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ANSC234 (Biochem2) > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q

5 methods of signaling?

A

hormone: brought to distant tissues (long distance)
paracrine: short distance communication between cells (signals diffuse through extracellular environment)
autocrine: message produced by a cell which acts on the cell itself
juxtacrine: signalling to neighbor cells (don’t travel). Helps cell understand its environment ( ie gap junctions)
pheromone: chemical signals that go from one organism to another of the same species

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2
Q

structure of glycerophospholipid?

A

2 FA attached to 1st and 2nd C of glycerol (ester link)

polar or charged group attached to 3rd C (phosphodiester link)

Can form different signals depending on where the molecule is cleaved

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3
Q

structure of sphingolipid

A

3 C spingosine backbone + FA chain (2nd C) + PO4 and X (3rd C)

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4
Q

what is ceramide

A

most simple sphingolipid

stabilizes lipid rafts = v important for signaling

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5
Q

glycosphingolipid structure? function?

A

formed when hydrophilic group contains a carb/sugar

function: determines blood groups by type of sugar added
- forms antigens for cells to recognize each other
- type of sugar is determined by glycosyltransferase

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6
Q

3 classes of eicosanoids?

A
  1. prostaglandins are synthesized from arachidonate precursor = causes smooth muscle contraction, regulates blood flow, body temp (ie fevers), etc…
  2. thromboxane: forms platelets important for blood clotting
  3. Leukotrienes: airway smooth muscle contractions (ie air system)
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7
Q

what are NSAIDs?

A

non steroidal anti inflammatory drugs

inhibits cycloxigenase = inhibits production of prostaglandin and thromboxane

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8
Q

precursor of steroids?

A

cholesterol

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9
Q

role of eicosanoids?

A

paracrine hormones

acts only on cells near the point of hormone synthesis (short distance)

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10
Q

structure of steroids?

A

4 ring structure

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11
Q

how do steroids travel?

A

carried in blood by carrier proteins

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12
Q

role of 1,25 dihydroxycholecalciferol?

what does it regulate?

A

aka calcitrol or vit D3

important for Ca metabolism

cleaves in photoreaction (UV light)

inactive in skin –> transferred to liver –> transferred to kidney where it becomes active

regulates:

  1. Ca absorption (intestine)
  2. Ca excretion (kidney)
  3. Ca storage (bone)
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13
Q

symptoms of vit D3 deficiency?

A

rickets = bow shaped legs

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14
Q

what are eicosanoids derived from?

A

arachidonic acid

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15
Q

prenol lipids acts as what?

A

hormones and pigments

ex: beta carotene –> retinol –> retinal –> neural signals to brain when retinal is hit

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16
Q

examples of tocopherols

A

vit E

Vit K (blood clotting)

warfarin: blood anticoagulant
ubiquinone: mitochondrial electron carrier
plastoquinone: electron carrier in chloroplast

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17
Q

describe 2 states of the lipid bilayer

A
  1. ordered state: gel (paracrystalline)
  2. disordered state: fluid

membrane can never be fully ordered or disordered state (always somewhere in between)

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18
Q

what causes the transition between ordered and disordered state of the membrane?

A

heat produces thermal motion of side chains

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19
Q

how does temp affect membrane fluidity?

A

increases thermal motion of side chains (higher temp = more fluid = more disordered)
-approx 20 to 40deg for mammals = fluid state

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20
Q

how does saturation of FA affect fluidity of membrane?

A

saturation of FA increases order

  • unsat FA = kinks = more disordered
  • sat FA = no kink = more ordered state
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21
Q

how does length of FA chains increase order?

A

uniform length = increases order

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22
Q

how does sterol content affect membrane fluidity?

A

sterols produces gaps = more disorder

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23
Q

how do cells regulate FA content of membrane?

A

by increasing saturated FA levels at higher temp

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24
Q

5 factors that affect fluidity of membrane?

A
  1. temp
  2. saturation of FA
  3. length of FA chains
  4. Sterol content
  5. cell regulation of FA content
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25
Q

3 types of movement in bilayer?

