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