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biosci 107 > cell structure and function > Flashcards

cell structure and function Flashcards

1
Q

similarities between all cells

A 
dna = heritable material
rna = messenger
proteins = workers
major cell organelles - functions + arrangements within cell
ATP as energy source
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2
Q

central dogma

A

DNA –> RNA –> PROTEIN

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3
Q

prokaryote vs eukaryote

A 
similarities = plasma membrane, cytosol, dna, rna protein, ribosomes 
E = membrane bound organelles, larger
P = no membrane bound nucleus
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4
Q

cytoplasm

A

everything inside plasma membrane NOT NUCLEUS

cytosol = water + dissolves & suspended (ions, amp. proteins, lipids)

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5
Q

endomembrane system

A 
nucleus
ER
Golgi
lysosomes
work together to package, label and ship molecules
(mitochondria + ribosomes NOT in system)
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6
Q

plasma membrane (basic not proteins)

A

selectively permeable
double layer of phospholipids with embedded proteins - physical barrier (separating inside & outside)
phospholipid - hydrophilic polar heads; hydrophobic lipid tails (fats = barrier to water) can form cells, organelles

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7
Q

proteins in plasma membrane

A

amphipathic - hydrophilic & phobic regions
cell specific and dynamic collection of mem proteins
INTEGRAL = embedded (partially/fully) into membrane
TRANSMEMBRANE = extends across entire lipid bilayer of plasma membrane, touches both intracellular & extracellular fluid
PERIPHERAL = associated w membrane; NOT embedded
TRANSPORT = channels, transporters, general/selective, gated/not, active/passive
ENZYMATIC ACTIVITY = chem. reactions, can be team of enzymes
SIGNAL TRANSDUCTION = external signal –> transduction of info INSIDE cell
CELL-CELL RECOGNITION = glycoproteins as molecular signature of extracellular side of cell
INTRACELLULAR JOINING = junctions
ATTACHMENT TO CYTOSKELETON & ECM = facilitate movement (eg. fibronectin - contact between cell surface integrins & ECM)

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8
Q

nucleus

A

enclosed by double lipid bilayer (nuclear envelope) continuous w RER
nuclear pores = entry & exit
nucleolus = rna prod, assembly of ribo subunits
house/protect DNA; assemble ribosomes; molecule segregation (temporal and spatial control of cell function)

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9
Q

dna

A

encodes phenotype
wrapped 2x around 8 histones –> nucleosomes (collective = chromatin)
cell division –> chromatin condenses –> chromatin fibre, condenses –> loops, stacks as cms
most of time DNA = chromatin & chromatin fibres
chromosome = many genes; genes = DNA segment contributing to phenotype/function

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10
Q

ribosomes

A 
2 subunits (small & large) made of ribosomalRNA (rRNA), in complex w many proteins
protein prod.
free in cytoplasm (used in cytosol - non endomem. destination)
attached to RER - non cytosolic proteins/endomembrane
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11
Q

endoplasmic reticulum

A

network of tubules stretched out from nuclear membrane
ROUGH
continuous from nuclear envelope
ribosomes
proteins enter lumen for folding
membrane surround proteins to form transport vesicles for golgi
PROD. of secreted, membrane, organelle proteins
SMOOTH
extends from rough
no ribosomes
housing of proteins & enzymes
synthesises lipids (steroids, phospholipids)
storage of cell specific proteins (not all make all proteins) –> function vary from cell-cell (cell/tissue specific)

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12
Q

golgi apparatus

A

modify, sort, package, transport proteins from RER using enzymes
formation of vessicles - secretory (exocytosis), membrane, transport (to lysosome)
CIS face = closer to ER, “receiving”; TRANS “shipping”
secretory cells = extensive Golgi
each sac/cisternae = enzymes w diff functions - modifications occur within each sac (formation of glycop., glycolipids, lipoproteins)

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13
Q

lysosomes

A

highly acidic (mem. proteins pump H+ in) for powerful digestive enzymes
vesicles formed from golgi
digestion of - substances entering cell; cell components (autophagy); entire cells (autolysis)
digest –> building blocks recycle

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14
Q

mitochondria

A

ATP through resp.
inner mem. w cristae; outer mem
matrix (fluid filled interior cavity
carry separate (37 genes) genome –> mito. specific products

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15
Q

cytoskeleton main structure; function

A

fibres & filaments –> maintain size, shape, integrity of cell
scaffolding
intracellular transport, cell movement
microtubules > intermediate filaments > microfilaments

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16
Q

microfilaments (cytoskeleton)

A

7nm
actin –> 2 chainz twisted around each other
periphery & lining interior cell
bear tension & weight - anchor cytosk. to plasma proteins
promote amoeboid motility (if req.)
dynamic - assembles/ disassembles as req.

