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BIO130 > Week 1 > Flashcards

Week 1 Flashcards

introduction to cells, model organisms and humans, info flow, introduction to nucleic acids, molecular interactions in the cell

1
Q

3 points of cell theory

A
  1. the cell is the basic organizational unit of life
  2. all organisms are comprised of 1 or more cells
  3. cells arise from pre-existing cells
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2
Q

examples of prokaryotic cells

A

bacteria and archaea

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3
Q

examples of eukaryotic cells

A

plants, fungi, animals, humans

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4
Q

differentiate prokaryotic and eukaryotic cells in regards
- nuclei presence
- cell#
- organelles (membrane)
- size
- complexity

A

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

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5
Q

describe the origins of the mitochondria in regards to the entangle engulf endogenize model (be detailed!)

A
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6
Q

name the more predatory mechanism of the origins of the mitochondria

A

phagocytosis (endosymbiotic theory from HS)

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7
Q

what is the E3 model

A

entangle engulf endogenize model

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8
Q

list 4 similarities between the phagocytosis model and the E3 model

A
  1. includes an ancient anaerobic archaeal cell
  2. ancient aerobic bacterium
  3. occurs over evolutionary time
  4. a symbiotic relationship between the two
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9
Q

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

A

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.

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10
Q

why is the e3 model preferred compared to the phagocytosis theory (2 reasons)

A
  • 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
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11
Q

explain how the e3 model can describe the evolution of chloroplasts (in brief)

A

a prokaryotic bacteria that can photosynthesize goes through the same process

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12
Q

why are mitochondria and chloroplasts a justification of the e3 model:
can _________ within the cell, have ______ dna, have _______ membranes

A

can reproduce within the cell, have their own dna, have double membranes

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13
Q

The endosymbiont thought to be a precursor of ____________

A

cellsw

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14
Q

what modern archaeal cell was found in the sediments of the ocean

A

ASGARD cell

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15
Q

t/f modern archaeal cells stopped entangling and engulfing!

A

false!

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16
Q

on an evolutionary timescale, what two divisions did the ancestral bacteria split into?

A

bacteria and archaea

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17
Q

on the evolutionary timescale, what factor may have caused bacteria to evolve into mitochondrion

A

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

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18
Q

on an evolutionary timescale, which came first: the evolution of mitochondria or chloroplasts

A

mitochondria

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19
Q

around how many years ago did the evolutionary timescale of ancestral bacteria begin

A

3.5-3.8 billion years ago

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20
Q

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

A
  1. mitochondria and chloroplasts still have remnants of their own (circular) genomes and their genetic systems resemble that of modern-day prokaryotes
  2. 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
  3. membranes in mitochondria and chloroplasts often similar to those in prokaryotes and appear to have been derived from engulfed bacterial ancestor
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21
Q

what is the information flow of the cell (central dogma)

A

dna to rna to protein

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22
Q

through what process can we change from the different parts of the central dogma

A

dna (transcription) rna (translation) protein

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23
Q

name the different RNAs

A

mRNA (messenger)
tRNA (transfer)
rRNA (ribosomal)

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24
Q

what is the roles of the different types of RNA

A

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

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25
Q

what is the genome

A

all the dna in the cell, usually includes mitochondrial and chloroplast dna

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26
Q

what is the transcriptome

A

all the rna that is in the cell at a particular point in time

27
Q

what is the proteome

A

all the proteins in a cell at a particular point in time

28
Q

what is the interactome

A

full set of protein-protein interactions that are happening in a cell at a point in time

29
Q

what is the metabolome

A

full set of metabolites that are found in a cell at a point in time

30
Q

what are metabolites

A

atp, vit, etc and tends to be smaller than proteins

31
Q

what is the phenome

A

all the other -omes (genome, transcriptome, proteome, interactome, metabolome) with some clinical observation

32
Q

t/f the transcriptome, proteome, interactome, metabolome are dynamic

A

true

33
Q

consider another reason for why scientists believed prokaryotes evolved into eukaryotes

A

similar genetic code which is essentially universal among all species

34
Q

how is info in RNA seq translated into AA sequences (via what)

A

genetic code

35
Q

dna, rna and proteins are synthesizes as ____________________________

A

linear chains of info with a definite polarity (polarity is directionality)

36
Q

what happens to the # of strands from dna to rna

A

dna is double, rna is single

37
Q

dna is able to determine what of the cell

A

the chemistry, the function of the cell

38
Q

dna is short for

A

deoxyribonucleic acid

39
Q

rna is short for

A

ribonucleic acid

40
Q

name the subunits/monomers that compose dna and rna

A

nucleotides

41
Q

list the 3 parts of the nucleotide

A

pentose sugar, nitrogenous base, phosphate group (backbone, 1/2/3 phosphate groups)

42
Q

which bases are pyramidines
(single ring)

A

C (1 nh2 and 1 double bonded O), T (ch3, 2 double bonded O) and U (only 2 double bonded O)

43
Q

which bases are purines (double rings)

A

A (had no double bonded O) G (has double bonded O)

44
Q

what are the nitrogenous bases of rna

A

gcau

45
Q

what are the nitrogenous bases of dna

A

gcat

46
Q

what is the names of the following
sugar + base + 1p
sugar + base + 2p
sugar + base + 3p

A

nucleoside monophosphate
nucleoside diphosphate
nucleoside triphosphate

47
Q

differentiate between a nucleoside and nucleotide

A

nucleoside: base and sugar
nucleotide: base and sugar and phosphate

48
Q

how are nucleotides linked and what direction

A

phosphodiester bonds, 5’ to 3’ (the polarity)

49
Q

dna is synthesized by ______ rna is synthesized by _______

A

dNTPs (deoxyribonucleoside triphosphates)
NTPs (ribonucleoside triphosphates)

50
Q

list the noncovalent attraction interactions between individual moelcules

A
  • electrostatic attraction: ionic, mid strong but not as strong in water
  • h bond
  • van der waals
  • hydro[hobic force
51
Q

explain van der waals and its signifance in DNA

A

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

52
Q

t/f the noncovalent interactions are very strong forces individually

A

no, very weak indiv, but can sum to generate strong binding between molecules

53
Q

how many h bond between cg and ag

A

cg is 3, ag is 2

54
Q

how to describe orientation of double stranded dna

A

antiparallel

55
Q

why is helix preferred

A

thermodynamically stable and it is the energetically favorable conformation

56
Q

what are the 3 forces that keep dna strands together

A
  1. h bond
  2. hydrophobic interactions: bases in (bases described as planar), rings out
  3. van der waals
57
Q

__________ contributes to the stability (not helix)

A

bases stracking

58
Q

proteins can recognize and make contact with specific dna sequences in the _______________

A

major and minor grooves (minor is narrower)

59
Q

t/f proteins only make contact with major groove

A

false! major and minor

60
Q

where does major and minor grooves come from

A

it is a result of the way the helix is coiled together

61
Q

the sequences of the two dna strands are _________ and can be ________

A

complementary, unzipped

62
Q

the complementary and unzipping nature is important for

A

dna replication (including pcr) and rna synthesis

63
Q

what composes the 5’ and 3’ end of the dna

A

5’ phosphate group (-PO4)
3’ hydroxyl group

64
Q

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

A

true

BIO130 (12 decks)

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