Cell Biology S1 Y1 Flashcards
1
Q
How is the issue of things not being visible if there is not enough photons overcome?
A
Use of a condenser lens to focus the light
2
Q
How is the issue of the photons not being right solved?
A
Use of detectors
3
Q
How is the issue of an object being too small to see solved?
A
Use of compound lenses
4
Q
How is the issue of an object not interacting with light solved?
A
Use of stains or labels
5
Q
How is the issue of the object interacting with light the same as the surroundings solved?
A
Use of optics to increase contrast e.g. phase contrast or DIC
6
Q
Magnification equation?
A
Magnification = actual object/image
7
Q
What are refractive indices and why are they an issue in magnification?
A
Level at which a material affects resolution - different materials have a different refractive index meaning there in a mismatch and the path of light changes and signal is lost
8
Q
What is numerical aperture?
A
The light-gathering ability and resolving power of the objective lens
9
Q
How are fluorphores used in fluorescence microscopy?
A
Energy emitted as photons that emit a longer wavelength when hit with shorter wavelength photons - as excited electrons return to ground state, photons are released as a form of energy
10
Q
What is a hybrid tagged protein?
A
Fluorescent proteins sequence at the start and end of a protein
11
Q
2 reasons why fluorescence microscopy has a better resolution?
A
- Less out of focus fluorophore excitation (via dichroic mirror that splits the beam so it goes down to speciment and back up to the eyepiece in widefield fluorescence and pinholes+a laser in confocal)
- Less out of focus emitted light collection
12
Q
Purpose of digital deconvolution?
A
Improving images using light diffraction information
13
Q
What is immunolabelling?
A
Use of antibodies to label cellular components
14
Q
How does immunolabelling work?
A
Antibodies bind to antigens at variable region - this recognises epitope (place it binds) - monoclonal antibodies bind to one epitope, polyclonal antibodies bind to many epitopes on one antigen
15
Q
Difference between direct and indirect immunolabelling?
A
Direct - primary antibody binds to antigen
Indirect - primary antibody binds, then secondary antibody to this (the antigen for the secondary antibody is the antibody’s constant region)
16
Q
What does fixation prevent?
A
Degradation and shrinking
17
Q
What is rapid freezing?
A
Aqueous systems cooled fast enough to prevent ice crystals forming - fixation method
18
Q
How is contrast established?
A
Staining with heavy metals exploits different electron densities in tissues
19
Q
What is tomography?
A
Serial sections orientated to reconstruct 3D images
20
Q
4 ways of localising cell components in light microscopy?
A
- Histochemical dyes
- Antibodies linked to FITC
- Green fluorescent proteins
- Chromogenic compounds (pigments)
21
Q
3 ways of localising cell components in electron microscopy?
A
- Antibody linked to colloidal gold (the different sizes of gold identify different compounds)
- Product is linked to heavy metals to localise enzymes
- Electron dense products can have enzymes localised
22
Q
What is central dogma?
A
Theory that genetic info only flows DNA to RNA to protein
23
Q
Why is ribose more reactive than deoxyribose?
A
Extra -OH group
24
Q
Purines vs pyrimidines?
A
Purines = A + G
Pyrimidines = T + C + U
25
2 poles of DNA/RNA subunits?
5' and 3' end
26
Which way does DNA polymerise?
5' to 3' semi-conservatively
27
3 stages of DNA transcription?
1. Initiation (RNA pol. II binds to promoter, double helix unwinds, RNA primers bind, transcription begins)
2. Elongation (RNA pol. joins nucleotides together, proof-read, RNA primer replaced with DNA)
3. Termination (termination signal causes replication complex release as RNA folds into hairpin to displace from DNA)
28
How is start site recognised in eukaryotes vs prokaryotes?
Eukaryotes = general transcription factors bind to it (and TFII recruits RNA pol. II)
Prokaryotes = sigma factor recognises it
29
DNA helicase role?
H-bonds broken between base pairs between origins of replication (where DNA replication begins)
30
DNA primase role?
Assembles and catalyses RNA primer synthesis
31
- DNA polymerase role?
- What makes sure it stays on strand?
- Adds nucleotides to primer and forms new strand
- Sliding clamp that is assembled at replication fork (where double helix is unwound)
32
DNA ligase role?
Joins strands
33
What is the difference between leading and lagging strand synthesis?
-Leading strand continuously synthesised and starts with RNA primer
-Lagging strand discontinuously synthesised in Okazaki fragments that all start with a RNA primer
34
Role of single strand DNA binding (SSB) proteins?
Prevents ssDNA from base pairing with other template strand
35
Role of topoisomerases?
Break DNA and rejoin it to prevent tension during replication by relaxing supercoiled DNA
36
Role of telomerase?
Allows ends of chromosomes to be replicated
37
Where are the regulatory DNA sequences in genes?
5' end upstream of coding region
38
Difference between exons and introns?
Exons are expressed, introns are not as they are internal interruptions
39
Structure of mRNA?
5'
cap
5' UTR
exons and introns
3' UTR
poly(A) tail
3'
40
What is de novo RNA synthesis?
