Topic 3 - Genomes, Genetics, Genomics Flashcards
Central Dogma of Life (information flow)
DNA –> transcription –> RNA –> translation –> Protein
also DNA replication where DNA is copied
DNA Structure! (6 major points)
don’t hate me for this one; it’s long
- Made up of nucleotide monomers (nucleotides are made up of 4 nucleobases)
- Deoxyribose (5 C sugar) with a 5’ Carbon phosphate
- Phosphodiester Bonds - connect nucleotides between 5’-phosphate groups and 3’ hydroxyl groups
- Sugar phosphate backbone
- Anti-parallel & double stranded - two complementary DNA strands that form a helix via nucleobase interactions
- Runs 5’ to 3’
What are the 4 DNA bases?
Adenine (A), Cytosine (C), Guanine (G), Thymine (T)
What DNA Bases are Pyrimidines + Explain Structure
Cytosine(C) and Thymine (T)
- have 6 membered rings (so there’s only one hexagon basically)
What DNA Bases are Purines + Explain Structure
Adenine (A) and Guanine (G)
- makes ‘Ag’ which is Silver in Chem - it’s ‘pure’ ==> purine
- fused 5/6 membered rings (a pentagon + hexagon stuck together)
What are the DNA base pairings and which ones are weaker?
A/T base pair - it’s wear with only 2 hydrogen bonds
C/G base pair - it’s stronger with 3 hydrogen bonds (more stable + harder to break 3 bonds)
DNA and RNA Differences (4)
also long, but you got this!
- RNA has a 2’-hydroxyl group (OH) on its ribose sugar
- RNA is less chemically stable than DNA (the 2’ OH can cause hydrolysis of sugar phosphate backbone)
- Thymine (T) replaced by Uracil (U) - Uracil doesn’t have a methyl group
- RNA is single stranded - but can fold into different structures!
- RNA basically does all the work
Prok. Chromosome Structure (3)
hint: hair ties
- Circular but is extensively supercoiled in order to fit inside cell (reminds me of those coiled hair ties)
- many proteins keep it in that circle shape - DNA must be compact to fit in cell
- Nucleoid - section of the cell where the chromosome lives (like the nucleus but is NOT sectioned off)
What are the 2 Exceptions learned that do not only have 1 circular chromosome?
- Vibrio Cholerae - has TWO circular chromosomes
- one has ~ 3 million base pairs (Mbp) and other has ~1 Mbp - Streptomyces - has LINEAR chromosomes
- they also make antibiotics (how coooool)
Eukaryotic Genomes (3)
- Multiple Linear Chromosomes
- Are generally larger and less compact
- Basic Rule: The smaller the size, the more compact genomes
_____ are segments of genetic material that encode a functional protein or RNA product
Genes :)
A typical microbial genome is comprised of:
~ 85-90% of protein encoded genes
~ 1-2% RNA coding genes (tRNA, rRNA)
~10% non-coding DNA (aka. junk DNA)
Genes are often organized into _________.
Functionally-related clusters
- where the function of surrounding genes can give you an idea of the gene’s function
Which type of microbes require a host? (2)
- Endosymbionts - can only live within cells of another organism
- Parasites
Both rely on the host for everything ==> small genomes
_______ is a parasite with the smallest genome ever (0.5 Mb genome (500 genes))
Mycoplasma
In prok. genomes, as genome size increases, the number of genes ______.
increases
Core genome
- genes in ALL members (usually conserved genes)
- its the middle part of the Venn diagram (shared by all)
Pan Genome
- all genes in any member (rare genes)
- one of the circles in the Venn diagram
Nucleosides v.s Nucleotides
Nucleosides - no phosphate group (just the tiny pentagon part of DNA)
Nucleotides - the entire thing
Homologous genes arranged in the same order in their genome is called _______.
hint: the word is kinda like synonym (‘same’)….
Synteny (the common arrangement of genes)
Genomic Islands vs Islets
Islands - large blocks of unique genes
Islets - smaller blocks of unique genes
An important Genome Island Example
hint: he talks about it all the time
Salmonella Pathogenicity Island-1 (SPI-1)
- encodes genes for type III secretion system which lets Salmonella enter host cells
- this island is found in all Salmonella but absent from close relatives (ex. E.coli)
What is a prophage?
