weeks 4-7

Question 1

Pq, Pc, Fd and cytochrome complex

Answer 1

plastoquinone - molecule and mobile electron carrier
Plastocyanine -protein and mobile electron carrier
Ferredoxin - protein that mediates electron transfer
Cytochrome complex - A proton pump found in the thylakoid membrane. This complex uses energy from excited electrons to pump protons from the stroma into the thylakoid compartment.

all in thylakoid membrane

Question 2

why you can’t measure photosynthesis globally

Answer 2

Varies between species and seasons
Scaling is challenging

Question 3

chlorophyll structure

Answer 3

Light absorbing head
Mg atom helps finetune electron structure to absorb key wavelengths
Hydrocarbon tail helps anchor pigment within thylakoid membrane

Question 4

photosystem structure

Answer 4

made up of chlorophyll, proteins and other pigments.

Has an antenna complex/ light harvesting complex: antenna pigment captures photons and channels them to the reaction centre. PSii has P680 - special chlorophyll molecules in RC. Energy passed from one pigment to another by resonance energy transfer.

Reaction centre - 1 or more chlorophyll a molecules in a matrix of protein, passes excited electrons out of photosystem.

Question 4

Factors limiting CO2 fixation

Answer 4

electron transport - regeneration of RuBP is limited by ATP and NADPH availability.
Environmental stress affecting enzymes - rate of Rubisco carboxylation

Question 4

Light reactions of photosynthesis

Answer 4

Photosystem 2 - energy transferred by resonance energy transfer until it reaches P680. P680 loses an electron to the primary acceptor, so it can now accept electron from water. Water is oxidised to from O2, e- and H+> in thylakoids

E- are passed form primary electron acceptor to Pq, through the cytochrome complex and into Pc. Generates proton-motive force/ electrochemical gradient so ATP is produced.

E- from Pc are passed to P700 in PS1. P700 is excited by light so electrons are passed to primary electron acceptor, then to Fd.
Then transferred from fd to NADP+ + a proton. Forms NADPH, catalysed by NADP+ reductase in the stroma

Question 5

Calvin cycle

Answer 5

Carbon fixation - CO2 + RuBP = 6 carbon compound, catalysed by rubisco. This splits into 2x 3-PGA

Reduction - 3-PGA is phosphorylated by ATP then reduced by NADPH, forming G3P

Regeneration - 1/6 of the triose phosphate is exported and the rest is used to make RuBP

in the stroma

Question 5

ATP generation chain in light reaction

Answer 5

H+ conc higher in the thylakoids. Diffuse into stroma via ATP synthase.
Occurs because of photolysis of water, cytochrome complex acts as H+ pump into the thylakoids, NADP+ reductase removes a proton from the stroma.

Question 6

Photorespiration

Answer 6

Results in loss of 25% of photosynthetically fixed carbon. Rubisco can also catalyse reaction between RuBP and O2. Produces 1 molecule of 3-PGA and 1 2-PG - toxic
Recycling of waste 2-PG uses and releases fixed CO2.

Higher temps = more photorespiration because rubisco has an increased affinity for O2 than CO2.

Can protect against products that build up when calvin cycle slows down

Question 7

C4 photosynthesis

Answer 7

Bundle sheath cells surround vascular tissue and mesophyll cells surround both.

CO2 is fixed into 4 carbon oxaloacetate, then converted into malate. Catalysed via PEP cayboxylase. Then moved from mesophyll to bundle sheath cells. NADP+ malate enzyme converts malate to pyruvate and CO2. Co2 enters calvin cycle

Question 8

How stomata open and close

Answer 8

Open - initiated by light, protons are pumped out of the guard cell, creating negative membrane potential in the cell. This activates K+ channels and K+ moves in. Decreases water potential so water moves in. Pressure increases and stomata opens.

Closing - proton pump deactivates, membrane depolarises and electrical potential is reduced. K+ channels close, pressure reduces

Question 9

CAM photosynthesis

Answer 9

Open stomata at night - opposite to normal plants. Co2 is taken up, fixed by PEP carboxylase and stored as malate overnight in the mesophyll cell vacuole.
Stomata close in morning preventing water loss.
Malate is transported to chloroplasts where NADP+ malic enzyme works and CO2 enters calvin cycle

Occurs in 1 cell not across 2

Question 10

Soil water stress

Answer 10

when water is limited stomatal closure is triggered by more ABA - abscisic acid. Accumulation depolarises guard cell plasma membrane, triggering an increase in Ca2+ levels in the guard cell. This deactivates K+ influc channels and activates eflux ones

Question 11

Actin in the cytoskeleton

Answer 11

Helps with mechanical support and movement.
Actin filaments are helical polymers with + and - ends.
Actin monomers bind to ATP, allowing association into a polymer
Actin-ATP is hydrolysed into actin-ADP. Then actin-ADP dissociates, because it now has a reduced affinity for the neighbouring subunit

Question 12

intermediate filaments in the cytoskeleton

Answer 12

Diverse family of proteins, help position nucleus and give mechanical strength.
Once they are formed they are stable and don’t break down

Question 13

microtubules in the cytoskeleton

Answer 13

Heterodimer of alpha and beta tubulin. Polymer has + and - ends
Heterodimer-GTP associates with polymer.
Tubulin heterodimer-GDP dissociates with polymer.
13 protofilaments are arranged in a hollow tube formation to make the filament.
Actin and microtubules have an actin-ATP/tubulin heterodimer-GTP cap at the end to prevent depolymerization during growth

Question 14

TEM vs SEM

Answer 14

in TEM electrons pass through the sample
In SEM electrons emitted from the surface of the object give the picture

Question 15

functions and locations of GAP and GEF

Answer 15

GAP= GTPase activating protein. Promotes hydrolysis of Ran-GTP to Ran-GDP. Found in cytosol so cytosol mainly contains Ran-GDP.

