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Molecular Animals > The Basic Shit > Flashcards

The Basic Shit Flashcards

1
Q

tun state

A

dormant state where tardigrades replace their blood with a matrix to prevent damage upon reawakening

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2
Q

mechanism of a biological process

A

the proximate cause - how it happens

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3
Q

origin of biological process

A

ultimate cause - WHY it happens

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4
Q

animal definition

A

multicellular, heterotrophic, eukaryotic, muscles, neuronal signals

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5
Q

factors regulated by many animals

A

energy-rich molecules, O2, waste (CO2, NH4, etc), water, salt, pH

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6
Q

optimal temp for most enzymes

A

37C

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7
Q

acclimation

A

time in condition allows some change like enzyme abundance to be made so that a condition becomes more liveable

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8
Q

changes in physiology from short- to long-term

A

protein abundance/folding (via PTM), ion movement, (<milliseconds). movement of proteins, hormone movement, protein/biomolecule synthesis, cell type and number, tissue structure/size, and genome eventually

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9
Q

what is phosphorylated during muscle contraction

A

myosin

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10
Q

parallel system of regulation

A

a negative feedback loop from 2 ends where one effector helps lower variable to the set point when it goes up and the other raises it when it drops

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11
Q

proportionality of r to sa and V

A

SA proportional to r^2, V proportional to r^3

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12
Q

2/3 of fluid in body is..

A

intracellular

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13
Q

ECF composition

A

80% is interstitial, 20 in blood

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14
Q

apical side of epithelial cell

A

absorption, has microvilli and endocrine cells. aka luminal, mucosal

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15
Q

follicle

A

tube with a closed end

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16
Q

epithelium function

A

barrier and transport

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17
Q

basolateral side of epithelia

A

has blood supply. aka basal, serosal

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18
Q

how are epithelial cells polarized

A

tight junctions seal sides

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19
Q

occluding junctions

A

include tight junctions (verts - only epithelial cells) and septate junctions (only occur in inverts)

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20
Q

desmosomes

A

physical glycoprotein connections in a single spot

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21
Q

gap junction

A

pore in both cells cytoplasm, used for communication

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22
Q

immunohistochemistry

A

using antibodies to tag spec elements in a tissue

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23
Q

mass action

A

his way of saying le chatliers principle?

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24
Q

vmax

A

max speed achieved by enzyme, based on saturation so can be modified by changing quantity of enzyme

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25
Q

km

A

inversely proportional to affinity for substrate; the x value where half the substrate is bound to an enzyme

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25
Q

how do soluble molecules/proteins get secreted (steps)

A

ribosome > rough er > golgi body > secretory vesicles.

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26
Q

exocytosis

A

secretion via vesicle fusing with cell membrane. takes milliseconds

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27
Q

advantages of multicellularity/ECF

A

communication - transport of nutrients and regulatory signals

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28
Q

disadvantage of multicellularity/ECF

A
29
Q

only some animals regulate

A

blood temp and blood pressure

30
Q

why no giant insects

A

they don’t have a true circulatory system.. must rely on diffusion + no hemoglobin or similar

31
Q

levels of organization

A

atom, molecule, macromolecule, organelle, cell, tissue, organ, organ system, body

32
Q

tissue types and function

A

connective tissue (structural support), muscle, epithelium(absorption, secretion, protection), nervous tissue

33
Q

what type of molecules need membrane channels

A

large, polar, charged

34
Q

desmosome purpose

A

strengthens connection between cells

35
Q

what can pass through gap junctions

A

less that 1000 Da, ions, water, some 2nd messangers

36
Q

how can proteins change from PTM

A

can destroy, cleave to modify, change or add or lose binding sites, tag proteins for a purpose

37
Q

phosphorylation

A

main ptm, done by kinases and undone by phosphatases, PO4-2 on a serine, threonine, or tyrosine. kinases have many targets as do phosphatases (518 kinases, 167 phosphatases)

38
Q

how many protein coding genes are there

A

22,000

39
Q

ubiquitynylation

A

transfers from E1 to E2 to a target Lysine, and often gets multiple ubiquinols before digestion by proteasome. more that 400 E2 ligases in genome

40
Q

calculating how many conformations are possible for a protein

A

possible states^(number of sites)