No primers needed, nucleotides just bound
41
3 ways RNA is processed?
1. Capping
2. Polydenylation
3. Splicing
42
What is mRNA capping?
A modified guanine nucleotide is the cap and has been methylated and acts as a recognition site for ribosomes
43
What is polydenylation of 3' tail?
String of adenine nucleotides that limit impact of degradation and export from nucleus to cytoplasm
44
Splicing:
- What is a spliceosome?
- Role of snRNA?
- What is alternative splicing used for?
- Complex of proteins and snRNPs (small nuclear ribonucleoprotein)
- Recognise splice sites and catalyse splicing
- Creating many proteins from one gene
45
What are cis-regulatory elements?
DNA sequences around the protein coding regions that control (activate and inhibit) mRNA transcription synergistically and antagonistically
46
How is upstream regulation of transcription carried out?
- Transcription factors bind to enhancer regions upstream
- PIC (pre-initiation complex) proteins recruited by transcriptional activators
- Mediator protein complex links activator transcription factors with PIC proteins
47
Role of co-factors in transcription?
Extra level of regulation of transcription factors
48
Structure of nucleosomes?
Beads on a string with a histone core with an octamer structure
49
How does DNA interact with histones?
Electrostatically (- phosphate, + residues in histone)
50
How is the structure of nucleosomes altered?
Chromatin remodelling factors slide along DNA and exchange histone octamers and subunits and remove core histones
51
Histone tail modifications:
- What does methylation cause?
- Acetylation?
- Chromosome condensation and tightening (gene repression)
- Chromosome decondensation and loosening (gene expression as transcription factors can now bind)
52
How are embryonic stem cells able to differentiate?
De-methylate (epigentically)
53
What does degenerate mean?
Multiple codons for the same amino acid
54
What are ribosomes made of?
Proteins and rRNA
55
What is a ribozyme?
RNA enzyme with a complex secondary structure to catalyse
56
What are snoRNAs?
Small nucleolar RNA processes rRNA and comes from introns
57
What is tRNA?
- Has D loop, T loop and an anticodon loop where mRNA binds
- Each tRNA codes for an amino acid (said to be charged with an amino acid by amino acylation whereby a protein binds and binds an amino acid to it)
58
How does the translation pre-initiation complex work?
Methionini-tRNA binds with small subunit with eIF2 (eukaryotic initiation factor 2) and GTP --> makes 40S complex --> mRNA binds to the 40S complex and folds as the polyA tail interacts with eIF4 complex --> eIF2 and eIF4 bind
59
How does mRNA bind with the 40S complex?
eIF4 binds to mRNA cap and mRNA folds in on itself as eIF4 interacts with polyA tail
60
What powers scanning of mRNA?
ATP hydrolysis
61
What does GTP hydrolysis lead to?
eIF protein release and Met-tRNA binds to large subunit (Met-tRNA in middle of 3 tRNA binding pockets)
62
What are the 3 tRNA binding sites on large ribosomal subunit?
1. A site = aminoacyl-tRNA
2. P site = peptidyl-tRNA
3. E site = empty/exit
63
What happens after Met-tRNA has bound?
Aminoacyl-tRNA binds to codon on A site
-- EF1α (elongation factor) and GTP are bound to aa-tRNA
-- Powered by GTP hydrolysis (changes ribosomal conformation to bring amino acids closer)
64
What is transpeptidation?
Ribozyme catalyses formation of peptide bond between 2 amino acids (after aa-tRNA has bound) and then peptidyl transferases transfer peptide onto chain
65
What is translocation?
Step after transpeptidation where polypeptide chain moves to the P site and empty tRNA moves to E site and is released (all powered by GTP hydrolysis)
66
What is termination?
Final step of translation where release factor protein complex binds to STOP codon and GTP hydrolysis causes complex to fall apart and release polypeptide
67
Why is base pairing loose in third position between tRNA and mRNA?
Base pair wobble accounts for redundancy in last letter of codons (can be different for same amino acid)
68
What are ribonucleoproteins?
RNA and protein complexes
69
What is the RNA world hypothesis?
Folded RNA ribozymes can act as catalysts for amino acid polymerisation, mRNA splicing and tRNA processing AND RNA can encode genetic information
70
What is membrane composition linked to?
Function (different membranes = different composition)
71
What do receptor proteins allow?
A cell to receive signals
72
What do transport proteins allow?
Import of molecules
73
- How do glycerophospholipids vary?
- 2 types?
- Other lipid in membranes?
- Different carbon chain lengths and head groups
- 1. Sterols
2. Sphingolipids (long amino alcohol with a fatty acid and varying head groups)
- Cholesterol
74
What do amphipathic lipids form in water?
A bilayer (normally 5nm wide) to form a sealed compartment so that there is no edges where tails could be in contact with water
75
4 ways phospholipids move?
1. Lateral diffusion
2. Flexion
3. Rotation
4. Flip-flop (flip sides of bilayer)
76
3 factors that affect membrane fluidity?
