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Eukaryotic cells (3)
- 10-100 um
- Nucleus with linear chromosomes, surrounded by 2 lipid bilayer membranes
- Nuclear membranes have pore complexes and are contiguous with rough ER
Eukaryotic Genome Size
varies greatly, from 2.9 million BP to 2,800 million BP
How many linear chromosomes are found in Eukaryotic cells?
3 to 50
Describe Chromosomes in Eukaryotic Cells (5)
- 3 to 50 linear chromosomes
- Basic unit of chromosomes is DNA coiled around histones
- Visible by electron microscopy
- reside in nucleus
- get replicated every time the cell divides
Genome size of Eukaroytic organisms
2.9 million BP to 2,800 million BP
Subcellular organelles that have their own DNA
Three RNA Polymerases in eukaryotes:
- rRNA, in nucleolus, amanitin - resistant
- mRNA, amanitin - very sensitive
- tRNA, aminitin - somewhat resistant
Regions of gene not coding for AA:
The structure of a nuclear pore complex in a Eukaryotic cell consists of (5):
- Inner Ring
- Outer Ring
- Anchor Protein
- Active Trasporter
sensitive to diptheria toxin and cycloheximide, not sensitive to tetracycline or chloroamphenicol
Separation of DNA Strands in Eukaryotic cells:
Prokaryotic molecular biology
- Most have a single circular chromosome
- few thousand genes located on it
- single origin of replication
Molecular Biology of Archaea
- Chromosome circular, haploid
- Genome Size: 0.5 to 5.8*10^6 BP
- Most DNA are supercoiling
- DNA Gyrase is like bacteria
- 1-3 origins of replication
- No introns in most genes
- mRNAs not spliced, but translated directly
- Promoter- TATA-Box, TATA-Binding Protein like Eukarya
- RNA Polymerase: 1, like Eukaryotic RNA Poly II
- Rifamipin-Insensitive, Like Eukarya
Archaea Translation (4)
- Ribosomes 70S
- sensitive to diphtheria toxin
- resistant to most antibacterial inhibitors of protein synthesis (tetracyclines, chloroamphenicol)
- AUG start codons use methionine
Eukaryotice Translation (6)
- Ribsosmes are 80S
- Large subunit has 3 rRNAs, not just 2
- Ribosomes not inhibited by most bacterial inhibitors of protein sysnthesis
- are sensitive to diphtheria toxin
- No shine Delgarno site by start codon (AUG)
- first amino acid is methionine
- replicate independently of the chromosome
- may be present in several copies
- typically have genes which are not essential for the cell under basic conditions, however may assist in resistance to antibiotics, etc (these are specialized genes)
- In a circle/star shape
- Super coils are tangled together and held together by proteins
- Few million BP long
Processing of Eukaryotic Pre-mRNA (3):
- Attach 5-Methylguanosine Cap
- Attach Poly-Adenosine Tail
- Splice out Introns
Exons Code for
Folding/ FunctionalDomains of Polypeptide
DNA Synthesis Needs (4)
- Template Strand
- dATP, dCTP, dGTP, dTTP
- Enzyme: DNA Polymerase
- Cleave DNA at specific 4-6 ntsequences.
- Methylation canprotect from them.
- Some antibiotics block protein synthesis only in bacterial ribosomes
tRNAs with amino acids enter
tRNAs with amino acid form peptide bond
Compare Bacteria, Archaea, and Eukarya in terms of: Range of genome size
Bacteria has a slightly greater range than archaea
Compare Bacteria, Archaea, and Eukarya in terms of: Chromosome number and topography
Eukaryotes usually have a greater chromosome number. In bacteria it is usually one circular chromosome
Compare Bacteria, Archaea, and Eukarya in terms of: Extent of extragenic regions in DNA
Only present in eukaryotes.
Compare Bacteria, Archaea, and Eukarya in terms of: Presence of histones
Bacteria does not have true histones, but Eukaya and some Archaea do.
Compare Bacteria, Archaea, and Eukarya in terms of: Number of RNA Polymerases, and their structure
- Bacteria has one polymerase with two sub unit parts
- Many sub units in Eukarya
- Archaea have one polymerase but the one polymerase has 8-12 sub units (so is more similar in structure to eukaryotic polymerase)
Compare Bacteria, Archaea, and Eukarya in terms of: Presence of genes in operons
Eukarya and bacteria have genes in operons
Compare Bacteria, Archaea, and Eukarya in terms of: Presence of introns in genes
Only in Eukarya
Compare Bacteria, Archaea, and Eukarya in terms of: Size of ribosomes
Eukarya 80S; Archaea 70S; Bacteria 70S
Compare Bacteria, Archaea, and Eukarya in terms of: Sensitivity of ribosomes to cycloheximide vs tetracycline
- Eukaryotic insensitive to cycloheximide, sensitive to tetracycline.
- Archaea are sensitive to cycloheximide and not tetracycline.
- Generally starts with a material being acted on by an enzyme converting it to an intermediate.
- Process continues until an end product is reach.
- Process can be regulated at various steps.
Allosteric Regulation of Enzymes
- Allosteric molecule binds to an allosteric site.
