ribosome structure photo

A
29
Q

Prokaryotic Ribosome structure

A
  • rRNAs are an integral part of ribosomal structures and are important parts of the protein synthesising machinery
  • Prokaryotes have 5S, 23S rRNA in their large ribosomal subunit
  • Prokaryotes have 16S rRNA in their small ribosomal subunit
29
Q

Ribosomal RNAs

A

The mRNA message is decoded on ribosomes

  • The ribosome is a very large multi-domain complex
  • It scans along the mRNA and captures the correct aminoacyl tRNA:
  • Correct complementarity (base-pairing) results in the covalent linking of aa onto the growing polypeptide chain

Ribosomes in the cytoplasm of a eukaryotic cell. Electron micrograph shows ribosomes as black dots (arrows).

Some are free, some attached to endoplasmic reticulum.

29
Q

Eukaryotic Ribosome structure

A
  • Eukaryotes have 5S, 5.8S and 28S rRNA in their large ribosomal subunit
  • Eukaryotes have 18S rRNA in their small ribosomal subunit
  • Despite differences in protein and rRNA components, both prokaryotic and eukaryotic ribosomes have nearly the same structure and function
30
Q

Elongation of
polypeptide photo

A
30
Q

Ribosomes have binding sites

A
  • Small subunit matches tRNA to the codon on the mRNA
  • Large subunit catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide
  • Each ribosome has one binding site for mRNA and three binding sites for tRNA tRNA binding sites:

A = aminoacyl-tRNA : new tRNA enters ribosomal complex

P = peptidyl-tRNA : tRNA attached to the polypeptide chain

E = exit : empty tRNA exits ribosomal complex

30
Q

Eukaryotic Ribosome structure photo

A
31
Q

Ribosomes have binding sites photo

A
32
Q

A single prokaryotic mRNA molecule can encode several different proteins

A
  • Unlike eukaryotic ribosomes, which recognize a 5’ cap, prokaryotic ribosomes initiate translation at ribosome-binding sites, which can be located in the interior of an mRNA molecule
  • This feature permits prokaryotes to synthesize more than one type of protein from a single polycistronic mRNA molecule
33
Q

A single prokaryotic mRNA molecule can encode several different proteins photo

A
34
Q

Proteins are translated by polyribosomes

A
  • Many ribosomes can simultaneously translate the same mRNA molecule
  • Increases the production capacity of a particular protein
35
Q

polyribosomes photo

A

Molecular Biology Flashcards (20 decks)

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