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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
km
inversely proportional to affinity for substrate; the x value where half the substrate is bound to an enzyme
25
how do soluble molecules/proteins get secreted (steps)
ribosome > rough er > golgi body > secretory vesicles.
26
exocytosis
secretion via vesicle fusing with cell membrane. takes milliseconds
27
advantages of multicellularity/ECF
communication - transport of nutrients and regulatory signals
28
disadvantage of multicellularity/ECF
29
only some animals regulate
blood temp and blood pressure
30
why no giant insects
they don't have a true circulatory system.. must rely on diffusion + no hemoglobin or similar
31
levels of organization
atom, molecule, macromolecule, organelle, cell, tissue, organ, organ system, body
32
tissue types and function
connective tissue (structural support), muscle, epithelium(absorption, secretion, protection), nervous tissue
33
what type of molecules need membrane channels
large, polar, charged
34
desmosome purpose
strengthens connection between cells
35
what can pass through gap junctions
less that 1000 Da, ions, water, some 2nd messangers
36
how can proteins change from PTM
can destroy, cleave to modify, change or add or lose binding sites, tag proteins for a purpose
37
phosphorylation
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
how many protein coding genes are there
22,000
39
ubiquitynylation
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
calculating how many conformations are possible for a protein
possible states^(number of sites)
41
transcription factors
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
why are hydrophobic molecules slower response
impossible to store in vesicles, must be synthesized when needed (ie sterol hormones)
43
hydrophobic molecules are often
modifiers of protein expression (such as hormones)
44
examples of hydrophilic molecules
peptides, ions, neurotransmitters
45
nuclear receptors
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
1st messengers
the ligand that comes from outside the cell usually to activate an ion channel and start a signal cascade
47
ion channels can be triggered by..
motion (cell stretch etc - hearing uses this), voltage, cold, heat
48
ligand-gated ion channels example
acetylcholine opens Na+ pump in muscle contraction
49
G protein coupled receptors
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
enzyme-linked receptors
ligand on extracellular side causes conformational change so enzyme does something inside the cell. ie. insulin receptor, growth factor receptor
51
2nd messenger/kinase cascade advantages
modulating how large end response is (lots of opportunity for regulation), and great amplification of single first stimulus
52
disadvantage of long cascade chain
malfunction with one protein in chain can ruin the result
53
common second messengers
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
adenyl cyclase
g-protein dependent, makes cAMP (guanyl makes cGMP)
55
genome size means..
nothing (except the amount of useless info)
56
human gene info breakdown
1.6% is coding, like 26 is introns, the rest is viral DNA (transposable elements)
57
NGS
revolutionized sequencing, it is affordable and now we want to move towards personalized healthcare based on genome
58
Krogh principle
model organisms are useful for a large number of problems
59
what makes model organisms good?
genetically tractable, sequenced genome, small, short generation time, can have genes spliced into them and RNAi used
60
model organism examples
mice, drosophilia, C elegans, zebrafish
61
genetic approaches
forward: characteristic of interest and scanning all genes/proteins for the cause, reverse: gene/protein of interest and tracking its result
62
Thomas Hunt Morgan
fruit fly genetics guy, figured out chromosomes
63
random mutagenesis and screening
chemically mutate, wait for homozygous for your trait of interest, and then sequence/screen that organism to see what changed
64
phospholipase C
activated by g-protein, cleaves phospholipid into DAG and IP3
65
transcriptomics
aka expression profiling- takes all mRNA being produced at a site with a process of interest and analyzes it
66
microarray
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
RNAseq
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
how are proteins separated
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
reverse techniques to see where/when a product is expressed
transgenics, immunohistochemistry
70
RNAi
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
gene knockout
permanently (heritably) removing genes from an organism

Molecular Animals (4 decks)

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