1. Temperature
2. Acyl chain length
3. Acyl chain saturation
77
What is lipid asymmetry?
Different phospoholipids and glycolipids on extracellular and cytosolic sides of membrane
78
- What are lipid bilayers impermeable and permeable to?
- What requires transporters?
- Impermeable = solutes and ions
Permeable = small hydrophobic molecules and small uncharged polar molecules
- Ions and large uncharged polar molecules
79
3 types of membrane proteins?
1. Integral (through whole membrane)
2. Peripheral (one side, lipid or protein associated)
3. Lipid anchored (covalently attached)
80
What membrane proteins would fall off in high salt washings?
Peripheral
81
What amino acids are best suited to the hydrophobic environment of the lipid bilayer?
Non-polar aliphatic
82
What are peptide bonds and why are they an issue sometimes?
- Polar (neg. carbonyl O, pos. amide H)
- Not energetically favourable in hydrophobic core of lipid bilayer but this is overcome with hydrogen bond between carbonyl O and amide H
83
- How many residues per turn in alpha helix?
- Where do side groups on each residue point?
- 3.6 (1.5A per residue)
- Away from one another
84
How do antiparallel beta sheets run?
- Adjacent beta-strands run in opposite directions and every other R group is above or below sheet
85
How thick is lipid bilayer?
50A (3/5 is hydrophobic core)
86
How many amino acids needed to span hydrophobic core in:
- Extended conformation?
- Alpha helix?
- 8 or 9 (each is about 3.5A)
- 20 (each is 1.5A) BUT needs more if it goes back through membrane
87
- How can you predict membrane protein structure?
- When does it not work?
- Hydrophobicity analysis (each amino acid has different value (hydrophobic are negative) - use average value over a number of amino acids)
- Beta barrels as there is not a deep enough trough
88
4 things integral proteins can be?
1. Transporters
2. Linkers
3. Receptors
4. Enzymes
89
2 types of membrane transport proteins?
1. Carrier proteins (specific binding site, switch conformation as only open to one side of membrane at a time - never continuous channel)
2. Channel proteins (open or closed, will be continuous channel if open, selective and gated)
90
3 types of gradient-driven pumps that carrier proteins transport by?
1. Uniport (one type of molecule in at a time)
2. Symport (one type of molecule in at a time but requires an ion conc gradient)
3. Antiport (as one type goes in, another moves out)
91
How do symporters (secondary active transporters) work?
- Use pumps to pump ions out with energy to create an ion concentration gradient so the molecules can move in
92
What is electrochemical gradient?
Concentration gradient and membrane potential (most effective if concentration gradient and membrane potential work in the same direction) - influences passive transport
93
What does active transport do?
Moves solutes against concentration and electrochemical gradients using symporters, pumps (e.g. ATP driven, light driven) - usually uses electrochemical gradient made by another molecule/ion to provide uphill transport for a second solute
94
Ion channels:
- How is gating controlled?
- How are ion channels measured?
- What are they like during refractory periods?
- By conditions inside and outside of cell
- Patch clamping - glass capillary used to remove small area and seals the end - can also measure activity of membrane as current only flows if they are open
- Inactivated (not closed)
95
Difference between channels and transporters?
Channels allow molecules with specific charge and size through
Transporters bind with specific solutes to allow them through
BOTH CAN MEDIATE PASSIVE TRANSPORT
96
What is osmolarity?
Total concentration of solute particles in a cell
97
Differences in approach to water in the cell between protozoans, animal cells and plant cells?
Protozoans = contractile vacuole to remove excess
Animal = osmotic equilibrium by pumping Na+ out to draw water in
Plant = use water in for turgor pressure
98
How does glucose cross plasma membrane?
- Passive transport via a transporter that conformationally changes when glucose binds
- Uses electrochemical Na+ gradient (symport) for uptake in gut lumen
- Uses uniport to release it to other tissues
99
How do pumps usually operate?
Linked to another factor e.g. ATP-driven pump also driven by gradient
100
How and why is cytosolic Ca2+ kept low?
- Ca2+ ATPase pumps transport out and return to their original conformation without a second ion binding
- Kept low so cell is more sensitive to a Ca2+ influx
101
What drives solute transport in plants, fungi and bacteria?
Electrochemical proton gradients generated by ATP or light-driven pumps
102
How is the pH of the cytosol kept neutral but some organelles are acidic?
ATP-dependent H+ pumps on lysosomes (in animals) and vacuoles (plants/fungi)
103
Why are ion channels used rather than ion transporters?
Conformational changes do not occur for each ion so it is much more rapid
104
- How is resting potential maintained?
- How are membranes allowed to reach their resting potential?
- K+ leak channels which allow free K+ movement across a membrane and Na+ pumps
- Na+ channels inactivated for recovery and repolarisation of membrane, K+ channels also help
105
How are these ion channels opened:
1. Mechanically-gated?
2. Ligand-gated?
3. Voltage-gated?
1. Pulled open by physical force application
2. Open when a molecule binds (intra/extracellular)
3. Membrane potential changes (have voltage sensors that detect when threshold potential is exceeded)
106
How is pressure responded to?