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17
Q

intermediate filaments (cytoskeleton)

A

8-12nm
diverse range
cytoplasm
bear tension & weight, scaffold for organlles
least dynamic –> most permanent (of cytosk.)

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18
Q

microtubules (cytoskeleton)

A 
25nm
tubulin dimers coiled --> tube
extend from centriole --> cytoplasm/nucleus 
support cell shape, size
guide for movement of organelles 
cms organisation (cell division)
support movement of cilia/flagella
very dynamic
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19
Q

fuel for ATP

glucose in body (functions)

A

fuel = cabs –> simple sugars; proteins –> aa’s; fats –> simple fats. ALL ABSORBED
glucose can go 2 ways -
1 = absorbed into bloodstream, –> cell (insulin) stored as glycogen (glucagon) into blood again
2 = in cell, cellular respiration –> cellular work

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20
Q

glycolysis

A 
cytosol
glucose --> 2 pyruvate (3C) + 2 H2O
2 atp in; 4 atp out --> net gain of 2 ATP
2NAD+ --> 2NADH electron carrier
monomers enter at different points
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21
Q

pyruvate oxidation

A 
matrix
pyruvate (loses carbon to form CO2) --> acetyl coA
1 NADH per pyruvate --> 2 per glucose
oxygen REQ.
no ATP
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22
Q

krebs cycle

A

matrix
per glucose = 6 NADH, 2 FADH2, 4 CO2, 2 ATP (half per acetyl coA
oxygen REQ.
completes extraction of energy from glucose
product of 1 reaction = substrate of other
intermediates in cycle used in OTHER metabolic pathways (eg. gluconeogenesis, fatty acid synth. etc)
monomers enter at different points

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23
Q

substrate phosphorylation

oxidative phosphorylationw

A 
SP = ADP + Pi --> ATP direct transfer (from sublate) of phosphate group  to ADP. glycolysis and krebs
OP = atp from oxidised NADH and FADH2. separate substrate required
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24
Q

electron transport chain

A

inner mitochondrial membrane
4 proteins: 1,3,4 = transmembrane; 2 = peripheral
NADH –> protein 1, FADH2 –> protein 2 –> donate (1 or 2) e- (become oxidised)
as e- moves from protein to protein (series of redox reactions) energy from e- pumps H+ form protein to intermem. space –> conc. gradient
chemiosmosis = H+ diffuses down through ATP synthase –> spins turbine –> ADP +Pi –> ATP (enable phosphorylation)
O2 “pulls” e- down chain, final e- acceptor –> red. to H2O
26 or 28 ATP per glucose

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25
Q

cyanide effect on ETC

A

blocks passage of e- to O2 –> cells die

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26
Q

effect of photofructokinase on respiration

A

rate limiting for glycolysis
INHIBITED by - atp, citrate
STIMULATED by - amp (prod. atp being used rapidly)

27
Q

function of insulin and glucagon

A 
insulin = hyperglycaemia. beta cells of islets of Langerhans --> blood --> glucose uptake to cells (--> storage, atp prod.)
glucagon = hypoglycaemia. alpha cells in islets of Langerhans --> blood --> breakdown of glycogen --> glucose --> blood (higher blood sugar)
28
Q

diabetes

A

function of insulin lost
TYPE 1 = insulin dependent. autoimmune (beta cells destroyed). genetic/environmental factors
onset in children/teens, 5-10% of diabetics
TYPE 2 - insulin resistance. body prod. insulin, receptors non-functional.
most diabetics, onset >40 yrs
can be linked to other pathologies and obesity.

