Week 1 Flashcards
origins of mitochondria (endosymbiosis) - entangle - engulf - endogenies (E^3) model
- archaean cell was anaerobic
- bacterial ecosymbiont was aerobic
- surface protrusions on archaea expanded over time
- this led to enclosure of ectosymbiont by archaeal membrane fusion
- escape of endosymbiont into cytosol and formation of new intracellular compartments
- over time, this evolved into modern-day mitochondria
did prokaryotes or eukaryotes form first?
prokaryotes formed much earlier, and then eukaryotes
what is an alternative model for endosymbiosis?
some models involve a more predatory mea hanse where the aerobic bacterium is engulfed via a process similar to phagocytosis
common features of both types of endosymbiosis models
- ancient anaerobic archaeal cell
- ancient aerobic bacterium
- over evolutionary time, a symbiotic relationship
Asgard cell
- type of archaea belonging to the group Asgard
- has a cell body and protrusions with ectosymbionts on their surface
describe and draw the sequence of the tree of life
ancestral prokaryote (3.5-3.8b years ago)
bacteria and archaea separated
1b years later, the first single-celled eukaryote was formed
lines of evidence to support endosymbiont hypothesis
- mitochondria and chloroplasts still have remnants of their own genomes, which are circular. their genetic systems resemble that of modern-day prokaryotes
- mitochondria and chloroplasts have kept some of their own protein and DNA synthesis components and these resemble prokaryotes too. they have their own ribosomes and multiply by pinching in half — the same process used by bacteria. are also sensitive to similar antibiotics.
- membranes in mitochondria and chloroplasts often similar to those in prokaryotes and appear to have been detached from engulfed bacterial ancestor.
general attributes of model organisms
- rapid development with short life cycles
- small adult (reproductive) size
- readily available (collections or wide-spread)
- tractability - ease of manipulation or modification
- understandable genetics
central dogma of molecular biology
DNA -(transcription)-> RNA -(translation)-> protein
tRNA
- transports amino acids
- protein synthesis
rRNA - ribosomal RNA
- part of the ribosome
- does catalytic work of making protein by creating peptide bonds
- has a structural role as part of RNA
refined central dogma
not all RNA is translated into protein - it has many other uses
draw a diagram for the elaborated central dogma information flow
genome
cell’s complete set of DNA, including mitochondria and chloroplasts
transcriptome
all the RNA in a particular cell at a particular point in time
genome vs transcriptome/proteome
transcriptome/proteome are much more dynamic
proteome
entire set of proteins in a cell at a particular point in time
how are the proteome and transcriptome related?
the proteome feeds information into the transcriptome
interactome
set of all protein-protein interactions taking place in a cell at a single point in time
metabolome
full set of small molecules that can be found in a cell at a certain point in time (anything that is generally smaller than a protein, like ATP, sugars, vitamins, some hormones)
example of metabolome affecting transcription
lac operon
phenome
comprised of everything (all the -omes), and together with the observable characteristics of what you’re looking at (cell, organ, etc)
describe the directionality of transcription and translation
- DNA, RNA, and proteins are synthesised as linear chains of information with a definite polarity
- info in RNA sequence is translated into an amino acid sequence via a genetic code which is essentially universal among all species
what are nucleic acids?
an organism’s blueprints - the genetic material in a cell
- DNA: deoxyribonucleic acid
- RNA: ribonucleic acid
three parts of a nucleotide
- pentose sugar - scaffold for base
- nitrogenous base
- phosphate group - backbone. There may be 1 (mono), 2 (di), or 3 (tri) phosphate groups
pyrimidines
UC The pyramids?
- single ring
- uracil
- cytosine
- thymine
purines
pure Animals Gobble
- double ring
- adenine
- guanine
where is the base attached?
1’
distinguish between ribose and deoxyribose in terms of functional groups
2’ carbon in ribose has a hydroxyl group - in deoxyribose it just has a hydrogen
nucleoside monophosphate
nucleoside vs nucleotide
nucleoside = base + sugar
nucleotide = base + sugar + phosphate
adenosine
sugar + adenine
guanosine
sugar + guanine
cytidine
sugar + cytosine
uridine
sugar + uracil
thymidine
sugar + thymine
nucleoside monophosphate
sugar + base + 1P
nucleoside diphosphate
sugar + base + 2P
nucleoside triphosphate
sugar + base + 3P
dNTPs
deoxyribonucleoside triphosphates
- DNA is synthesised from them
- N stands for A, C, T, G
NTPs
- N stands for A, C, U, G
- ribonucleoside triphosphates
- RNA is synthesised from them
nucleotides are linked by
phosphodiester bonds
overall charge on nucleic acids
negative all the way along
interactions between individual molecules are usually mediated by
noncovalent attractions:
1. electrostatic attractions (happen within and between large molecules) - weakened by water
2. hydrogen bonds - strongest in a straight line
3. van der Waals attractions - two atoms very close together, causing temporary dipole due to uneven distribution of electrons. not weakened by water
4. hydrophobic force - water pushing non-polar things away from itself. individually weak, but add up.
individually, very weak forces - BUT can sum to generate strong binding between molecules
Cell theory
- the cell is the basic organisational unit of life
- all organisms are comprised of 1 or more cells
- cells arise from pre-existing cells: the ability to reproduce is characteristic of living matter, which must be able to duplicate DNA, create proteins, etc
two main types of cell
eukaryotic and prokaryotic cells
prokaryotic
- no nuclei
- single celled (but communities may exist)
- bacteria and archaea (domains)
eukaryotic
- nuclei with membrane
- single-celled (eg algae) or multicellular
- plants, fungi, animals, humans, protozoans
describe and draw a prokaryotic cell
- no membrane-bound organelles; localised DNA may be in nucleoid or not localised at all
- smaller size than eukaryotes (~1micrometer)
- less DNA than eukaryotes
draw and describe a eukaryotic cell (plant)
- nucleus
- several membrane-bound organelles
- larger size and more complex (~5micrometers)
draw and label a eukaryotic cell (animals)
describe cytoskeletons in eukaryotic cells
- simple diffusion is not enough to guide transport
- cytoskeleton includes microtubules and actin filaments