Mechanically-gated Piezo channels that are stretch-activated
107
What does the size of the change in membrane potential affect and not not affect?
Does not affect how wide a channel opens but does change probability it will open
108
Ion channels and nerve signalling:
- How is a change in membrane potential spread along axon?
- Why can this not be used for long-distance communication and what is the solution?
- Passively down plasma membrane adjacent to site where signal was received
- Too slow and would weaken signal, so active signalling is used to propagate electrical signal (action potential) along axon without weakening
109
How do voltage-gated Ca2+ channels convert electrical signal to a chemical signal?
Open and trigger vesicles containing neurotransmitter to fuse with membrane to release neurotransmitters into synaptic cleft etc...
110
Why are toxins that affect neurotransmitters so dangerous?
Can change inhibitory and excitatory effects of neurotransmitters
111
What does GABA cause?
Acts an inhibitor and causes Cl- influx when GABA binds to receptor on Cl- channel which neutralises Na+ influx which means there is no change in membrane potential
112
Role of neurons?
- Generate, relay, combine, interpret and record signals
113
What are ligand-gated ion channels used for?
Transiently activate/inactivate neurons in living animals - they are taken from algae and put into animal cells as a gene (Na+ flows when exposed to blue light) (optogenetics)
114
3 cytoskeletal elements (and their subunit)?
1. Microfilaments (actin)
2. Microtubules (αβ-Tubulin dimer)
3. Intermediate filaments (various)
115
4 roles of the cytoskeleton?
1. Gives cells structure
2. Establishes and maintains polarity
3. Drives cellular movement
4. Generates and transmits physical forces
116
How does the cytoskeleton generate and transmit physical forces?
- Cell-cell adhesions
- External mechanical forces from extracellular matrix and the lumen
117
Actin microfilaments:
- What do they generate?
- What do they underlie?
- What are the linked to?
- 2 types of actin (what do they both have)?
- Contractile forces
- The membrane as structural elements
- Cell-cell and cell-matrix adhesions
- G (globular) and F (fibrous) actin - both have barbed/plus and pointed/minus end
118
Actin microfilaments:
- What controls F-actin dynamics?
- What type of actin is most energetically favourable and why?
- ATP hydrolysis as monomers bound to ADP dissociate from the minus end and monomers bound to ATP add to the plus end (rate either way is stable normally)
- ATP-actin as plus end is growing
119
4 types of actin microfilament organisation?
1. Filopodia, microvilli (stiff parallel)
2. Lamellipodia (branched network)
3. Cortex (gel-like mesh underlying plasm membrane)
4. Stress fibres (contractile bundles)
120
Why do actin microfilaments drive protrusion and migration?
- As actin monomers are added the plus end is pushed out of membrane
- Filopodium is thread foot, lamellipodium is sheet foot
121
What are filopodia and 4 roles?
- Bundled actin protrusions
- Allow neuronal cells to make growth cones - Pathfinding and making connections
- Found in most migrating cells
- Allow interdigitation in epithelial cell sheets
122
How are actin microfilaments organised?
By actin binding proteins (crosslink microfilaments in filopodia, crosslink cortical meshwork, nucleate branched network)
123
Myosins:
- What are they?
- How is contractile force generated?
- 3 roles?
- Actin-binding motor proteins with conserved heads and variable tail domains
- Moving F-actin filament towards plus end
- 1. Transport cargo along filament
2. Slide filaments relative to organelle/cell membrane and to eachother
3. Bundle F-actin filaments
124
- 6 steps of the mechanism of myosin-actin binding?
- How does this generate contraction?
1. Myosin head binds tightly to actin
2. ATP binding leads to release
3. ATP hydrolysis causes conformational change
4. ADP-bound myosin makes contact with next subunit and inorganic phosphate is released
5. "Power stroke" as actin moves
6. Myosin released when ATP replaces ADP
- As actin-myosin filaments slide relative to eachother, F-actin filament bundles and F-actin meshwork behind lamellipodia contract
125
3 main roles of microtubules?
1. Resist compressive force (bones of cell)
2. Ensure chromosome separation
3. Tracks for vesicle trafficking
126
- The repeating αβ-Tubulin dimer subunits of microtubules both bind to GTP but what does β-tubulin do differently?
- How are they organised?
- Hydrolyses it to GDP
- Lengthwise (αβαβαβαβ...) and form lateral associations (α-α and β-β) which are staggered to form a spiralling tube
127
What determines microtubule dynamics?
GTP hydrolysis (stronger with β-tubulin bound, and more likely if it is polymerised) - αβ heterodimers assemble at plus end and as conformational changes curve the filament, depolyerisation occurs as the bonds between subunits are weakened
128
When can microtubule growth occur?
Rate of addition > rate of GTP hydrolysis
- If GTP hydrolysis catches up = catastrophe (breakdown) BUT this is part of the cycle of growth and collapse
129
How are microtubules formed?
