Synthetic Biology Exam 2

Viral, bacterial, and eukaryotic genomes.

virus

obligate intracellular parasite

extracellular virus particles

Virions

key virus components

Nucleic acid

Capsid

Sometimes an envelope

viral location of nucleic acid

Capsid

bacterial nucleic acid location

nucleoid

eukaryotic nucleic acid location

nucleus

viral extrachromosomal DNA elements

none

bacterial extrachromosomal DNA elements

plasmid

eukaryotic extrachromosomal DNA elements

mitochondria

viral DNA structure

nucleocapsid

bacteria DNA structure

HU proteins

eukaryotic DNA structure

histones

viral tertiary DNA structure

none

bacterial tertiary DNA structure

supercoiling

eukaryotic tertiary DNA structure

chromatin fiber

viral genome segmentation

either

bacterial genome segmentation

(usually) non-segmented

eukaryotic genome segmentation

segmented

viral genome size

1K-10Ks bp

bacterial genome size

1.5-10 millions bp

eukaryotic genome size

billions bp

viral number of genes

3 - couple hundred

bacterial number of genes

hundreds to thousands

eukaryotic number of genes

10 thousands

viral gene density

very compact

bacterial gene density

dense with overlapping genes

eukaryotic gene density

not dense

a lot of space in between genes

viral gene structure

varies by host

bacterial virus no introns

eukaryotic virus yes introns

bacterial gene structure

no introns

eukaryotic gene structure

yes introns

requires splicing

virus repetitive DNA?

no

bacteria repetitive DNA?

small amounts of transposons

eukaryotic repetitive DNA?

tons

bacterial gene arrangement

operons

eukaryotic gene arrangement

gene families

virus genomes can be…

circular or linear

segmented or non-segmented

single or double stranded

DNA or RNA

reverse transcriptase

enzyme that converts RNA to DNA

virus classification system

Baltimore classes

why do viral genomes contain have overlapping genes?

time and space-saving mechanism to optimize time in the host

glycoprotein spikes

proteins found on virus envelope that attach to the host cell

retrovirus

contains 3 genes and long terminal repeats

integrates into host DNA permanently

what does a virus NOT have?

ribosomes

ATP

amino acids

lytic life cycle

viral latency period to build up replicants before bursting the cell to spread

steps of the lytic life cycle are:

attachment and uncoating

transcription and translation of proteins

replication of the genome

assembly

release (burst)

viruses use what in a cell to complete its life cycle:

organelles

what is used to visualize bacteriophage lysis?

plaque assay

what is a plaque?

missing space on plate that shows where bacteria have burst

PFU

plaque forming units

lysogenic phase

good environment

virus stays within host cell

lytic phase

bad environment

virus wants to burst cell quickly and leave

eukaryotic viruses

retrovirus integration

uses reverse transcriptase to convert viral RNA into DNA and inserts into the host genome

retroelement

stays within the cell

copies itself and re-integrates

amount of our genomes made of retroelements:

40%

HA glycoprotein

gets virus INTO cells

NA glycoprotein

gets virus OUT of cells

virus limitations

species

tissue type

what determines a viral infection?

specific binding of glycoproteins and host cell receptors

what causes a pandemic?

viruses that come from other species

what species do flu viruses often come from?

birds

reassortment

substantial change in virus DNA

mutation

virus with some changes

synthetically replicated virus example

1918 spanish flu

HATX91:1918

1 HA gene from TX virus

7 genes from 1918

inactivated vaccine

dead virus

structure changed by heat

requires a lot of live virus to produce

live attenuated

alive but weakened/changed form

may revert to infectious form

protein subunit

uses only a portion/the toxin product

mRNA

limited by how the protein is coded for mutates

requires a booster for new variants

codon deoptimization

substituting suboptimal codon pairs to slow translation

amino acid sequence is unchanged

overall codon usage is unchanged

SAVE

synthetic attenuated virus engineering

COVI-VAC

live covid vaccine

prevents reversal to infectious form

broad immune response