29
Q

local/long distance cell signalling

A

local = signals act on nearby target cells eg neurotransmitters
long distance = signals act from distance eg. hormones prod. by specialised cells –> travel via circulatory system –> act on specific cells

30
Q

3 main steps in cell signalling

A
  1. RECEPTION - signalling protein (primary messenger) bind to receptor –> change shape/chemical state change
  2. TRANSDUCTION - receptor protein activates another protein –> relay of changes (relay molecules = secondary messengers) - proteins activated via phosphorylation
  3. RESPONSE all activates proteins –> 1< functions occur
31
Q

receptors, types of receptors

A

only target receptors interact with ligand
3D molecular shape of proteins - STRUCTURE DETERMINES FUNCTION
can have different receptors at diff times –> transmission of signal only when needed
intracellular = primary messenger hydrophobic, small (lipid soluble) can enter cell. least common
membrane bound/cell surface = primary messenger large, hydrophilic, most common

32
Q

G protein coupled receptors

A

transmembrane - pass 7x
many diff types; many diff ligands; diverse functions
1. receptor unbound, rest, G protein bound to GDP, enzyme inactive
2. ligand binds to receptor, binds GP. GTP displace GDP, enzyme still inactive
3. active GP disassociates from receptor, enzyme activated –> cell response
4. GP has GTPase activity (hydrolysed to GDP + Pi) - release from enzyme, resting shape

33
Q

ligand gated ion channels/receptors

A

binding of ligand –> change shape (open/close gate) –> ions can pass
membrane protein, specific ions can travel in response to ligand binding
1. rest, gate closed
2. ligand bind –> gate open –> ions into cell
3. ligand dissassoiates –> gate closes

34
Q

signal transduction (phosphorylation cascade)

A

p kinase transfer Pi group (from ATP) to another protein –> activated –> series of ( now active) proteins adding phosphate to next kinase
phosphatases = dephosphorylate –> inactive, recyclable. for control

35
Q

cAMP and calcium as secondary messengers

A

secondary messengers = not proteins, small
cAMP
- activates downstream protiiens - can start phos. cascade
- prod by adenylyl cyclase (activated by GP) - converts ATP to cAMP
CALCIUM
- low Ca in cell; high outside maintain conc. of Ca via Ca pumps - high Ca in cell = damage so OUT of cell, int ER, into MITOCHONDRIA
- phospholipase C activated (GP) –> cleaves PIP2 into DAG, IP3
- IP3 diff –> cytosol –> bind to gated channel in ER
- Ca+ out of ER –> activate other proteins –> cascade

36
Q

reasons for signal cascade and cell response examples

A

amplifying response - eg. 1 adrenalin molecule –> 10^9 glucose-1-phosphates
multiple control points
specificity of response despite molecules in common
coordination of other signalling pathways
RESPONSE = gene expression, open/close ion channel, alter protein –> gain/lose activity, movement of cytoskeleton

37
Q

deactivating response in signalling

A

signals for limited time; activation promotes start of deactivation –> signal short = homeostatic equilibrium, cell ready to respond again
phosphodiesterase (PDE) breaks down cAMP
inhibition of specific PDEs - therapeutic eg. viagra

38
Q

adrenaline signalling pathway

A

through GPCR –> activates cAMP + 2 p kinases in cascade

active glycogen phosphorylase = convert glycogen –> glucose-1-phosphate –> glycolysis –> ATP when needed

39
Q

gene expression = ?

A

process of going from DNA to functional product

40
Q

3 main steps of gene expression

A
  1. transcription of RNA from DNA
  2. processing of pre-mRNA transcript
  3. translation of mRNA –> protein
41
Q

control points in gene expression

A

transcription factors (TF) assemble, DNA needs to be accessible
regulatory proteins - block translation
specific proteins assist in nuclear export in DNA
capping, splicing

42
Q

why is gene expression control important

A

temporal (time) and spatial (place) control - achieve right thing at right place at right time
housekeeping proteins - continually made, mRNA available in large quantities, longer half life
other proteins - prod in response to stimuli as req. cell signalling –> nucleus –> activate transcription. short lived

43
Q

main steps in transcription and translation (gene expression)

A

INITIATION
ELONGATION
TERMINATION

44
Q

transcription (gene expression)