- Catabolic pathways: starting material may be allosteric activator of enzymes, may activate transcription of genes.
- Anabolic pathway: end-product mat act as allosteric inhibitor, decrease transcription of genes.
Two-component Transcriptional Regulatory System:
- 1. Sensor kinase in plasma membrane.
- 2. Response regulator acts as transcriptional activator when phosphorylated.
A repressor protein can bind operator, blocking binding of RNA polymerase to promoter-blocks transcription.
A transcription activator protein must bind near promoter, and assist RNA poly binding at promoter.
Example of positive transcriptional regulation
- E. Coli prefers glucose as energy source
- Glucose used up, cAMP produced
- Signals to switch to other sugars (like lactose)
- cAMP binds Catabolite Activator Protein
- Stimulates transcription
another mechanism of regulating transcription of the trp operon
Control of Transcription in Archaea
- Mainly similar to Bacteria
- Repressor proteins bind TATA box and nearby BRE regions near promoter
- Block access of (TBP) and TFB general transcription factors
- Transcriptional activator proteins enhance binding of TBP at promoter
Most mRNAs in bacteria have a short half-life, and are degraded by ribonucleases, some of which target secondary structures.
Operons regulated by repressor proteins are known from some:
Transcriptional activators known from some:
Post-Transcriptional Regulationof Gene Expression:
- mRNAs degraded by RNAases
- Antisense RNAs bind to mRNAs
Total size from less than 2 kBP to over 200 kBP (3-100 genes)
- protein coat
- may be helical, Icosahedral, or complex
- consists of host membrane lipids and viral proteins
- may have role in binding and infection of host cells
Viral Life Cycle (5)
- virus binds to a host cell
- viral Genome is replicated
- viral proteins are made on host cell ribosomes
- new virions are assembled
- mature virions are released from the host cell
- Viruses of bacteria
- have virions binding to cell wall of host
- inject DNA genome into host cytoplasm
- capsid remains outside
entire virion taken into the host cell by endocytosis or membrane fusion
DNA viruses (dsDNA)
- Includes many bacterial viruses (bacteriophages)
- (–) strand DNA is template for making mRNA by RNA polymerase
- Genome of dsDNA replicated by DNA polymerase
DNA Viruses (ssDNA)
- must first make complementary DNA
- then DNA can replicate
- (–) strand serves as template for making viral mRNA
RNA genome viruses
May involve 2 kinds of RNA dependent RNA polymerases (Transcriptase & Replicase)
transcribes (-)strand RNA into mRNA
transcribes (+) strand RNA into ds replicative form (RF) RNA
- Have a RNA genome which is made into a DNA copy.
- The DNA copy is then made back into an RNA copy. An example is HIV.
Can replicate - move to new location in chromosome or plasmid
kills host cell
bacterial DNA carried alongin phage from cell to cell.
Replicating, infectiousRNAs, encode no proteins.
Misfolded proteins, infectious, catalyse misfolding of intact proteins
What accounts for the high rate of mutation in RNA genome viruses?
- DNA Polymerase has a mechanism where it
- changes mutations – RNA does not check.
Viral taxonomy determined by (4)
- type of nucleic acid
- capsid and envelope characteristics
- genome size and sequence
- host infected
What unique kinds of enzymes and unique information flow occur in life cycles of RNA genome viruses?
Genome RNA → + RNA / - RNA → - RNA
Bacteriophage T4 of E. Coli (5)
- has a genome that is moderatly large (~160k base pairs)
- icosahedral head, a stalk, and a base plate
- has a linear genome
- has a unique base in to prevent destruction of phage by host restriction endonucleases
Bacteriophage Lambda (3)
- About 48k base pairs long
- one of the earliest genomes to be sequenced
- looks like the other phages, but does not have the base plate
- rolling-circle replication mechanism
M13 Bacteriophage (4)
- single strand of DNA genome
- cylindrical virus that binds to the sex phylos that are produced to do conjugation
- viral DNA is transcribed to produce viral proteins
- host cell survives the entire process
M2 Bacteriophage (5)
- Have 3600 base pairs
- RNA can be translated directly by the host cell
- To replicate, replicase must be used.
- Takes single-stranded RNA and makes a (-) copy to make more (+) strand genomes.
- Kills host
Change in Physical Structure of DNA- such as changes in nucleotidesequence.
Errors in DNA polymerase but DNA poly. can proofread
- UV light, X-rays, Ionizing Radiation, Chemicals.
- Excision-repair enzymes can fix some damage
can grow on minimal, defined media with minerals (N, P, S sources) and C-source (glucose)
- Can’t grow on minimal media
- Mutation in a biosynthetic pathway, require amino acid, vitamin, ect.
- (-) stranded RNA genome
- The virus binds to receptors and is brought into the host cell by endocytosis.
- genomes then get into the nucleus of the host cell
- negative strands of RNA are transcribed by Transcriptase and assembled by Replicase
- Replicase does not proofread.
Antigenic Drift in Influenza virus:
- Host anitbodies no longer protect against virus.
- surface proteins will change
What is a sigma factor?
is a prokaryotic transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.
How does a sigma factor influence transcription of genes?