VBS 2032. Exam 2
- What is a genome?
- How do the genomes of eukaryotic, prokaryotic microorganisms differ?
- How about viruses/bacteriophages? - answer Genome: the genetic material of an
organism
*For prokaryotes and eukaryotes this is all the DNA in a cell
*For virus this could be DNA or RNA
Eukaryote genome:
- Linear chromosomes composed of double-stranded DNA (2 copies "diployed")
- linear chromosomes are in the cell nucleus
Prokaryote genome:
- Circular double-stranded DNA chromosomes
- Chromosome is not bounded by a membrane, it is organized in the nucleoid
- Have smaller circular pieces of DNA (plasmids)
- Their genome is a combination of chromosomal DNA and plasmid DNA
Viruses "bacteriophages" genome:
- have the greatest diversity in their genomes
- linear or circular DNA or RNA either double- or single-stranded present as a single
strand of nucleic acid or divided into many segments
- How does the Central Dogma state how information transmitted?
- What is a viral exception to this? - answerCentral Dogma states: DNA is replicated
(DNA replication), Information from DNA is passed to RNA (process of transcription),
then the RNA passes the information to protein (process of translation)
Viral exception:
- Viruses have a different paradigm than what the central dogma states
EX: Retroviruses
- Have an RNA genome that's copied into DNA
Many enzymes are required:
- What are the functions of the enzymes? - answerEnzymes:
- DNA helicase: unwind the DNA helix at the replication fork
- DNA gyrase (antibiotic target): temporarily breaks the strands of DNA, relieving the
tension caused by unwinding the 2 strands of the DNA helix
,- DNA primase: synthesizes small fragments of RNA to serve as primers for DNA
synthesis
- DNA polymerase: synthesize DNA
*Use 1 strand of DNA as a template to make the complementary strand
- DNA ligase: joins 2 DNA fragments together by forming a covalent bond between the
sugar and phosphate residues of adjacent nucleotides
For DNA replication
1. DNA must be unwound by DNA helicase and DNA gyrase
2. DNA primase produces short RNA primers where DNA polymerase can begin
3. DNA fragment is generated on the lagging strand and fragments are joined together
by DNA ligase
Semi-conservative replication - answer- When DNA is copied this is a ____________.
Definition: 2 DNA molecules each contain 1 strand of original DNA and 1 new
Process:
1. Replication of chromosomal DNA starts at the origin of replication and then proceeds
in both directions
2. Bidirectional replication creates 2 advancing forks where DNA synthesis is occurring
3. The replication forks ultimately meet at a terminating site
4. DNA replication is semiconservative, meaning each of the 2 molecules created
contains 1 original strand paired with 1 newly synthesized strand
- How do prokaryotes replicate?
- How do eukaryotes replicate? - answerProkaryotes cell division:
- Binary Fission
Eukaryote cell division:
- Mitosis
*Involves more steps and regulation because several chromosomes must be divided
equally between daughter cells
- How does the arrangement of DNA in eukaryotes differ from that in prokaryotes?
- What are the differences between DNA and RNA?
- Which base is unique to DNA? to RNA? - answerEukaryote genome:
- Linear chromosomes composed of double-stranded DNA (2 copies "diployed")
- linear chromosomes are in the cell nucleus
*DNA does not code for RNA or protein
Prokaryote genome:
- Circular double-stranded DNA chromosomes
- Chromosome is not bounded by a membrane, it is organized in the nucleoid
- Have smaller circular pieces of DNA (plasmids)
,- Their genome is a combination of chromosomal DNA and plasmid DNA
Differences between DNA and RNA:
DNA:
- Bases: (A) adenine, (T) thymine, (G) guanine, (C) cytosine
- Base pair: A-T and G-C
- Sugar: deoxyribose
- Structure: usually double-stranded
RNA:
- Bases: (A) adenine, (U) uracil, (G) guanine, (C) cytosine
- Base pair: A-U and G-C
- Sugar: ribose
- Structure: usually single-stranded
What is initiation, elongation, and termination? - answerInitiation: RNA polymerase
binds to the promoter and melts a short stretch of DNA
Elongation:
- Sigma factor dissociates from RNA polymerase, leaving the core enzyme to complete
transcription.
- RNA is synthesizes in the 5' to 3' direction as the enzyme adds nucleotides to the 3'
end of the growing chain
Termination: When RNA polymerase encouters a terminator, it falls off the template and
releases the newly synthesized RNA
- How is information transmitted in replication, transcription and translation?
