Biology 3 (Microbiology)

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Virus

Back 1

- Obligate intracellular parasite
- Can only reproduce in other host's cells
- NOT LIVING
- Can't synthesize ATP on its own, have to hijack the host's cell

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Virus Genome

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- Either DNA or RNA (not both)
- Single or double stranded
- Linear or circular
- Contained in a protein capsid shell

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Bacteriophage

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Virus that infects bacteria

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Bacteriophage Genome

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- Rigid and economical in size
- Carries only really necessary genes and relies on host for transcription/translation proteins
- Can overlap reading frames to code for two proteins

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Bacteriophage Structures (4)

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- Head
- Tail Fiber
- Sheath
- Capsid

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Head

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Genome located here

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Tail Fiber and Base Plate

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What attaches to the cell's surface

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Sheath

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- Injects Genome into host by contracting
- Uses stored ATP as energy
- Need to puncture cell walls

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Capsid

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Protein coat surrounding viral genome structure used to classify viruses

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Animal Viruses
Envelope

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- Surrounds capsid
- Derived from the membrane of its host

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Animal Viruses
Budding

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- How a virus gets the envelope covering

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Animal Viruses
"Naked" Virus

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- Don't have envelopes, don't need them
- Associated with cell walls, plant viruses, phages...

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Lytic Cycle

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- Rapid increase in numbers
- Destroys host cell in the process
- Phage genome made from dNTP of degraded host genome

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Hydrolase

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- Lytic Cycle
- "Early Gene" which is transcribed first, degrades host genome
- Expressed immediately after infection

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Lysozyme

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- Typical "Late Gene"
- Destroys bacterial cell wall (which protects against osmotic pressure)
- Cell bursts, releases viruses

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Lysogenic

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- Clever girls...
- Virus genome incorporates itself into host genome
- When host replicates genome it replicates prophage

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Prophage

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- Virus phage genome
- "Silent". Genes not expressed, progeny not made directly
- Prevented from replicating itself by host proteins that bind to to operator
- The trick is that the virus doesn't care. It sits there..waiting..until it removes itself and enters lytic.

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Animal Virus Replication
Protein Receptors

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- Animal virus likes to hijack receptors on a cel that have a normal function, virus uses these to recognize its target cell (smart)
- Host can't change this process because they have normal physiological functions too

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Endocytosis

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- Animal Virus Replication
- How the virus gets in, host cell engulfs it and internalizes it (recall membrane coat)

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Provirus

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Same thing as a prophage (virus DNA inserted into DNA of host)

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Life Cycles of Animal Virus

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- Lytic
- Lysogenic
- Productive

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(+) RNA Virus

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- MUST encode RNA dependent RNA polymerase
- Don't have to carry this
- Simplest kind of viral genome
- Makes (-) strand before generating new (+) genomes
- Host can't distinguish between virus mRNA and its own, so it's replicated

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(-) RNA Virus

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- Must carry RNA dependent RNA polymerase and encode it
- Makes a (+) strand when it infects host, and uses this (+) strand to make (-) strands.

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Retroviruses

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- Must encode reverse transcriptase
- They are basically (+) RNA viruses that incorporate themselves into host genome as proviruses
- Lysogenic viruses
- Enter as RNA, use enzyme to turn to DNA

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What's special about Prokaryotes?

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- No membrane bound organelles (nucleus, mitochondria, lysosome)
- Can still do cellular respiration and photosynthesis!

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Shapes (3)

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Cocci - Round
Bacilli - Rod
Spiralla - Spiral

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Prokaryotic Cytoplasm

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- No nucleus, so the genome is here (circular)
- Plasmid is here
- Transcription and translation occur in the same place, at the same time

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Plasmid

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- Circular piece of ds-DNA smaller than the actual genome
- Has genes that are advantageous, help with exchange of info in conjugation

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Prokaryotic Cell Wall

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- Has a lipid bilayer, outside of which is a cell wall (prevent lysis from osmotic pressure)

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Peptidoglycan

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- Unique construction of cross-linking sugars
- What's actually in the cell wall of prokaryotes

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Gram (+) Stains

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- Cell wall with peptidoglycan
- Lipid Bilayer
- Cytoplasm

- Stain DARK!

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Gram (-) Stains

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- Outer Membrane
- Periplasmic space with peptidoglycan
- Inner Membrane

- Stain LIGHT

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Prokaryotic Flagella

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- Whiplike filaments used for moving
- Can have one, at both ends, or many
- Different from eukaryotic!

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What affects Bacterial Growth?