A

INITIATION
- template strand 3’-5’ = inverse of non-template strand
- TATA box = promoter, upstream (around 25nt)
-TF inc. TATA box binding protein (TBP) assembly
- RNA pol bind, more TFs bind –> transcription initiation complex
ELONGATION
- complimentary RNA nt add to 3’ end of growing transcript
- h bonds between bases, phosphodiester bonds between nt
- double helix reforms, transcript leaves template strand
TERMINATION
- after trans of polyadenylation signal –> enzymes release pre-mRNA; RNA pol dissociates
- fidelity (proofreading) is less than for DNA rep

45
Q

processing, introns, exons, UTRs (gene expression)

A 
capping = modified G add to 5'
tailing = 50-250 A add to 3'
c & t = facilitate export & ribosome binding, stability
splicing = remove introns from transcript
exons = coding regions (inc. UTR)
introns = non-coding regions 
UTR = untranslated parts at 5' & 3'
SPLICING
spliceosome (large complex of proteins & small RNAs in nucleus
introns removes, exons rejoined --> mature mRNA
alt. splicing = diff combinations of exons toned together --> multiple forms of mRNA from single pre-mRNA --. multiple gene products from same gene
46
Q

ribosomes, tRNA and translation (parts)

A

mRNA binding site on small subunit
A site = holds next in line tRNA (w anticodon carrying aa - physical link between RNA and aa seq.)
P site = holds tRNA carrying growing polypep (middle)
E site = exit

47
Q

translation steps (gene expression)

A

INITIATION - GTP (energy) req.
initiator tRNA (methionine)
small ribo w initiator tRNA ALREADY BOUND, bonds 5’ cap of mRNA
small R scnas DOWNSTREAM –> find translation site (aug)
h bonds between mRNA & initiator
big R binds
ELONGATION
1. codon recognition - bp w complimentary anticodon, GTP invested –> increase accuracy/ efficiency
2. peptide bond formation - large R catalyses, removes polypep chain from tRNA in P
3. translocation - tRNA from A –> P, P –> E exit. GTP needed
empty tRNA reloaded in cytoplasm
TERMINATION
1. ribo reaches stop codon (A), –> release factor bind
2. release factor = promote hydrolysis - bond between P tRNA and last aa –> release polypep
3. ribo + others dissociate (can be recycled), 2 GTP hydrolyses

48
Q

amino acid properties & structures

A

side chains determine properties (amino group, carboxyl group, side chain)
PRIMARY
DNA seq.
covalent bonds (relatively strong) between aa
N terminus = 5’; C terminus = 3’
leave ribo –> 2º structure
SECONDARY = weak H-bonds–> alpha helix and beta sheets
TERTIARY = 3D shape stabilised by SIDE CHAIN interactions
QUATERNARY = multiple proteins associated together –> functional protein (not all)

49
Q

processing and sorting proteins (ribosomes, golgi)

A

proteins for function in cytosol –> complete translation on free ribosomes - ALL translation starts here –> many processed & sorted through RER & GOLGI
proteins go through endomem. system = complete trans. at RER

50
Q

signal peptides (gene expression)

A

direct ribosomes to RER; at N terminus; signal recognition particle binds to SPs

  1. polypeptide synth
  2. SRP binds to SP
  3. SRP binds to receptor on RER
  4. SRP detaches –> polypep synth. resumes (now in RER)
  5. signal cleaving enzyme cuts off SP
  6. complete polypep –> fold. SECRETORY proteins = solubilised in LUMEN; MEMBRANE proteins = anchored to mem; BOTH = go to GOLGI (via vesicles) –> maturation
51
Q

post translation modifications

A

translation complete but protein (may) not (be) yet functional
phosphorylation; methylation; acetylation, carboxylation
some in golgi; others cytosol
confer activity
ability to interact w/ other molecules
direct to particular locations

52
Q

interphase

A

cells mostly in interphase
G1 (growth/gap phase 1) = most cell activities, duration variable (cell specific). G1 CHECKPOINTS = DNA undamaged, correct cell SIZE & NUTRITION, appropriate SIGNALS. if NOT –> exit to G0
S = synthesis of DNA - DNA replication. strands separated (H bonds sep.) new strand of DNA synthesised opposite each of old strands. DNA polymerase
G2 = checks for correct DNA synth –> prep for M: synth of proteins, enzymes, reactants, replication of centrosomes completed