- Difference in eukaryotes and prokaryotes - answerDNA replication: Double-stranded
DNA is duplicated so its encoded information can be passed on to the next generation.
Gene expression (2 events):
1. Transcription: information encoded in DNA is copied into RNA
Transcription:
Prokaryotes
- transcripts (mRNA) often contain sequence for several genes
- transcription and translation happen at the same time, as soon as mRNA beings to
form ribosomes attach and begin making proteins
Eukaryotes
- transcripts contain sequence from a single gene
- mRNA transcripts are transported out of nucleus or they can be translated in
cytoplasm
, Discuss the different types of RNA and the significance of each. - answerRibosomal
RNA (rRNA):
- Not translated
- They make up the ribosome structure
- Serve structural and catalytize the bonds between amino acids in the newly
synthesized protein
tRNA:
- Not translated, but participate in translation process
*plays a critical role in protein synthesis
- involved in interpreting genetic code (each molecule carries a specific amino acid)
mRNA: is translated as a 3-letter-code
- translated during protein synthesis
- used to synthesize the encoded protein
- How many nucleotides are used to encode an amino acid?
- What does it mean that the genetic code is degenerate (redundant)? - answer- Various
combinations of 3 bases could code for 64 different amino acids, but codes for 20
- RNA code is redundant
*Redundancy allows some level of mutation to occur in DNA or RNA without changing
the protein
- What is a polycistronic message?
- Are they found in prokaryotes or eukaryotes? - answerPolycistronic message: mRNA
molecule encodes information to multiple genes for different proteins
*Found in prokaryotes as mRNA molecules carry the information for one or multiple
genes
- What is an operator? What binds to this element?
- What is a promoter? What binds to this element? - answerOperator:
- Region located immediately downstream of a promoter to which a repressor can bind
- Binding of the repressor to the operator prevents RNA polymerase from progressing
past that region (blocking transcription)
- Binds a regulatory protein
Promoter: DNA (nucleotide) sequence to which RNA polymerase binds to start
transcription
What is the difference between an inducible system and a repressible system? -
answerHow are genes regulated?
1. Inducible: are usually "off", not transcribed until specific inducing molecules are
present
- What is a genome?
- How do the genomes of eukaryotic, prokaryotic microorganisms differ?
- How about viruses/bacteriophages? - answer Genome: the genetic material of an
organism
*For prokaryotes and eukaryotes this is all the DNA in a cell
*For virus this could be DNA or RNA
Eukaryote genome:
- Linear chromosomes composed of double-stranded DNA (2 copies "diployed")
- linear chromosomes are in the cell nucleus
Prokaryote genome:
- Circular double-stranded DNA chromosomes
- Chromosome is not bounded by a membrane, it is organized in the nucleoid
- Have smaller circular pieces of DNA (plasmids)
- Their genome is a combination of chromosomal DNA and plasmid DNA
Viruses "bacteriophages" genome:
- have the greatest diversity in their genomes
- linear or circular DNA or RNA either double- or single-stranded present as a single
strand of nucleic acid or divided into many segments
- How does the Central Dogma state how information transmitted?
- What is a viral exception to this? - answerCentral Dogma states: DNA is replicated
(DNA replication), Information from DNA is passed to RNA (process of transcription),
then the RNA passes the information to protein (process of translation)
Viral exception:
- Viruses have a different paradigm than what the central dogma states
EX: Retroviruses
- Have an RNA genome that's copied into DNA
Many enzymes are required:
- What are the functions of the enzymes? - answerEnzymes:
- DNA helicase: unwind the DNA helix at the replication fork
- DNA gyrase (antibiotic target): temporarily breaks the strands of DNA, relieving the
tension caused by unwinding the 2 strands of the DNA helix
,- DNA primase: synthesizes small fragments of RNA to serve as primers for DNA
synthesis
- DNA polymerase: synthesize DNA
*Use 1 strand of DNA as a template to make the complementary strand
- DNA ligase: joins 2 DNA fragments together by forming a covalent bond between the
sugar and phosphate residues of adjacent nucleotides
For DNA replication
1. DNA must be unwound by DNA helicase and DNA gyrase
2. DNA primase produces short RNA primers where DNA polymerase can begin
3. DNA fragment is generated on the lagging strand and fragments are joined together
by DNA ligase
Semi-conservative replication - answer- When DNA is copied this is a ____________.
