11 - Evolution of Eukaryotes: endomembranes and endosymbiosis

Question 1

Relative sizes of typical mitochondrial, chloroplast and nuclear genomes

Answer 1

Chlamy has three different genomes

• in the nucleus wich is 120000kb
• in mitochondria which is 16kb
• and in chloroplast which id 200kb
• through evolution the amount of genome of a chloroplast went from 5000kb to 115kb
• in mitochondria it went from 5000kb to 16kb

Question 2

Rubisco structure and assembly from components coded by different genomes

Answer 2

• cube shaped and contains eight small subunits and eight large subunits
• each large subunit contains an active site
• the small subunits do not have a role in catalysis but do serve an importnat regulatory role
• synthesis of rubisco requires the coordinated expression of genes in two different genomes
• the lagre subunit is encoded by a gene in the chloroplast genome
• the small subunit is encoded by a gene that is found in the nucleus
• After the small subunits polypeptide is synthesized in the cytosol, it is imported into the chloroplast, where it associates with large subunit monomers to make the functional enzyme.

Question 3

possible reasons why modern organelle genomes have become dramatically smaller over evolutionary time

Answer 3

• a specific gene is already in the nucleus, so it can be deleted from the mitochondrial genome
• organelles want to get rid of genes that are already present because it will make it easier to transcrip and translate the DNA
• you can get rid of the genes by mutation and deletion, or by lateral gene transfer to the nucleus

Question 4

Possible reasons why genes have moved to the nucleus from organelles over evolutionary time

Answer 4

• coordinated control
• Maybe the cell doesn’t need that gene anymore
• Genes need enzymes for glycolysis
• If you are in the nucleus you can engage in sexual recombination
• These organelles are involved in electron transport, which means that there is lots of oxygen and a lot of electrons (reactive oxygen species) that can damage nucleic acid.

Question 5

Possible reasons why certain genes have not moved to the nucleus from organelles

Answer 5

• It is simpler to have them locally
• It might be convenient to have the genes that code for protein right there ready for use
• Proteins that can’t be moved out of the nucleus will be inconvenient, therefore it will be better to keep it in the organelle, which has ribosomes
• They haven’t had time to get out the organelle to the nucleus
• Might be to big

Question 6

Basic mechanism of transcription and translation in prokaryotic organelles vs. eukaryotic nuclear environments.

Eukaryotes

Answer 6

• RNA polymerase synthesizes a precursor-mRNA containing extra segments that are removed by RNA processing to produce a translatable mRNA.
• This mRNA exits the nucleus through a nuclear pore and is translated on ribosomes in the cytoplasm

Trascription

• Initiation:
  
  • RNA polymerase II cannot directly bind to DNA; it is recruited to the promoter once transcription factors have bound
• Elongation:
• Termination:
  
  • there is no transcription terminator.
  • Near the 3’ end of the gene is a DNA sequence that is transcribed into the pre-mRNA.
  • Proteins bind to this polyadenylation signal in the RNA and cleave it just downstream.
  • This signals the RNA polymerase to stop transcription.
  • A poly (A) tail is added at the 3’ end. There is no base-paring of the poly (A) tail.
• Translation
• Initiation:
  
  • The Met-tRNA, GTP and ribosomal subunit complex binds to the 5’ cap of the mRNA and moves along the mRNA (scanning), until it reaches the AUG start codon in the P site.
  • Base-pairing occurs between the codon and the anticodon of the initiator Met- tRNA.
  • The large ribosomal subunit binds and GTP is hydrolyzed, completing initiation.
• Elongation: turns at a rate of 1-3 times per second.
• Tremination:
  
  • the ribosome arrives at a stop codon, at which point a protein release factor causes the previous tRNA to release the amino-acid chain and the ribosomal large and small units separate.

Question 7

Basic mechanism of transcription and translation in prokaryotic organelles vs. eukaryotic cells.

Prokaryotes

Answer 7

• RNA polymerase synthesizes an mRNA molecule that is immediately available for translation on ribosomes
• DNA is circular

Transcription

• Initiation:
  
  • RNA polymerase binds directly to DNA; it is directed to the promoter by a protein factor that is then released once transcription begins
• Elongation:
• Termination:
  
  • There are two types of specific DNA sequences called terminators that signal the end of transcription of the gene. They act after they have been transcribed
    
    • First type; the terminator sequence on the mRNA uses complementary base-paring with itself to form a “hairpin”.
    • Second type; a protein binds to a particular terminator sequence on the mRNA

Translation

• Initiation:
  
  • The small ribosomal subunit, the initiator Met-tRNA and GTP bind directly to the region of the mRNA with the AUG start codon.
  • This initiation complex is then guided by the ribosome binding site, in this case SD box, just upstream of the start codon on the mRNA that base-pairs with a complementary sequence of rRNA in the small ribosomal subunit.
  • The large ribosomal subunit then binds to the small subunit to complete the ribosome.
  • GTP hydrolysis then begins translation.
• Elongation: turn at a rate of 15-20 times per second
• Termination:
  
  • the ribosome arrives at a stop codon, at which point a protein release factor causes the previous tRNA to release the amino-acid chain and the ribosomal large and small units separate.

Question 8

Basic structure and function of ribosome

Answer 8

• is made up of two parts of dissimilar size, called the large and small ribosomal subunits.
• Each subunit is made up of a combination of ribosomal RNA (rRNA) and ribosomal proteins.
• the RNA is catalytic.
  the protein is structural.
• they recognize mRNA sequences as codons for translation.
• tRNA enters ribosomes and holds the appropriate anti-codon and the respective amino acid to be added on to the chain

Question 9

Basic structure and function of RNA polymerase

Answer 9

• RNA polymerase is a protein that reads DNA 3’-5’ and synthesizes RNA 5’-3’.
• RNA polymerase is the structure that understands the information in a promoter
• it binds to the promoter and begins to transcribe
• in prokaryotes about 50 nucleotides per second the polymerase is chugging along.

Question 10

conceptual connections between RNA and DNA polymerase

Answer 10

• All polymerases read in the 3’-5’ direction and synthesize in the 5’-3’ direction.
• they are both enzymes.
• the difference is that RNA polymerase is used in transcription whereas DNA polymerase is used in DNA replication and cell cycling processes

Question 11

Examples of complementary base pairing in gene expression

Answer 11

• mRNA basepairs with itself, for prober function
• in DNA structure
• in transcription: making RNA form DNA
• tRNA basepairs with itself to form 3D shape
• tRNA anticodon basepairs with mRNA codons
• mRNA base-pairs with rRNA in translation initiation (SD box, 5’ cap)
• base-paring between snRNA and mRNA in the removal of introns
• in prokaryotes, mRNA base-pairs with itself to form a hairpin in termination of transcriptionstronger hairpin loop when there are more G and C pairs
• Some RNA’s such as micro RNA also base pair with other RNA’s (mRNA) and stop translation from occurring
  
  • Ex:translational control, which can be used to control gene expression.