Gamma-tubulin forms scaffold for αβ dimers and they are nucleated by the microtubule organising centre (MTOC)
130
What is a centrosome?
Large aggregation of microtubule nucleating complexes
131
What are the two microtubule motor proteins?
Kinesins and dyneins
132
Kinesins:
- What are they?
- What do they cause?
- Mechanism?
- Plus-end directed microtubule motors with a similar structure to myosin
- Anterograde transport (vesicle dispersion)
- Walk along microtubule via hand-over-hand mechanism which is driven by ATP hydrolysis
133
Dyneins:
- What are they?
- What do they do?
- Mechanism?
- Minus-end directed microtubule motors with a highly conserved structure
- Retrogade transport but require adaptor proteins as they cannot bind directly to cargo
- ATP hydrolysis-driven "power stroke" to move along microtubule
134
Intermediate filaments:
- 5 characteristics?
- How do they vary in different cell and tissue types?
- What do they interact with?
- 'Ligaments of the cell', rope-like (tough, inelastic), non-polar, more diverse, help cells withstand mechanical stress
- Different types expressed
- F-actin and microtubules
135
4 types of intermediate filaments (and what type they are)?
1. Keratin/cytokeratin (cytoplasmic-epithelial)
2. Vimentin-related (cytoplasmic-mesenchyma)
3. Neurofilaments (cytoplasmic-neuronal)
4. Lamins (nuclear - in all cell types)
136
How are intermediate filaments formed?
Non-polar helical bundles - coiled-coil dimers bind to form tetramers which associate laterally
137
Difference between desmosomes and hemidesmosomes?
Desmosomes = cell-cell junctions
Hemidesmosomes = cell-matrix adhesions
138
What do neurofilaments do?
Protect long axons
139
Role of nuclear lamins?
Form mesh under nuclear envelope to protect nuclei from mechanical stress
140
How are intermediate filament dynamics controlled?
By phosphorylation (e.g. nuclear lamins break down due to phosphorylation during cell division)
141
Where are internal organelles thought to be from?
An archaeon that lost its cell walls so it could uptake genes via horizontal gene transfers to speed up evolutionary processes which then uptook bacteria and achaeons to become organelles
142
How did the nucleus form?
Invaginations in the membrane enclosed the DNA to protect it
143
What did mitochondrial development allow?
That there was energy for evolution and developing cellular systems
144
How do peroxisomes generate energy?
Fatty acid beta oxidation
145
- What is the endomembrane system?
- What are the parts?
- A system whereby cargo never crosses a membrane but can get from compartment to compartment in a cell as the compartments are topologically equivalent and vesicles just move and fuse with compartments to transfer cargo
- Plasma membrane, nucleus, rough ER, lysosomes, secretory vesicles, Golgi apparatus
146
How is the endomembrane system involved in the production of a protein?
There are different compartments involved with the sequential processing and modification of secreted proteins so that the differing reactions are kept separate
147
What is the entry point for newly synthesised proteins into the endomembrane system?
The ER (first assembled in the ER lumen and then moved where relevant)
148
ER lumen:
- N-glycosylation takes place here, what is this?
- What other part the production of a protein takes place here?
- The post-translational modification of a protein by adding an oligosaccharide to the protein that is normally lipid-linked in the ER lumen (catalysed by oligosaccharyl transferase)
- Folding and quality control as the protein will not be released until properly folded
149
What happens to proteins and sugars after they leave the ER?
Move to the cis-Golgi network and down to the trans-Golgi network (where they undergo their last modifications and are stored) and then they go into lysosomes and secretory vesicles and to the plasma membrane
150
What is an example of how sugar modifications affect the body?
ABO blood types are as a result of different sugar modifications like adding fucose, galactose, N-acetylglucosamine and N-acetylgalactosamine
151
What is the different between N and O-linked glycosylation?
N-linked glycosylation is when oligosaccharide sugar is added to a N atom on an asparagine residue on a protein
O-linked glycosylation is when an oligosaccharide sugar is added to an O atom on a serine or threonine residue on a protein
152
What are lysosomes?
Degradative organelles that lower the pH of their contents using ATP hydrolysis pumps to pump in protons so acid hydrolases in them can break things down
153
- What are the options that signals (stretch of amino acids) trigger proteins to have when they are synthesised and are in the cytosol?
- Stay put, go to the nucleus, import into ER, import into peroxisomes or enter mitochondria
154
What is nuclear targetting?
Use of positively charged amino acids such as lysine and arginine (act as uclear localisation signals) on the surface of proteins to tag them for import into the nucleus
155
What are the nuclear membrane the ER said to be?
Contiguous (membrane is linked)
156
Why is the nuclear membrane leaky to small molecules?
Nuclear pores
157
How do large molecules enter nucleus?
Actively transported through nuclear pores
158
What is the mechanism of protein import through the nuclear pore complex?
1. Nuclear import receptors recognise nuclear localisation signals (NLS) on the prospective nuclear protein
2. Complex of receptor and protein is guided to a nuclear pore by fibrils
3. Binding of nuclear protein opens pore more
4. GTP hydrolysis then drives the active transport in
159
Ran-GTPase:
- What are its two forms?
