Topic 1 - Intro and Background Flashcards
What is a key limitation of CRISPR gene editing?
Can only edit genomic DNA, not mtDNA (because the machinery cannot cross the mitochondrial membrane)
Who was the first person to identify and describe cells?
Robert Hooke
What was Robert Hooke looking at under the microscope when he first observed cells? Describe the state of the cells
Looking at cork (dead plant material)
Wasn’t actually looking at cells, he was looking at where cells used to be (plant cell walls being observed)
Who was the first person to observe living cells?
Antony van Leeuwenhoek
What was Antony van Leeuwenhoek observing when he first observed cells?
Volvox (an alga)
Why are cells called “cells”?
Robert Hooke thought they looked like the cells that monks used to live in but in miniature
What three statements make up the cell doctrine?
- Cells are the smallest living unit
- Cells are distinct units with specific tasks
- A cell can only derive from another cell by cell division
What kind of organism does NOT follow the rules of the cell doctrine?
Viruses
What are the 3 domains of life?
Bacteria, Archaea, and Eukarya
Why are phylogenetic trees of the whole tree of life constructed using rRNA instead of genomic DNA? (3)
- rRNA is in all cells
- It is easy to clone and get a lot of for analysis
- It follows predictable patterns of mutation
What are the 7 universal features of all cells?
- Store hereditary info as cells
- Replicate hereditary info
- Transcribe DNA into RNA
- Translate RNA into proteins
- Use proteins as catalysts
- Use the same molecular building blocks to produce materials
- Are enclosed by a plasma membrane
Describe the lipids in the membrane of Archaea, bacteria, and eukaryotic cells
Archaea: Branched hydrocarbons
Bacteria and Eukarya: Unbranched hydrocarbons
Why may it be useful for archaea to have branched hydrocarbon-lipids embedded in their membranes?
This might help stabilize organisms in environments where temperatures are extreme, help them to grow and proliferate under these conditions
Which domain(s) of life lack peptidoglycan in their cell walls?
Archaea and eukarya
The only domain(s) of life whose cells have membrane-bound organelles is/are…
Eukarya
No pathogens belonging to this domain of life have yet to be found
Archaea
What are the 4 basic features of all cells (think: prokaryotic/archaea cells, less complex)
- Plasma membrane
- DNA
- Ribosomes
- Cytosol
The smallest living organism is…
A bacteria, specifically: Mycoplasma spiroplasma
What are the 4 possible metabolic pathways in which organisms can create energy?
- Photoautotrophy
- Photoheterotrophy
- Chemoautotrophy
- Chemoheterotrophy
What 2 methods can be employed to identify bacteria?
- Growing bacteria in medium, in culture
2. Gene sequencing
What kind of metabolic pathway (chemo/photo, auto/hetero) pathway do humans use?
Chemoheterotrophy
Why can’t all bacteria be grown in a lab culture?
May not know their needs (some need light, pH, specific nutrients, etc.)
What is the biggest bacterium? How big is it?
Thiomargarita magnifica, over 1 cm long
What is atypical about Thiomargarita magnifica compared to other bacteria, other than its size?
It has membranes inside it enclosing different regions, similar to compartmentalization of eukaryotic cells
What organelles (not including the 4 required features for all cells) are specific to eukaryotic animal cells? (2)
- Centrosome with a pair of centrioles
2. Lysosomes
Do plants have centrosomes and centrioles?
Just centrosomes
What organelles (other than the 4 foundational components of all cells) are specific to plant eukaryotic cells? (4)
- Large central vacuole
- Chloroplasts
- Cell walls
- Plasmodesmata (not an organelle)
Describe fungal cells
Have cell walls, vacuoles (not always but often)
Sometimes their cell walls have large holes - this effectively links cells into one environment: effectively one large multinucleated cell
What are plasmodesmata?
Holes in the cell walls of plants or fungal cells
What are two examples of factors which can influence differentiation of cells into distinct cell types
- Differential expression of proteins/transcription factors
2. Epigenetic changes
Different sets of genes are usually activated in response to…
The environment - chemical processes and cues
What is the advantage of having compartmentalized cells?
Barriers allow for distinct regions to have different chemical environments. This is advantageous because:
- Some proteins are pH activated
- Chemical gradients (like proton gradients) are key in processes to create ATP
Why is it useful for proteins to be arranged within the cell?
