cell structure and function Flashcards
similarities between all cells
dna = heritable material rna = messenger proteins = workers major cell organelles - functions + arrangements within cell ATP as energy source
central dogma
DNA –> RNA –> PROTEIN
prokaryote vs eukaryote
similarities = plasma membrane, cytosol, dna, rna protein, ribosomes E = membrane bound organelles, larger P = no membrane bound nucleus
cytoplasm
everything inside plasma membrane NOT NUCLEUS
cytosol = water + dissolves & suspended (ions, amp. proteins, lipids)
endomembrane system
nucleus ER Golgi lysosomes work together to package, label and ship molecules (mitochondria + ribosomes NOT in system)
plasma membrane (basic not proteins)
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
proteins in plasma membrane
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)
nucleus
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)
dna
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
ribosomes
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
endoplasmic reticulum
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)
golgi apparatus
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)
lysosomes
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
mitochondria
ATP through resp.
inner mem. w cristae; outer mem
matrix (fluid filled interior cavity
carry separate (37 genes) genome –> mito. specific products
cytoskeleton main structure; function
fibres & filaments –> maintain size, shape, integrity of cell
scaffolding
intracellular transport, cell movement
microtubules > intermediate filaments > microfilaments
microfilaments (cytoskeleton)
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.
intermediate filaments (cytoskeleton)
8-12nm
diverse range
cytoplasm
bear tension & weight, scaffold for organlles
least dynamic –> most permanent (of cytosk.)
microtubules (cytoskeleton)
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
fuel for ATP
glucose in body (functions)
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
glycolysis
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
pyruvate oxidation
matrix pyruvate (loses carbon to form CO2) --> acetyl coA 1 NADH per pyruvate --> 2 per glucose oxygen REQ. no ATP
krebs cycle
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
substrate phosphorylation
oxidative phosphorylationw
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
electron transport chain
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
cyanide effect on ETC
blocks passage of e- to O2 –> cells die
effect of photofructokinase on respiration
rate limiting for glycolysis
INHIBITED by - atp, citrate
STIMULATED by - amp (prod. atp being used rapidly)
function of insulin and glucagon
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)
diabetes
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.
local/long distance cell signalling
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
3 main steps in cell signalling
- RECEPTION - signalling protein (primary messenger) bind to receptor –> change shape/chemical state change
- TRANSDUCTION - receptor protein activates another protein –> relay of changes (relay molecules = secondary messengers) - proteins activated via phosphorylation
- RESPONSE all activates proteins –> 1< functions occur
receptors, types of receptors
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
G protein coupled receptors
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
ligand gated ion channels/receptors
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
signal transduction (phosphorylation cascade)
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
cAMP and calcium as secondary messengers
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
reasons for signal cascade and cell response examples
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
deactivating response in signalling
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
adrenaline signalling pathway
through GPCR –> activates cAMP + 2 p kinases in cascade
active glycogen phosphorylase = convert glycogen –> glucose-1-phosphate –> glycolysis –> ATP when needed
gene expression = ?
process of going from DNA to functional product
3 main steps of gene expression
- transcription of RNA from DNA
- processing of pre-mRNA transcript
- translation of mRNA –> protein
control points in gene expression
transcription factors (TF) assemble, DNA needs to be accessible
regulatory proteins - block translation
specific proteins assist in nuclear export in DNA
capping, splicing
why is gene expression control important
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
main steps in transcription and translation (gene expression)
INITIATION
ELONGATION
TERMINATION
transcription (gene expression)
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
processing, introns, exons, UTRs (gene expression)
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
ribosomes, tRNA and translation (parts)
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
translation steps (gene expression)
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
amino acid properties & structures
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)
processing and sorting proteins (ribosomes, golgi)
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
signal peptides (gene expression)
direct ribosomes to RER; at N terminus; signal recognition particle binds to SPs
- polypeptide synth
- SRP binds to SP
- SRP binds to receptor on RER
- SRP detaches –> polypep synth. resumes (now in RER)
- signal cleaving enzyme cuts off SP
- complete polypep –> fold. SECRETORY proteins = solubilised in LUMEN; MEMBRANE proteins = anchored to mem; BOTH = go to GOLGI (via vesicles) –> maturation
post translation modifications
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
interphase
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
M phase
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
sister chromatids
DNA replicated during INTERPHASE condenses to 2 identical sister cmt during PROPHASE (2 sides of cms = identical)
meiosis
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
sources of variation in meiosis
independent assortment at metaphase 1
crossing over/chiasma in P1
fusion between 2 gametes
effect of DNA sequence changes (germ line, somatic, large scale etc.)
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
substitution, insertion/deletion (INDEL) mutations
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)
sickle cell anaemia
substitution from Glu to Val –> missense substitution mutation
val = non-polar; hydrophobic
glu = negatively charged; hydrophilic
MPF
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
“stop” and “go” signals
gene product is associated with checkpoints - many = stop and go
stop = keep cell proliferation in CHECK
go = STIMULATE cell proliferation
how can mutations causing cancer arise?
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
what are 2 of the genes that, when mutated, can cause cancer?
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)
development of cancer requires..
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