- What activates it (turns it off)?
- What turns it on?
- GTP-bound (on) and GDP-bound (off) - allows it to act as a molecular switch
- A GAP (GTPase activating protein) which adds amino acid to active site to make it GDP-bound and is found in the cytoplasm
- A GEF (guanine nucleotide exchange factor) that exchanges GDP for GTP in the nucleus
160
Ran-GTPase:
- How does protein release occur?
- How is it related to protein export?
- Ran-GTP associates with nuclear import receptor and changes its conformation so it releases the protein
- Ran-GDP is released into the cytoplasm by a nuclear import receptor, at the same time proteins can be exported as they can bind to the nuclear import receptors if they are bound to Ran-GTP
161
What are mitochondrial targeting sequences?
Short amino acid chains that are most positively charged and make an amphipathic alpha-helix and they are always at the N-terminus - outer-membrane receptors recognise helices
162
What is the difference between proteins imported into the nucleus vs the mitochondria and ER?
Nucleus only imports folded proteins, whereas the mitochondria and ER cannot take folded conformations
163
- How is a protein kept unfolded so it can enter the mitochondria?
- What happens when it is time for it to enter?
- Chaperones (heat shock proteins)
- Energy is used to release the protein (ATP hydrolysis) and then it enters the mitochondria by translocated channels
164
What is active import?
Mitochondria pump proteins in inter-membrane space make the matrix negative so charged amino acid residues are attracted
165
2 reasons why mitochondrial protein import is more complex?
1. Proteins can be inner-membrane, outer-membrane, inter-membrane space or the matrix
2. Mitochondria have their own genome and protein synthesis machinery
166
What is used for ER targetting?
Hydrophobic signal sequence at N-terminus (protein with signal sequence is insulin)
167
How does ER targetting and translocation work?
When a mRNA sequence binds to a ribosome, a SRP (signal recognition particle) recognises a hydrophobic signal sequence and stops the translation and binds to the ribosome. This ribosome with the SRP binds to a SRP receptor on the rough ER and translation continues and translocation begins (co-translational translocation) and the protein is pushed into the ER lumen - signal peptide is then either cleaved as it only showed protein was hydrophobic (but this forms a new N-terminus and a lumenal protein) OR it is not cleaved and a transmembrane protein is left
168
What does the ER usually act as?
The first step to another destination for newly synthesised proteins
169
3 pathways involved in protein trafficking?
1. Endocytic (cell exterior --> early endosome --> late endosome --> lysosome)
2. Anterograde (ER to cell exterior)
3. Retrograde (cell exterior to ER)
170
4 steps of molecules moving between compartments via vesicles in endomembrane system?
1. Vesicle buds from donor compartment
2. Vesicle pinches off and translocates from donor to acceptor compartment
3. Vesicle docks with acceptor compartment
4. Vesicle fuses with acceptor compartment and releases its contents
171
What helps buds to form?
Coats (different on different membranes)
172
Clathrin coats:
- Structure?
- Where do they form?
- What do they produce?
- What binds and why?
- What do they form?
- How does pinching off occur?
- Triskelion with light and heavy chains
- At plasma membrane and Golgi
- Endocytosis due to different adaptor proteins
- Adaptor proteins as they have sequences for budding and as more get recruited, more cargo is imported into bud that is forming
- A sphere as membrane is deformed
- By scission via mutations to dynamin so that the neck to the membrane is removed by constriction
173
- What is COPI used for?
- COPII?
- Involved in budding from Golgi to ER so proteins can return to the ER
- Involved in budding from ER to cis-Golgi so proteins can leave the ER
174
What controls coat recruitment?
Coat recruitment GTPases (controlled by GEFs and GAPs)
175
3 ways of selecting cargo?
1. Active recruitment
2. Selective exclusion
3. Passive inclusion
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Budding from the ER:
- What is SARI?
- What does SARI - GEF cause?
- What does SARI - GAP cause?
- How are the cargo and coat indirectly linked?
- ER GTPase
- Release of GDP and binding of GTP (this GEF is only in ER membrane)
- Recruitment of adaptor proteins to form inner coat
- Protein-protein interactions
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- What is a DXE motif?
- What occurs when it is recognised?
- A specific amino acid sequence in cytoplasmic tail on cargo that is recognised by coat proteins
- Adaptors recruited and they bind to coat proteins and a coat-protein coated vesicle forms
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Why must vesicle uncoating occur?
So a vesicle can bind with a membrane
179
What controls vesicle uncoating?
GTP hydrolysis as it changes the conformation and the coat falls off when it fuses with a membrane
180
Why may a protein be excluded from budding vesicles and how?
If they are misfolded a CHAPERONE will bind and hold it back
181
- What cargo will be returned to the ER?
- What is this transport?
- Cargo receptors to be recycled
- Bidirectional
182
How are vesicles targeted to the correct membrane?
By having a complimentary molecular structure
183
What is used for targeting and fusion?
Rabs and SNAREs
184
Steps of targetting to release?