Arrangement allows for signalling to occur faster due to increased efficiency of sorting
How do prokaryote and eukaryote genome sizes relate to each other, generally
Trend: Eukaryote genomes are larger than prokaryote genomes
Describe the trend in eukaryote genome size and level of organization of the organism
There is no trend
What is the size of the average bacterial genome (in # of genes)
1000-6000
What is the size of the average archaea genome (in # of genes)
1000-6000 (same as bacteria)
The largest bacterial genomes is over…
8000 genes
How many genes does a human have (range)
20,000-30,000
What does it mean for eukaryotes to have “hybrid DNA”
They have genomic DNA but also other kinds of DNA such as mtDNA
What organelles contribute to the hybrid genomes of eukaryotes?
Mitochondria and chloroplasts
What are 2 reasons eukaryotes tend to have larger genomes than prokaryotes?
- Have hybrid genomes
2. Have large amounts of non-coding DNA
How much of the human genome is protein coding (%)
2%
How much of the E. coli genome is protein coding?
89%
Explain why there is such a large difference in the percentage of protein coding genes between humans and E. coli
Bacteria don’t maintain their physical forms, humans do. Therefore, bacteria just replicate when they have nutrient availability, when you need to reproduce quickly it makes more sense to have less DNA to replicate - tightly regulated genes
humans do other things with their nutrient availability and this has to be REGULATED, a lot of human non-coding DNA is regulatory.
What do bacteria and mitochondria have in common?
- No nucleus but have their own DNA
2. Have their own ribosomes
Plant cells have both mitochondria and chloroplasts, which did they take up first?
Mitochondria
Are mitochondrial ribosomes more similar to eukaryotic cytosolic ribosomes or bacterial ribosomes?
Bacterial ribosomes
What is the difference between the zebrafish genome and the Fugu genome?
Have the same number of genes but zebrafish has a 4x larger genome due to larger areas of noncoding DNA
Why do plants have such a huge range of genome sizes?
Polyploidy is common in plants - depending on the Xn (e.g. 3n, 9n) the genome size varies
Define the term Karyotype
A complete set of human chromosomes
A situation where chromosomes 4 and 6 transfer segments to create “hybrid chromosomes” is an example of…
Reciprocal chromosomal translocation
Reciprocal chormosomal translocation is often observed in (1) patients
Cancer
How are different chromosomes fluorescently labelled?
DNA probes can be inserted into a chromosome “pool” and bind to specific sequences - unique to a particular set of chromosomes
Does the number of chromosomes in a species correlate with its complexity?
No
Describe the gene density of yeast compared to humans
Gene density is higher in yeast than it is in humans (for a given number of bases, how many genes are within that sequence)
Describe the intron size as it relates to the human vs. Fugu Huntingtin gene
Same number of exons in both species for that gene, but the entire gene is much longer in humans due to larger introns/repetitive sequences
If humans and mice are both mammals, why do mice have smaller genomes?
Humans have experienced several genome duplication events, some sequences have been lost/added resulting in a different (but very similar) number of genes between the two species
How much smaller (%) is the mouse genome compared to the human one?
20% smaller
Sequences which are conserved across species tend to be in these areas of a gene (2)
- Exons
2. Regulatory regions
About how similar (%) are humans to a banana
50% sequence identity
What are 4 processes which can eventually give rise to new genes?
- Intragenic mutation (e.g. base change in the gene exon)
- Gene duplication
- DNA segment shuffling (take 2 genes and “cross over”)
- Horizontal transfer (in plants mostly)
Describe Horizontal gene transfer
Transfer of a gene from one individual to another within its cohort (not its offspring)
Describe Vertical gene transfer
Transfer of genes from parent to offspring
Plants with tumors/galls often look like this due to…
Horizontal gene transfer of a bacterium to a plant
Orthologs and paralogs fall under the umbrella term of (1) genes
Homolog
What is an ortholog?
An ancestral gene mutates causing two distinct species, orthologs are often very similar with slight differences
E.g. hemoglobin gene in mice and humans
What is a paralog?
A gene duplicates and multiple versions of the gene are within the genome of the offspring which can now diverge
e.g. Hemoglobin and myoglobin, both in humans
What are transposable elements?
Genes which can “jump” from one region of the genome to another, they replicate themselves
What is a pseudogene?
Has the anatomy of a gene (promoter region, start and stop sequences, etc.) but never produces a protein product
What likely causes pseudogenes to be nonfunctional?
A mutation in the promoter region of the gene
What is a non-coding RNA gene?
Produces functional RNA as opposed to proteins
What 2 factors cause human genomes to differ from one another?
- SNPs
2. Duplication and deletion events
Why is it important to be able to identify humans by their DNA?
- Forensic investigations
- Identification of family members, paternity tests
- Therapies