Definition: 2 DNA molecules each contain 1 strand of original DNA and 1 new
Process:
1. Replication of chromosomal DNA starts at the origin of replication and then proceeds
in both directions
2. Bidirectional replication creates 2 advancing forks where DNA synthesis is occurring
3. The replication forks ultimately meet at a terminating site
4. DNA replication is semiconservative, meaning each of the 2 molecules created
contains 1 original strand paired with 1 newly synthesized strand
- How do prokaryotes replicate?
- How do eukaryotes replicate? - answerProkaryotes cell division:
- Binary Fission
Eukaryote cell division:
- Mitosis
*Involves more steps and regulation because several chromosomes must be divided
equally between daughter cells
- How does the arrangement of DNA in eukaryotes differ from that in prokaryotes?
- What are the differences between DNA and RNA?
- Which base is unique to DNA? to RNA? - answerEukaryote genome:
- Linear chromosomes composed of double-stranded DNA (2 copies "diployed")
- linear chromosomes are in the cell nucleus
*DNA does not code for RNA or protein
Prokaryote genome:
- Circular double-stranded DNA chromosomes
- Chromosome is not bounded by a membrane, it is organized in the nucleoid
- Have smaller circular pieces of DNA (plasmids)
,- Their genome is a combination of chromosomal DNA and plasmid DNA
Differences between DNA and RNA:
DNA:
- Bases: (A) adenine, (T) thymine, (G) guanine, (C) cytosine
- Base pair: A-T and G-C
- Sugar: deoxyribose
- Structure: usually double-stranded
RNA:
- Bases: (A) adenine, (U) uracil, (G) guanine, (C) cytosine
- Base pair: A-U and G-C
- Sugar: ribose
- Structure: usually single-stranded
What is initiation, elongation, and termination? - answerInitiation: RNA polymerase
binds to the promoter and melts a short stretch of DNA
Elongation:
- Sigma factor dissociates from RNA polymerase, leaving the core enzyme to complete
transcription.
- RNA is synthesizes in the 5' to 3' direction as the enzyme adds nucleotides to the 3'
end of the growing chain
Termination: When RNA polymerase encouters a terminator, it falls off the template and
releases the newly synthesized RNA
- How is information transmitted in replication, transcription and translation?
- Difference in eukaryotes and prokaryotes - answerDNA replication: Double-stranded
DNA is duplicated so its encoded information can be passed on to the next generation.
Gene expression (2 events):
1. Transcription: information encoded in DNA is copied into RNA
Transcription:
Prokaryotes
- transcripts (mRNA) often contain sequence for several genes
- transcription and translation happen at the same time, as soon as mRNA beings to
form ribosomes attach and begin making proteins
Eukaryotes
- transcripts contain sequence from a single gene
- mRNA transcripts are transported out of nucleus or they can be translated in
cytoplasm
, Discuss the different types of RNA and the significance of each. - answerRibosomal
RNA (rRNA):
- Not translated
- They make up the ribosome structure
- Serve structural and catalytize the bonds between amino acids in the newly
synthesized protein
tRNA:
- Not translated, but participate in translation process
*plays a critical role in protein synthesis
- involved in interpreting genetic code (each molecule carries a specific amino acid)
mRNA: is translated as a 3-letter-code
- translated during protein synthesis
- used to synthesize the encoded protein
- How many nucleotides are used to encode an amino acid?
- What does it mean that the genetic code is degenerate (redundant)? - answer- Various
combinations of 3 bases could code for 64 different amino acids, but codes for 20
- RNA code is redundant
*Redundancy allows some level of mutation to occur in DNA or RNA without changing
the protein
- What is a polycistronic message?
- Are they found in prokaryotes or eukaryotes? - answerPolycistronic message: mRNA
molecule encodes information to multiple genes for different proteins
*Found in prokaryotes as mRNA molecules carry the information for one or multiple
genes
- What is an operator? What binds to this element?
- What is a promoter? What binds to this element? - answerOperator:
- Region located immediately downstream of a promoter to which a repressor can bind
- Binding of the repressor to the operator prevents RNA polymerase from progressing
past that region (blocking transcription)
- Binds a regulatory protein
Promoter: DNA (nucleotide) sequence to which RNA polymerase binds to start
transcription
What is the difference between an inducible system and a repressible system? -
answerHow are genes regulated?
1. Inducible: are usually "off", not transcribed until specific inducing molecules are
present