Tethering --> docking --> fusion --> release
185
4 steps of targetting to release explained?
1. Tethering occurs as a tethering protein on the acceptor membrane binds to Rab-GTP protein on vesicle membrane
2. Docking then occurs as a SNARE protein on a vesicle binds to other SNARE proteins on the acceptor membrane
3. Fusion then occurs
4. Cargo is then released into acceptor lumen
186
How do SNARE proteins interact to allow fusion of a vesicle and the acceptor membrane?
Interact to form a stalk (trans-SNARE complex) which undergoes hemifusion and fusion so the vesicle can fuse (when it is fused this is the cis-SNARE complex)
187
What does Botox do?
Cleaves certain SNARE proteins to prevent neurotransmitter release so the synapses are paralysed
188
What explains how proteins move between Golgi stacks?
Vesicular transport model and the cisternal maturation model
189
What is the vesicular transport model?
Different compartments have different enzymes which means different types of modification occur
190
How does the cisternal maturation model work?
- Only retrograde transport (no forward movement)
- Medial Golgi becomes trans-Golgi as enzymes from trans-Golgi are transported into medial and medial enzymes to cis-Golgi
191
What happens to proteins in the trans-Golgi when they have been modified?
Packed into vesicles and taken to different places
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Is membrane fusion regulated or unregulated?
Both
193
What do lysosomes contain?
Acid hydrolases
194
What does mannose-6-phosphate cause?
Proteins to be transported to lysosomes
195
Process of endocytosis?
A protein/molecule binds to a receptor and triggers vesicle formation and the protein and receptor are added to an endosome by fusion and the receptor is then recycled by a recycling endosome which returns to the plasma membrane
196
What does the matrix of the mitochondria have?
Enzymes for the Krebs cycle
197
Uses of ATP:
- What kind of reactions for growth and repair?
- Where does energy for those reactions come from?
- What does it link and couple?
- Where does it transfer energy from respiration to?
- Anabolic
- Catabolic reactions
- Energy yields to energy requiring processes
- Areas of the cell that use energy
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- Where do cells obtain most energy from?
- How?
- Membrane-bound mechanisms
- ATP-synthase and large multi-subunit F-type ATPase
199
ATP-synthase:
- Where?
- How does it generate ATP?
- On inner mitochondrial membrane (ATP synthesised in matrix) and thylakoid membrane in chloroplasts (ATP synthesised in stroma)
- When 3H+ are pumped through, 1 ATP forms
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Large multi-subunit F-type ATPase:
- What is it made up of?
- How does it generate ATP?
- Why does ATP form when the stalk spins?
- F0 (integral) and F1 (peripheral)
- As H+ passes through the stalk is spun and ATP is generated
- Different conformations form as the motor turns and conformational energy is turned into ATP chemical bond energy
201
What does a proton gradient act as?
A form of stored energy
202
Proton gradient across mitochondrial membrane:
- What releases energy to pump H+ across membrane?
- Where do electrons come from?
- What do conformational changes of the proton pump using energy allow?
- High energy electron transport chain electron transfers
- Oxidation of food molecules from the Krebs cycle
- Proton uptake and release and return to the high affinity position
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Electron transport chain:
- What do electrons pass through to release energy for proton pumping?
- How do electrons move along ETC?
- NADH dehydrogenase, cytochrome bc1 complex, cytochrome oxidase complex
- Oxidation and reduction reactions (as one reactant is oxidised, another is oxidised)
204
2 mobile electron carriers?
1. Ubiquinone - carries electrons from NADH dehydrogenase to cytochrome bc1 complex
2. Cytochrome c - carries electrons from cytochrome bc1 complex to cytochrome oxidase complex
205
Order of mitochondrial ETC?
NADH dehydrogenase --> ubiquinone --> cytochrome bc1 complex --> cytochrome c --> cytochrome oxidase complex
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What is chemiosmotic coupling?
Linkage of electron transport, proton pumping and ATP synthesis (oxidative phosphorylation)
207
How are reducing agents ranked?
According to electron transfer potential (increases along ETC, NADH is high and H2O is low)
208
What do NADH and FADH2 do?
Donate electrons
209
What does ___ have for respiration:
- Matrix?
- Inner mitochondrial membrane?
- Outer membrane?
- Inter-membrane space?
- Enzymes for citric acid cycle
- Electron transfer proteins, ATP-synthase, transport proteins
- Large pores, lipid synthesis and lipid conversion to metabolites
- Enzymes that use ATP passing out of matrix to phosphorylate nucleotides
210
Does NADH produced in cytoplasm or matrix produce more ATP per molecule?
Matrix
211
What agents interfere with oxidative phosphorylation?
Cyanide and CO - inhibit cytochrome oxidase by blocking the passage of electrons to O2 to stop ATP synthesis as the proton gradient dissipates
212
What do mitochondrial uncouplers do?
Prevent protons flowing through ATP synthase so heat is generated instead of ATP
213
Why does photophosphorylation require energy from light?