– it’s the part of a bacteriophage genome inserted into the genome of another bacterium
What’s a bacteriophage?
they’re like cute spiders with giant heads
- are viruses that infect bacteria
How will some bacteria benefit from a prophage?
- prophages can carry cargo genes: extra genes that could end up being helpful for the host bacteria :)
for ex. many bacterial toxins are encoded by prophage
Genomic Diagram
the fancy circle
- key info. + strain name is in the middle
- shows key features + locations of genes
- sometimes, some genes are highlighted for special attention
Plasmids
- are circular DNA molecules replicated in the cytoplasm
- use host cell machinery to replicate itself
- many Bacteria + Archaea have them (separate from genome)
- vary in size and copy number (how many per cell)
Gene Naming Convention (for prok.)
Four letters
- first 3 are lowercase, describe the gene function (acronyms)
- last letter UPPERCASE, describes a specific gene (ABCDEF…)
Gene names are italicized
ex. btuC (imagine this is italicized)
Protein Naming Convention
4 letters
- first 3 are gene function, first letter is CAPITAL
- last one is specific gene (ABCDE..)
- NOT italicized
ex. BtuC
ex. RpoS is a _________ and purF(in italics) is a ________.
hint: check the naming convention
protein; gene
Mutation
heritable change in the DNA (ex. addition/deletion of a base)
Mutant
the organism whose genome carries a mutation
Wild-Type Strain
- isolated from nature, naturally occurring
- or one being used as the parental strain in a genetic study
Genotype
genetic makeup of an organism (can’t see it)
Phenotype
observable characteristic of an organism
types include: metabolic, virulence, morphology etc.
A _______ is a specific position on the chromosome
Genomic locus (loci = plural)
Mutation Naming Convention
Wild Type base/a.a, then number, then mutant base/a.a
ex. HisC (A77K) - residue 77 mutated from alanine (A) to lysine (K)
What symbol do you use when naming a deletion mutation?
the delta symbol!
ex. ΔbtuC
Phenotype Naming Convention
3 Letter Acronyms:
First letter= capitalized
Strains are shown with a + or - for the phenotype
ex. His+ strain can make histidine; His- cannot.
What are point mutations + name the 3 types?
mutations to a single base pair
silent, missense & nonsense
Silent mutations
is a different codon but ==> ends up being the same amino acid (no change to a.a sequence)
Mutations that lead to a change from one amino acid to another are called ______
Missense mutations (quote common too!)
Nonsense Mutations
leads to an early stop codon –> results in premature protein
This makes no sense!
Truncation
the shortening of the protein (due to nonsense mutations)
Which mutations result in DNA being taken out? (lost)
Deletion mutations (and giant deletions can happen!)
Which mutations result in DNA being added?
Insertion mutations
Frameshift Mutations
- occur due to deletion/insertion mutations
- when the reading frame all shifts downstream and scrambles it all
How many base pairs can be deleted without resulting in a frameshift mutation?
3,6 or 9!
Reversions
a mutant which acquires another mutation to ‘revert’ back to wild type
Suppressor Mutations
hint: they ‘fix’ the problem
mutations that compensate for the effects of a previous mutation (it ‘fixes’ the previous mutation)
What is the natural mutation rate?
~10e-6 per 1000 bp per round of replication for prok.
1 in a million to ten million of a chance to get mutations
Horizontal Gene Transfer
getting new genetic material from foreign DNA from the environment, a virus or another organism
What are the 3 ways Foreign DNA can enter a prok. cell?
- Transformation
- Transduction
- Conjugation
What can foreign DNA do once inside a cell? (3)
- Be degraded/lost/not used
- be replicated separately (plasmids, phage)
- be integrated into the chromosome
What is Genetic Recombination?
it’s the physical exchange of DNA between genetic elements.
DNA 1 DNA 2 (bits of each DNA are shared with one another
Homologous Recombination
a specific type of genetic recombination (HR) that’s used to repair DNA double strand breaks.
- damaged DNA is repaired used homologues template
What is RecA?
hint: mediates strand invasion!
- an enzyme used in homologous recombination where it binds single stranded DNA and searches for a homologous double stranded DNA
- DNA strand from one source fused to DNA strand of another
What is the conservative mechanism for transposable elements?
hint: it’s like the cut + paste mechanism!
