Week 1 Flashcards
introduction to cells, model organisms and humans, info flow, introduction to nucleic acids, molecular interactions in the cell
3 points of cell theory
- the cell is the basic organizational unit of life
- all organisms are comprised of 1 or more cells
- cells arise from pre-existing cells
examples of prokaryotic cells
bacteria and archaea
examples of eukaryotic cells
plants, fungi, animals, humans
differentiate prokaryotic and eukaryotic cells in regards
- nuclei presence
- cell#
- organelles (membrane)
- size
- complexity
prokaryotic: no nuclei, single celled, smaller, no membrane bound organelles, less DNA than eukaryotes
eukaryotic: nuclei, single celled or multicellular, several membrane bound organelles, larger size and more complex
describe the origins of the mitochondria in regards to the entangle engulf endogenize model (be detailed!)
name the more predatory mechanism of the origins of the mitochondria
phagocytosis (endosymbiotic theory from HS)
what is the E3 model
entangle engulf endogenize model
list 4 similarities between the phagocytosis model and the E3 model
- includes an ancient anaerobic archaeal cell
- ancient aerobic bacterium
- occurs over evolutionary time
- a symbiotic relationship between the two
describe the process of e3 (very long, goodluck)
hints: 2 parter: enclosure of ectosymbiont by archael membrane fusion then escape of endosymbiont into cytosol and formation of new intracellular compartments
Over time, the archaeal protrusions expanded to completely engulf the bacterial endosymbiont.
It begins with an anaerobic prokaryote with archaeon DNA beginning to envelop a bacterial ectosymbiont. the archaeal protrusions (surface) expand and entangle the bacteria (this is where it is becomes a aerobic prokaryote? - own dna, membranes, not completely enclosed within the cell). the bacterial ectosymbiont is named the bacterial endosymbiont at this stage
the bacterial endosymbiont becomes the presursor of the mitochondria. the prokaryote begins forming the nuclear envelope, the eR, and is the precursor to the aerobic eukaryote.
why is the e3 model preferred compared to the phagocytosis theory (2 reasons)
- Phagocytosis models make it seem as an amoeba; nothing about er, nothing about nuclear envelope evolution
- This model can show the development when there might be fusions for the nuclear envelope and beginnings of the ER
explain how the e3 model can describe the evolution of chloroplasts (in brief)
a prokaryotic bacteria that can photosynthesize goes through the same process
why are mitochondria and chloroplasts a justification of the e3 model:
can _________ within the cell, have ______ dna, have _______ membranes
can reproduce within the cell, have their own dna, have double membranes
The endosymbiont thought to be a precursor of ____________
cellsw
what modern archaeal cell was found in the sediments of the ocean
ASGARD cell
t/f modern archaeal cells stopped entangling and engulfing!
false!
on an evolutionary timescale, what two divisions did the ancestral bacteria split into?
bacteria and archaea
on the evolutionary timescale, what factor may have caused bacteria to evolve into mitochondrion
As o2 levels increase in the planet, what may have happened in the E3 of aerobic bacterium around here, which is what led to mitochondria precursor and over time, created the eukaryote
on an evolutionary timescale, which came first: the evolution of mitochondria or chloroplasts
mitochondria
around how many years ago did the evolutionary timescale of ancestral bacteria begin
3.5-3.8 billion years ago
list the 3 lines of evidence to support the endosymbiont hypothesis
fun fact! Antibiotics that affect bacteria, mito and etc are sensitive to the same types
- mitochondria and chloroplasts still have remnants of their own (circular) genomes and their genetic systems resemble that of modern-day prokaryotes
- mitochondria and chloroplasts have kept some of their own proteins & DNA synthesis components and these also resemble prokaryotes - own ribosomes, machinery for dna replication, grow and divide similarly to bacteria
- membranes in mitochondria and chloroplasts often similar to those in prokaryotes and appear to have been derived from engulfed bacterial ancestor
what is the information flow of the cell (central dogma)
dna to rna to protein
through what process can we change from the different parts of the central dogma
dna (transcription) rna (translation) protein
name the different RNAs
mRNA (messenger)
tRNA (transfer)
rRNA (ribosomal)