A
  1. uncatalyzed lateral diffusion
  2. uncatalyzed transbilayer
  3. catalyzed transbilayer translocations (floppases, flippases, scramblases)
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26
Q

describe uncatalyzed lateral diffusion

A

FA can move very fast

membrane needs to be fluid for this movement

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27
Q

describe uncatalyzed transbilayer diffusion

A

“flip flop” diffusion

very slow if not catalyzed by protein

more difficult movement

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28
Q

describe catalyzed transbilayer translocation.

types?

A

movement of FA across membrane with a protein catalysis = thus much easier movement than uncatalyzed transbilayer

types:
1. flippases:
- outer to inner leaflet
- uses ATP
- P-type ATPase

  1. floppases:
    - inner to outer
    - uses ATP
    - ABC transporter
  2. scramblase:
    - moves lipids in either direction towards equilibrium
    - doesn’t use ATP
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29
Q

why is it important that flippases put phosphatidylserine on outer leaflet?

A

so that the outer leaflet can trigger apoptosis (cell death) and phagocytosis = important for clot formation

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30
Q

what are lipid rafts?

A

stable and rigid domain of sphingolipids and cholesterol in the outer leaflet (on top of cell membranes). Enriched with membrane proteins

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31
Q

what are caveolae?

A

type of lipid raft that involves both leaflets of the bilayer

caveolin monomers forms dimers which forces lipid bilayer to curve inward = caveolae on surface of cell (“little caves”)

important for cell localization and integration

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32
Q

examples of uses of membrane fusion?

A

endo and exocytosis

budding of vesicles from golgi complex

fusion of sperm and egg

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33
Q

describe membrane fusion at synaptic space

A

(refer to diagram?)

  1. neurotransmitter-filled vesicle approaches plasma membrane
  2. increased calcium (from voltage gated CA ion channels) acts as a signal
  3. v-SNAREs and t-SNARES recognizes each other > zips > initiates fusion of lipid bilayers
  4. hemi fusion: outer leaflet and inner leaflet diffuses
  5. fusion pore opens
  6. vesicle contents are released outside of the cell to the synaptic space
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34
Q

what does fusion of 2 membranes require?

A
  1. triggering signal
  2. recognize each other
  3. close apposition
  4. local disruption of bilayer
  5. hemi fusion
  6. fusion protein
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35
Q

What are the types of solute transport across membranes?

A
  1. simple diffusion: small particles. moves down conc gradient. no ATP used
  2. facilitated diffusion: moves down gradient through a protein channel. no ATP
  3. primary active transport: against gradient = uses ATP
  4. secondary active transport: against gradient. driven by ion moving down its gradient
  5. ion channel: down gradient. may be gated by ligand or ion
  6. ionophore-mediate ion transport: small molecules that transports down electrochemical gradient
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36
Q

carrier vs channel transporters?

A
  1. carriers:
    - primary or secondary passive transporters
    - slow and saturable
    - can reach max saturation state where it can’t go further
  2. channels:
    - fast and not saturable
    - movement is restricted by conc gradient or time before the gate closes
37
Q

describe glucose transporter?

A

passive transporters (moves down conc gradient). No ATP

  1. glucose transporters stored within cell in membrane vesicles
  2. insulin interacts with receptor = vesicle moves to surface = fuses with membrane = increases # of glu transporters in membrane
  3. insulin level drops = glu transporters are removed from membrane (endocytosis) = forms small vesicles
  4. smaller vesicles fuse with larger endosome
  5. glu transporters become small vesicles = ready to return to surface when insulin rises again

(refer to diagram)

38
Q

describe the chloride bicarbonate exchange protein

A

(aka anion exchange protein)

  • increases rate of bicarb transport across membrane
  • allows entry and exit of bicarb without changing membrane potential
  • increases co2 carrying capacity of blood

refer to diagram

39
Q

describe role of anhydrase in respiration

A

essential in co2 transport to lungs from tissues

waste co2 released from respiring tissues into blood enters the erythrocyte (RBC) where it is converted to bicarb by anhydrase

40
Q

describe Chloride bicarb exchange in respiring tissues?

in lungs?