- a transposase gene flanked by inverted repeats
- the transposase enzymes will recognize these inverted repeats, cut out the transposable element in the middle and insert it into another DNA!
===> process called transposition
What is the replicative mechanism for transposable elements?
Hint: copy + paste
transposon remains at locus and a copy is produced and inserted elsewhere
A cell that is capable of taking up free DNA is called ________.
competent
some bacteria/archaea are naturally competent, some aren’t
Can DNA freely cross the cell membrane?
this one’s easy to boost confidence :)
nope, it’s a large and charged molecule!
How is DNA brought into the cell of competent organisms?
pili bind to the DNA and retract it into the periplasm
-one stranded degraded, other passed through membrane via competence system
What are virus DNA packaged into?
virions; they have a protein coat to protect DNA
Difference between Lytic and Lysogenic Pathway for bacteriophage infections?
Lytic: phage DNA is replicated, then viruses lyse the host cell
Lysogenic: viral DNA integrated into host (prophage) and can be induced —> can trigger lytic pathway
True/False: Phages can either be purely lytic or temperate (both lytic and lysogenic pathway)
Trueeee!
When a virus (phage) transfers DNA from one cell to another, it’s called _________.
transduction!
What are the two types of transduction?
generalized; specialized
Generalized Transduction?
- during lytic cycle when host DNA is accidentally packaged into a viral particle and injected into a new cell instead of phage DNA
Specialized transduction?
- when a prophage is induced, its DNA is packaged into phage particles along with some neighboring DNA by mistake
- this is then injected into a new cell by phage particle
What type of horizontal gene transfer requires cell-cell contact?
conjugation (mating)
What mediates conjugation?
- mediated by conjugative F plasmids with F+(donors) and F- (recipients)
What are F-plasmids?
- fertility plasmids originally found in E.coli
- strains with F plasmid are F+ donor cells
- strains without are F- recipient cells
True/False: In conjugation, DNA transfer occurs bidirectionally
False! DNA transfer is unidirectional, only from donor F+ cells to recipient F- cells.
tra (transfer) genes in conjugation?
- encoded by F-plasmids
- these genes can encode conjugative pilus which reaches out and grabs F- cells
Role of oriT in conjugation?
- DNA is nicked off at beginning of origin of Transfer (oriT)
- single strand is copied
Type IV secretion system in conjugation
- when DNA is nicked off and copied, the single strand is passed down this secretion system
- transfers F plasmid DNA from F+ to F= cell through conjugative bridge
How is a conjugative bridge formed?
when pilus connects two cells together
True/False: After conjugation, the F+ donor cell becomes F- cell.
False. F+ cell remains F+, and F- recipient cell becomes F+.
Conjugative transfer for Hfr strains
High frequency recombination
- doesn’t transfer the full plasmid, so F- cell remains F-.
How can you tell if a microbial genome contains a lot of horizontally-acquired DNA?
checking the %GC content - when it’s different than the rest of the genome and absent from loci in related lineages
Craig Venter
hint: he was super influen…tial
- used shotgun sequencing
- major name in DNA sequencing!
- first complete genome of H. influenzae
True/False: DNA sequencing became more expensive over time.
False. It’s wayyyy less than it once was!
What is Shot Gun Sequencing?
-sequence random bits of DNA - then let the computer figure out the rest
Sanger Sequencing
- by Fredrick Sanger
- a DNA polymerase to build a complementary strand using: dNTPs and rare special dNTPs without an 3’OH
- different length DNA that end with a labelled ddNTP
True/False: Special ddNTPs are labelled a different way using different fluorophores in Sanger sequencing.
True!
Illumina sequencing (next-generation sequencing)
- generating millions of copies of different DNA molecules being sequenced
- uses reversibly terminated dNTPs and unblock the 3’ end to add another residue
_______ is the study of proteins which uses mass spectrometry to identify proteins/protein levels.
Proteomics
What is metagenomics?
the study of a complete genetic content of an environmental sample
________ is the process when RNA is converted back to DNA, which can then be sequenced via next-generation methods.
reverse transcription!
True/False: This topic is such a ‘doozy’.
VERY TRUE