what is the roles of the different types of RNA
mRNA (messenger): undergoes translation to protein
tRNA (transfer): transports AAs, for protein synthesis, structural role and function
rRNA (ribosomal): part of the ribosome, catalytic function
what is the genome
all the dna in the cell, usually includes mitochondrial and chloroplast dna
what is the transcriptome
all the rna that is in the cell at a particular point in time
what is the proteome
all the proteins in a cell at a particular point in time
what is the interactome
full set of protein-protein interactions that are happening in a cell at a point in time
what is the metabolome
full set of metabolites that are found in a cell at a point in time
what are metabolites
atp, vit, etc and tends to be smaller than proteins
what is the phenome
all the other -omes (genome, transcriptome, proteome, interactome, metabolome) with some clinical observation
t/f the transcriptome, proteome, interactome, metabolome are dynamic
true
consider another reason for why scientists believed prokaryotes evolved into eukaryotes
similar genetic code which is essentially universal among all species
how is info in RNA seq translated into AA sequences (via what)
genetic code
dna, rna and proteins are synthesizes as ____________________________
linear chains of info with a definite polarity (polarity is directionality)
what happens to the # of strands from dna to rna
dna is double, rna is single
dna is able to determine what of the cell
the chemistry, the function of the cell
dna is short for
deoxyribonucleic acid
rna is short for
ribonucleic acid
name the subunits/monomers that compose dna and rna
nucleotides
list the 3 parts of the nucleotide
pentose sugar, nitrogenous base, phosphate group (backbone, 1/2/3 phosphate groups)
which bases are pyramidines
(single ring)
C (1 nh2 and 1 double bonded O), T (ch3, 2 double bonded O) and U (only 2 double bonded O)
which bases are purines (double rings)
A (had no double bonded O) G (has double bonded O)
what are the nitrogenous bases of rna
gcau
what are the nitrogenous bases of dna
gcat
what is the names of the following
sugar + base + 1p
sugar + base + 2p
sugar + base + 3p
nucleoside monophosphate
nucleoside diphosphate
nucleoside triphosphate
differentiate between a nucleoside and nucleotide
nucleoside: base and sugar
nucleotide: base and sugar and phosphate
how are nucleotides linked and what direction
phosphodiester bonds, 5’ to 3’ (the polarity)
dna is synthesized by ______ rna is synthesized by _______
dNTPs (deoxyribonucleoside triphosphates)
NTPs (ribonucleoside triphosphates)
list the noncovalent attraction interactions between individual moelcules
- electrostatic attraction: ionic, mid strong but not as strong in water
- h bond
- van der waals
- hydro[hobic force
explain van der waals and its signifance in DNA
When 2 atoms close enough together, there becomes flickering dipoles which allows those atoms to be attracted to each other - these are weak on their own, but when you have many atoms packed together (eg in dna) they can become strong
When you have stacked bases, you have many atoms close together which provides the situation to have the transient flickering of dipoles which helps to hold the DNA strands
t/f the noncovalent interactions are very strong forces individually
no, very weak indiv, but can sum to generate strong binding between molecules
how many h bond between cg and ag
cg is 3, ag is 2
how to describe orientation of double stranded dna
antiparallel
why is helix preferred
thermodynamically stable and it is the energetically favorable conformation
what are the 3 forces that keep dna strands together
- h bond
- hydrophobic interactions: bases in (bases described as planar), rings out
- van der waals
__________ contributes to the stability (not helix)
bases stracking
proteins can recognize and make contact with specific dna sequences in the _______________
major and minor grooves (minor is narrower)
t/f proteins only make contact with major groove
false! major and minor
where does major and minor grooves come from
it is a result of the way the helix is coiled together
the sequences of the two dna strands are _________ and can be ________
complementary, unzipped
the complementary and unzipping nature is important for
dna replication (including pcr) and rna synthesis
what composes the 5’ and 3’ end of the dna
5’ phosphate group (-PO4)
3’ hydroxyl group
t/f separating and rejoining dna strands is a reversible process that is performed by proteins in the cell and with heat in the lab
true