It uses a poor electron donor (H2O) so it needs to be made better
214
What do chloroplasts couple?
Electron transfer and proton pumping
215
What do protons from H2O oxidation contribute to?
Electrochemical proton gradient
216
What produces high energy electrons?
Light energy (sunlight absorbed by chlorophyll and electrons interact with photons to raise their energy level)
217
What are photosystems?
Functional and structural units of protein complexes involved in photosynthesis (has a reaction centre surrounded by light-harvesting centres called antennae)
218
When do electrons move to the next step?
When they are raised in energy and move from high to low energy
219
Where are electrons in chloroplasts from?
Photolysis of water by manganese
220
Order of electron transport in chloroplasts?
Electrons from photolysis --> photosystem II --> plastoquinone --> cytochrome b6-f complex --> plastocyanin --> photosystem I --> ferredoxin --> NADP reductase
221
3 mobile electron carriers in chloroplasts?
1. Plastoquinone
2. Plastocyanin
3. Ferredoxin
222
Where and how is light energy converted to chemical energy in chloroplasts?
By development of a proton gradient at cytochrome b6-f complex
223
How many ATP and NADPH required for a 3 carbon sugar fixation in Calvin cycle?
9 ATP, 6 NADPH
224
Role of Rubisco?
Fixes carbon (C in CO2) to a 5C compound
225
What does thylakoid contain?
PSI, PSII, ATP synthase, NADP reductase
226
- What happens in the stroma?
- What does it contain?
- ATP and NADPH are synthesised, carbon fixed
- DNA
227
3 differences between mitochondria and chloroplasts?
1. Mitochondrial high energy electrons from NADH, chloroplasts have low energy electrons from H2O (but are excited)
2. Mitochondrial ultimate electron acceptor is O2, in chloroplasts it is NADP+
3. In mitochondria, chemical bond energy is used in cellular processes. In chloroplasts chemical bond energy (and reducing power) is used in carbon fixation
228
Which statement is false about the events/conclusions from studies during the mid-1800s surrounding the discovery of cells?
Scientists confirmed new cells can form spontaneously from the remnants of ruptured cells
229
What type of microscopy uses two types of filters?
Fluorescence microscopy
230
What type of microscope employs a light microscope and requires that samples derived from thick tissues be fixed and stained to reveal cellular components?
Bright-field
231
What microscope can resolve as small as 2nm?
TEM
232
What microscope scans specimens with a focused laser to obtain a series of 2D optical sections by exciting fluorescent molecules that can be used to reconstruct a 3D image?
Confocal
233
Which membrane lipid does not have a fatty acid tail?
Cholesterol
234
How does a bilayer arrangement of phospholipids result in higher entropy for the system and thus make membrane formation energetically favourable?
Water molecules form cagelike structures around hydrophobic molecules, causing the latter to cluster together and limit their contact with water
235
What do membrane lipids often do?
Diffuse laterally along the plane of the membrane
236
A bacterium is suddenly expelled from a warm human intestine into the cold world outside. What would the bacterium do?
Add lipids with hydrocarbon tails that are shorter and have more double bonds
237
You have a piece of DNA that includes the following sequence
3' CGTAAGCTAGGCCTATCGTA 5'
5' GCATTCGATCCGGATAGCAT 3'
Which of the following RNA molecules could be transcribed from this piece of DNA?
5' AUGCUAUCCGGAUCGAAUAC 3'
238
Which phospholipids are most mobile?
Short chain, more double bonds
239
Why may the amino acid coding sequence between two organisms for an enzyme be very similar, but the surrounding sequences vary a lot?
Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences
240
What enzyme is responsible for establishing the asymmetry in the phospholipid bilayer?
Flippase
241
How does the cell relieve the torsional stress created along the DNA duplex during replication?
Topoisomerases break the covalent bonds in the backbone, allowing the local unwinding of DNA ahead of the replication fork
242
Where is the catalytic site for peptide bond formation primarily formed?
rRNA
243
What will happen to glucose transport on the apical membrane if the Na+/K+ pump is inhibited?
Inward glucose transport will slowly decrease into the epithelial cells because of the slow accumulation in intracellular Na+
244
What are the 3 most common ways of performing active transport?
1. Na-coupled
2. ATP-driven
3. Light-driven
245
What DNA strands can form a DNA duplex by pairing with itself at each position?
Sequences that are palindromic (read the same backwards and forwards)
246
How are microtubules different to actin microfilaments?
Actin filaments are formed from monomeric subunits
247
Do myosin filaments move toward the plus or minus end of actin and what powers it?
Plus by ATP hydrolysis
248
What would be true if a GFP-tagged protein moves from the tip of an axon to the nucleus of a neuronal cell?
It binds dynein through an adaptor protein
249
Where are ribosomes that translate mRNA encoding ribosomal proteins found?
The cytosol
250
What is a nuclear localisation signal rich in?
Lysine and arginine
251
How are lysosomes kept at a low pH?
ATP-driven proton pumps
252
How does 2,4-DNP inhibit ATP synthesis?
Acts as a mitochondrial uncoupler
253