41
Q

transcription factors

A

on enhancer or promoter, change abundance of proteins. natural selection can change their uses and cause certain genes to be expressed differently ie. lactase. there are like 478 transcription factor genes

42
Q

why are hydrophobic molecules slower response

A

impossible to store in vesicles, must be synthesized when needed (ie sterol hormones)

43
Q

hydrophobic molecules are often

A

modifiers of protein expression (such as hormones)

44
Q

examples of hydrophilic molecules

A

peptides, ions, neurotransmitters

45
Q

nuclear receptors

A

collect hydrophobic molecules in the nucleus, they are often transcription factors with a receptor for the hormone so they are impacted by this molecule to modify protein expression

46
Q

1st messengers

A

the ligand that comes from outside the cell usually to activate an ion channel and start a signal cascade

47
Q

ion channels can be triggered by..

A

motion (cell stretch etc - hearing uses this), voltage, cold, heat

48
Q

ligand-gated ion channels example

A

acetylcholine opens Na+ pump in muscle contraction

49
Q

G protein coupled receptors

A

guanine-binding protein coupled receptors. over 1000 genes for this. used in sight, smell, adrenaline secretion. ligand binds to protein that signals G protein which then signals smth else

50
Q

enzyme-linked receptors

A

ligand on extracellular side causes conformational change so enzyme does something inside the cell. ie. insulin receptor, growth factor receptor

51
Q

2nd messenger/kinase cascade advantages

A

modulating how large end response is (lots of opportunity for regulation), and great amplification of single first stimulus

52
Q

disadvantage of long cascade chain

A

malfunction with one protein in chain can ruin the result

53
Q

common second messengers

A

cAMP and cGMP activate kinases, IP3 from membrane phospholipids activates Ca channels in the ER for muscle contraction, Ca activates calmodulin which activates kinases, diacylglycerol (DAG) is the other membrane component (hydrophobic) which activates membrane kinases

54
Q

adenyl cyclase

A

g-protein dependent, makes cAMP (guanyl makes cGMP)

55
Q

genome size means..

A

nothing (except the amount of useless info)

56
Q

human gene info breakdown

A

1.6% is coding, like 26 is introns, the rest is viral DNA (transposable elements)

57
Q

NGS

A

revolutionized sequencing, it is affordable and now we want to move towards personalized healthcare based on genome

58
Q

Krogh principle

A

model organisms are useful for a large number of problems

59
Q

what makes model organisms good?

A

genetically tractable, sequenced genome, small, short generation time, can have genes spliced into them and RNAi used

60
Q

model organism examples

A

mice, drosophilia, C elegans, zebrafish

61
Q

genetic approaches

A

forward: characteristic of interest and scanning all genes/proteins for the cause, reverse: gene/protein of interest and tracking its result

62
Q

Thomas Hunt Morgan

A

fruit fly genetics guy, figured out chromosomes

63
Q

random mutagenesis and screening

A

chemically mutate, wait for homozygous for your trait of interest, and then sequence/screen that organism to see what changed

64
Q

phospholipase C

A

activated by g-protein, cleaves phospholipid into DAG and IP3

65
Q

transcriptomics

A

aka expression profiling- takes all mRNA being produced at a site with a process of interest and analyzes it

66
Q

microarray

A

uses chips with DNA strands and mRNA fluorescently labelled for 2 conditions to see based on hybridization with each of the many many sections of DNA which RNAs are expressed in each condition

67
Q

RNAseq

A

used for transcriptomics, it simply sequences the 2 samples of which RNA appears so you can compare them. benefit - you don’t need the genome to already have been sequenced. problem - expensive, the data is really complex

68
Q

how are proteins separated

A

2D gel with axes of molecular weight and charge (isoelectric point), so differences like PTMs are also detectable. from there you use mass spec.

69
Q

reverse techniques to see where/when a product is expressed

A

transgenics, immunohistochemistry

70
Q

RNAi

A

natural process harnessed to knock down genes, used in reverse methods. dicer cuts up dsRNA and RISC destroys it. maybe used to kill viral mRNA in nature

71
Q

gene knockout

A

permanently (heritably) removing genes from an organism

Molecular Animals (4 decks)

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