53
Q

M phase

A

mitotic phase = mitosis + cytokineses
INTERPHASE = uncondensed, centrosomes
PROPHASE = mitotic spindle forming, cms (2 sister cmt), condensed cms, nuclear envelope gone
METAPHASE = cms line up
ANAPHASE = sister cmt pulled apart, drawn to opposite poles
TELOPHASE = cleavage, nuclear envelope reforms

54
Q

sister chromatids

A

DNA replicated during INTERPHASE condenses to 2 identical sister cmt during PROPHASE (2 sides of cms = identical)

55
Q

meiosis

A

M1
P1 = synapsis - 2 pairs of sister cmt from each pair of homologous cms line up –> TETRAD; chiasma occur - non-sister cms in tetrads cross over –> recombination
MET1 = independent assortment
A1 = whole (homologous) cms pulled
M2
similar to mitosis but not preceded by DNA replication (since cms pulled in M1, not cmt)
A2 = sister cmt separate –> haploid

56
Q

sources of variation in meiosis

A

independent assortment at metaphase 1
crossing over/chiasma in P1
fusion between 2 gametes

57
Q

effect of DNA sequence changes (germ line, somatic, large scale etc.)

A 
CAN affect structure and function (coding region more likely; introns less likely but still can)
germ line = passed to future progeny
local/somatic = during cell division (eg. tumours)
large scale alterations = chromosomal rearrangements
small scale (point mutations) = 1/few nt altered; substitution, insertion/deletion
58
Q

substitution, insertion/deletion (INDEL) mutations

A

SUB:
silent - no effect
missense - change in aa –> effect depends of ROLE of RESIDUE (∴major/minor/good/bad)
nonsense - stop codon –> truncated protein
INSERTION/DELETION
frameshift via insertion; frameshift via deletion = extensive missense - downstream residues from point of deletion altered –> catastrophic effect.
3 NT PAIR MUTATION - NOT frameshift - downstream residues in tact
* EFFECT of all mutations depend on WHERE mutation happened eg. closer to N terminus = worse (closer to start)

59
Q

sickle cell anaemia

A

substitution from Glu to Val –> missense substitution mutation
val = non-polar; hydrophobic
glu = negatively charged; hydrophilic

60
Q

MPF

A

at G2 checkpoint
maturation (m phase) promoting factor = specific cyclin / CDK complex - KEY for G2 checkpoint
Cyclin = protein, fluctuates throughout cell cycle
cyclin dependent kinase (CDK) = kinase, activated when attached to cyclin
MPF function = phosphorylation of (many) other proteins, allows mitosis to occur
END of M phase, cyclin DEGRADES –> no MPF until needed again
ACTIVITY DEPENDENT ON MANY CELL SIGNALS

61
Q

“stop” and “go” signals

A

gene product is associated with checkpoints - many = stop and go
stop = keep cell proliferation in CHECK
go = STIMULATE cell proliferation

62
Q

how can mutations causing cancer arise?

A

GENETIC PREPOSITION - all cells of body. inherited by parents, issue/deficiency in a gene
ACQUIRED LOCALLY - in one cell initially, eg. UV radiation, smoking, carcinogens, treatments, drugs
in BOTH - altered protein function –> (can) loss of cell cycle control

63
Q

what are 2 of the genes that, when mutated, can cause cancer?

A

PROTO - ONCOGENES (“go”) –(mutate)–> ONCOGENE - over activation –> increased function. eg. Ras (GTPase); Myc (transcription factor)
TUMOUR SUPRESSOR GENES (“stop”) –(mutation)–> deactivation –> loss of function. eg. TP53, BRCA1, BRCA2 - all inhibitors (stop DNA replication if DNA not good eg. damaged)
both –> uncontrolled cell growth (ie tumour)

64
Q

development of cancer requires..

A

MULTIPLE DNA CHANGES
not just one change (very rare)
eg. 1 mutation increases chance of 2nd mutation, 2nd mutation increases chance of 3rd mutation ETC ETC –> malignant cell

biosci 107 (5 decks)

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