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- Temperature
- Nutrition

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Chemoautotroph

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Build stuff from carbon dioxide using chemical energy

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Chemoheterotroph

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Rely on organic cmpounds for carbon and use energy from chemicals (this is us)

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Photoautotroph

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Use carbon dioxide as carbon source and light for energy (plants)

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Obligate Aerobes

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Love oxygen, need it to live

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Facultative Anaerobes

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Don't need oxygen, but will use it if it's there

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Tolerant Anaerobes

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Grow with oxygen or without it, won't use it

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Obligate Anaerobes

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Hate oxygen, it's a poison to them because they lack the enzyme that gets rid of oxygen free radicals

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Binary Fission

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- Bacteria don't have mitosis or meiosis
- They grow in size until they've got enough genome for two of them, and then split in half
- Genetically identical cells

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Lag Phase

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- Cell division doesn't happen here even in good times
- Need time to get division materials ready (genome)

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Log Phase

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- Major Groph
- If time to double is 20 minutes, and we start with 1 bacteria, after 4 hours we get 4096 bacteria

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Stationary

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- No dividing, because nutrients are getting limited

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Carrying Capacity

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- Maximum number the population that can withstand in an environment
- Limited by nutrients

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Endospores

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- Gram (+) Bacteria
- Form in unfavorable conditions
- Thick shells made of peptidoglycan, inside is everything needed to be metabolically active
- Sleep through bad times

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Sex in Bacteria (3)

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- Tranduction
- Transformation
- Conjugation

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Transduction

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Transfer of one genome to another

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Transformation

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Eat DNA, get new genes

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Conjugation

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- Physical contact, bridges mae from F+ (males) to F- (females)
- Transfer "factor" to females, which then become males
- Only occurs in the presence of females

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F Plasmid

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Has genes to produce sex pillus

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Fungi Composition

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- Multicellular eukaryotes
- Cell walls are rigid and made of chitin
- Chemoheterotrophs that feed primary through absorption (digestion outside cells)

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Fungi Reproduction (Asexual - 3)

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- Budding
- Fragmentation
- Spore Formation

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Fungi Reproduction (Sexual)

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- Adults are haploid (n)
- Fuse to form diploid (2n), which produce by meiosis to get more haploids.
- Do this through having opposite hyphae (+ and -)

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Define: Eukaryotic Translation

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Using:
1) A ribosome (including rRNA)
2) tRNA's coupled to amino acids
3) An mRNA transcript to make a peptide chain

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General function of Eukaryotic and Prokaryotic Translation

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A process in which mRNA issues orders that are read by the ribosome and carried out by molecules of tRNA coupled to amino acids.

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Difference between Prokaryotic and Eukaryotic Translation: Ribosomal

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Eukaryotic: Ribosome contains 40S and 60S subunit, making an 80S ribosome. They are synthesized in the nucleolus (site of rRNA synthesis via transcription, and where ribosomes are assembled from rRNA and proteins imported from the cytoplasm).

Prokaryotic: Ribosomes comprise 30S and 50S subunit, making a 70S ribosome.

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Difference between Prokaryotic and Eukaryotic Translation: Source of mRNA

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Eukaryotic: Transcription occurs in the nucleus, so after processing, the mRNA must move through nuclear pores from the nucleus to the cytoplasm. All Translational machinery in a eukaryote is housed in the cytoplasm.

Prokaryotic: No nucleus, therefore no nuclear membrane. Transcription (mRNA synthesis) and Translation (protein/peptide synthesis) both occur in the cytoplasm.

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Difference between Prokaryotic and Eukaryotic Translation: 5' UTR

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Eukaryotic: Kozak Sequence.

Prokaryotic: Shine–Dalgarno Sequence. Located 10 nucleotides upstream of the start codon.

Both are similar in that they function generally in assembly of the translation initiation complex.

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Difference between Prokaryotic and Eukaryotic Translation: First Amino Acid

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Eukaryotic: Methionine (AUG) Codon sequence for Methionine can be found in other places too.

Prokaryotic: N–Formylmethionyl tRNA

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Nucleolus

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Site of rRNA synthesis and ribosome synthesis. Eukaryotic cells.

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Difference between Prokaryotic and Eukaryotic Translation: Timing of Transcription and Translation

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Eukaryotic: Cannot occer at the same time due to the different locations of the processes. Transcription and RNA processing = Nucleus. Translation = Cytoplasm/Cytosol. mRNA processing must take place between Transcription and Translation.

Prokaryotic: Once the 5' end of the transcript has been made by RNA Polymerase, it undergoes Translation. Transcription and Translation occur simultaneously – RNA Polymerase can be building the 3' end of the mRNA as ribosomes are already reading the 5' end of the mRNA.

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the initiation phase begins with what binding to what in both prokaryotes and eukaryotes?

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Binding of a small ribosomal subunit to the mRNA.

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What happens to this sequence when it undergoes Transcription then translation?

5'–C G G–3'

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Transcribed:
Produces complementary mRNA molecule:

5'–C C G–3'

Translated:
The codon is presented at the ribosome's A site, where it is joined by the tRNA that carries the anticodon:

3'–G G C–5'

Front 66

Which sequences are written in a 5 –> 3
and which in a 3 –> 5?

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5 –> 3: DNA and mRNA sequences

3 –> 5: tRNA anticodon

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Definition of Genetic Code

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The association between each mRNA Codon and the amino acid for which it codes.

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Degenerate Genetic Code

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Means that more than one triplet codon can correspond to the same amino acid, part of the definition of the genetic code.

The Genetic code is degenerate!

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A codon is a nucleotide sequence situated on a molecule of ?

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mRNA