A

resp tissues:
co2 goes in -> carbonic anhydrase converts to bicarb –> bicarb goes out of chloride bicarb exchange protein into blood plasm as Cl goes in

in lungs: bicarb enters into erythrocyte as Cl goes out –> carbonic anhydrase converts bicarb into Co2 –> Co2 leaves erthrocyte and is exhaled

41
Q

types of ion passage?

A

uni port: carries only 1 substrate in 1 direction

symport: 2 solutes both moving in same direction
( form of cotransport)

antiport: 2 solutes moving in diff directions (cotransport)

42
Q

types of active transport?

A
  1. primary active transport: uses ATP
  2. secondary active transport: when endergonic transport of one solute is coupled to exergonic flow of a different solute tht was originally pumped by primary active transport
43
Q

example of antiport?

A

NA+ K+ ATPase –> maintains polarity and resting potential of the cell membranes –> H+ pumps present in kidney to regulate sodium potassium in blood

44
Q

describe the sodium potassium pump

A

responsible for generating membrane potential

  1. transporter binds 3 Na from inside of cell
  2. phosphorylation is initiated
  3. transporter releases 3 Na+ to outside and binds 2 K+ from outside of cell
  4. dephosphorylation
  5. transporter releases 2K+ to inside
45
Q

describe f-type ATPase

A
  • active transmembrane protein transporters that transports ions through membrane
  • can convert ATP to ADP or ADP to ATP (if H+ comes in = ADP becomes ATP. if H+ goes out = ATP becomes ADP)
  • catalyzes uphill transmembrane passage of H+ drive by ATP hydolysis
46
Q

what are ABC transporters

A

“ATP binding CAssette” : ATP dependent transporters

pumps AA, peptides, lipids, drugs, etc… out of cells against a concentration gradeint

solutes can come in or out

47
Q

describe steps in regulation of genes

A
  1. transcription
  2. posttranscriptional mRNA
  3. RNA stability
  4. translational regulation
  5. protein modification
  6. protein transport
  7. degredation
48
Q

what are 2 classes of genes?

A
  1. housekeeping: genes are expressed by all cells in the body in all cells in the organism
  2. regulated: based on cell environment, type, life, etc…
49
Q

2 classes of regulating gene expression

A
  1. inhibitors (negative regulation)

2. activators (pos regulation)

50
Q

role of RNA polymerase

A

enzyme that makes RNA polymer

regulated by regulator protein (transcription factors, activators, repressors…) which regulates RNA transcription

51
Q

what is upstream? what is downstream?

A

up: left
down: right

52
Q

where does RNA polymerase bind to DNA?

A

at promoters

where transcription starts

53
Q

what do repressors and activators do?

A

repressors: blocks binding of RNA polymerase to DNA
activators: enhances RNA polymerase-promoter interactio

54
Q

what are operators

A

binding sites on DAN that repressors bind to

55
Q

describe negative gene regulation

A

effector binds to repressor and causes conformational change –> repressor binds to operators (binding sites) –> RNA polymerase binding is blocked –> transcription is blocked

56
Q

what does the effector do?

A

molecular signal that regulates the binding of repressor to DNA

binds to the repressor –> causes a conformational change –> doesn’t allow repressor to bind to DNA

57
Q

describe pos regulation

A

effector binds to activators –> activators bind to DNA and enhances RNA polymerase activity at promoter

58
Q

5 DNA binding motifs?

A
  1. helix turn helix domain
  2. zinc finger domain
  3. homeodomain
  4. leucine zipper
  5. helix loop helix
59
Q

what is the helix turn helix domain?

A

-20 amino acids long
-2 alpha helical segments (one of the 2 acts as a recognition helix to read sequences and interact)
crucial to regulation

60
Q

describe zinc finger domain

A
  • 30 AA long
  • loops are coordinated by Zn2+
  • DNA binding is weaker
  • Proteins may have less than one Zn finger
  • Can also act as RNA binding motif can read and bind to RNA sequence
61
Q

describe homeodomain

A
  • 60 AA long
  • only in eukaryotes
  • similar to helix turn helix domain function
62
Q

describe leucine zipper

A
  • leu (AA) occurs at every 7th position

- partially interacts with DNA (Lys and Arg)

63
Q

how does chromatin structure affect access to promoters?

A

how tightly chromatin is bound together

tightly bound =denies access to promoters

loosely bound = allows access to promoters

64
Q

what is chromatin?

A

DNA + histones

65
Q

what is multimeric?

A

comes in groups

66
Q

5 types of histones?

A 
H1
H2A
H2B
H3
H4
67
Q

what are the 4 important histone types?

A

H2A
H2B
H3
H4

(H1 is not important)

these makes an optomer block around which DNA is wound around

68
Q

transcriptionally active chromatin are… (2)

A

deficient in H1

enriched with H3.3 (variant of H3) and H2AZ (variant of H2)

69
Q

how are histones covalently modified?

A 
methylation
phosphorylation
acetylation
ubiquitiniation
sumoylation

these are post transcriptional modifications that can change protein function

70
Q

what is important for histone modifications?

A

SW1 and SNF enzymes

71
Q

what are HATs?

A

histone acetyl transferase

enzymes that acetylate Lys residues

72
Q

what are HDACs?

A

histone d-acetylases

they remove acetyl groups from histones when transcription of a gene is no longer required

73
Q

what is UAS

A
  • upstream activating sequences
  • far from promoter
  • influences gene expression by regulating access to promoter region
  • causes DNA to bend so that UAS can come near to promoter
  • achieved by HMG proteins (causes bending of DNA)
74
Q

what does the HMG protein do?

A

facilitates DNA looping so that UAS can bind to promoter

[?]

75
Q

what do activation domains do?

A

activates mediators

  • asp and glu
  • proline
  • Gln
76
Q

3 domains that regulate transcription factors?

A
  1. transcription activation
  2. DNA binding domain
  3. hormone binding domain
77
Q

describe alternative splicing

A

-only in eukaryotes

exons are taken out. introns are kept

results in diffcombinations of DNA sequences = diff proteins can be created

78
Q

what is miRNA? how do they affect translation of mRNA

A

miRNA = microRNA

miRNA cleas or blocks mRNA = prevents translation = silences genes

79
Q

what is siRNA

A

small interfering RNAs

short segments that were cleaved by dicer proteins

80
Q

what is siRNA

A

small interfering RNAs

short segments that were cleaved by dicer proteins

81
Q

why is homeostasis required?

A
  1. precursor levels are not constant
  2. energy requirements are not constant
  3. cells maintain dynamic steady state
  4. organisms maintain dynamic steady state
82
Q

steps of regulation of enzymes?

A
  1. extracellular signals
  2. transcriptional regulation
  3. mRNA degradation
  4. mRNA translation on ribosome
  5. protein stability
  6. enzyme localization
  7. changes of levels of substrate
  8. enzyme binding allosteric effectors
  9. covalent modifications
  10. interactions with regulatory proteins
83
Q

describe extracellular signals (step 1)

A

can be hormonal, neuronal, growth factors or cytokines

84
Q

describe transcriptional regulation (step 2)

A

regulated by transcription factors –>proteins that bind to specific DNA regions near a promoter that activates or represses transcription of that gene = increases or dereases synthesis of the encoded protein

85
Q

describe mRNA degradation (3)

A

degrades by cellular ribonucleases

amount of mRNA in cell is a function of tis rates of synthesis and degradation

86
Q

describe regulation of activity of enzymes by levels of substrate (7)

A

activity depends on substrate amount

recall michaelis menten equation

87
Q

how do covalent modifications of enzymes affect activity?

A

phosphorylation or dephosphorylation can regulate function

covalent modifications occur soon after a regulatory signal

88
Q

pathways in opposite directions are….

A

not favoured simultaneously

ie glycolysis and gluconeogenesis

89
Q

common regulatory mechanisms at organism level…

A
  1. don’t simultaneously favour pathways in opposite directions (ie glycolysis and gluconeogenesis)
  2. maximizes product utilization
  3. ability to partition metabolites between alternate pathways (ie glycolysis pr pentose phosphate pathway)
  4. draws on fuel best suited for the need
  5. slows down synthetic pathways when products accumulate (ie regulation)

ANSC234 (Biochem2) (2 decks)

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