GEF= guanine exchange factor. Converts Ran-GDP to Ran-GTP. found in nucleus so nucleus mainly contains Ran-GTP.

Question 16

fluorescence microscopy

Answer 16

samples are tagged with fluorescent substance eg GFP (green fluorescence protein - from jellyfish, can be fused onto proteins)
emission can be detected, giving high contrast image

often incorporates confocal microscopy - scans a laser across a sample to improve resolution and generate 3D images

Question 17

Protein targeting into nucleus

Answer 17

Controlled by nuclear localisation signals (NLS) - amino acid sequence that tags protein

Cargo binds to receptor and moves into the nucleus. Cargo dissociates due to Ran-GTP binding. Ran-GTP competes with the cargo for the receptor, effectively pushing it out.
The receptor binds to ran-GTP and the complex is recycled back to the cytoplasm.
(It is then hydrolysed into Ran-GDP by GAP)

Question 18

Protein targeting out of nucleus

Answer 18

Controlled by nuclear export signals (NES) - amino acid sequence that tags protein

Cargo binds to receptor. Receptor is bound to Ran-GTP, which promotes cargo binding (rather than causing dissociation like in import)
Complex moves out of the nucleus
Ran-GTP is hydrolysed, forming Ran-GDP, causing cargo to dissociate

Question 19

preventing Ran-GDP build up during protein targeting

Answer 19

Ran-GDP binds to nuclear transport Factor 2 (NTF2) in the cytoplasm
The complex moves into the nucleus and dissociates due to Ran-GDP conversion to Ran-GTP

Question 20

protein targeting to the ER

Answer 20

Signal sequence on a protein being translated by a ribosome is recognised by a signal recognition particle (SRP)
SRP-ribosome complex binds to a SRP receptor on the ER membrane
The SRP receptor directs the ribosome to the translocator
The translocator binds ton the ribosome, pushing out the SRP-SRP receptor complex
The protein resumes being translated and is translocated across the ER membrane
SRP and SRP receptor dissociate and are recycled

Question 21

vesicle trafficking

Answer 21

important for moving substances between membrane bound compartments
Coat proteins help define a vesicle - different coat proteins for different compartments

Question 22

Movement along the cytoskeleton - actin

Answer 22

Myosin move along actin towards + end. Myosin is made up of 2 heavy and 2 light chains. N terminal binds to actin, C terminal binds to cargo. Myosin releases from actin after ATP binding

Question 23

Movement along the cytoskeleton - microtubules

Answer 23

Kinesin and dynein move along microtubules Kinesin moves towards + end, dynein moves towards - end. Kinesin releases from microtubule after ATP hydrolysis

Question 24

movement of chloroplasts

Answer 24

Move in response to light Uses specialised actin filaments and binding proteins like chloroplast unusual positioning 1 (CHUP1)

Question 25

movement via flagella and cilia

Answer 25

Flagella have undulating motion, cilia have whip like motion Both made of axoneme - bundles of microtubules Dynein arms connecting microtubule doublets slide microtubules over one another Cross bridging linking proteins stop sliding and cause axoneme to bend Bacteria flagella are made of flagellin, forms a rigid helical filament motor in bacterial membrane rotates flagella

Question 26

animal cell + amoeba cell migration

Answer 26

Most animal cells crawl rather than swim crawl through mesh-like lamellipodia Lamellipodia use actin to extend, and microtubules and intermediate filaments for structural support. They help to close wounds protrusion - actin polymerisation pushes plasma membrane out The extended cell becomes attached The trailing cytoplasm is pulled forwards Protrusion of lamellipodia and in amoebas depends on actin polymerisation

Question 27

how sister chromatids move

Answer 27

tubulin depolymerizes at the kinetochore (attachment sites for microtubule firbes) - gets shorter motor proteins in the kinetochore move the chromosome along the microtubule spindle fibres move past each other sister chromatids are held together by cohesins

Question 28

cytokinesis in animals vs plants

Answer 28

animals: ring of actin forms around cell, contracts and divides it in 2 plants: cell wall prevents division by cleavage. Golgi derived vesicles move along microtubules towards the middle of the cell. Vesicles coalesce to form a cell plate. A new cell wall forms inside the cell plate.

Question 28

cell cycle checkpoints

Answer 28

allow integration of internal and external signals G1 - decides whether cell will start dividing or differentiate. Controlled by cyclin complex. G2- commits cell to mitosis. Controlled by cyclin complex. depends on replication of DNA. mitosis - depends on number of chromosomes + their attachment to microtubules. Controlled by anaphase promoting complex (APC)

Question 29

CDKs in control of mitosis

Answer 29

cyclin-dependent kinase phosphorylates target proteins, only when bound to cyclin Regulated by protein abundance CDK + cyclin = mitosis promoting factor (MPF)

Question 30

what does PBS do

Answer 30

phosphate-buffered saline stabilises pH

Question 31

what does CaCl2 do in bacterial cell transformation + name of plasmid carrying gene for antibiotic resistance in E coli

Answer 31

Ca 2+ neutralises negative DNA. Used in chemical + heat shock method of transformation. allows dna to bind to cells more easily beta- lactamase/ bla gene

Question 32

where is PTC gene TAS2R38 found

Answer 32

chromosome 7 at position 34

Question 33

meiosis 1

Answer 33

prophase 1 - homologous chromosomes form pairs, recombination occurs. Synaptonemal complex is a protein complex that holds homologous pairs together, forming a tetrad/bivalent. 2 chromatids of a homologous pari align, the corresponding alleles align, DNA of 2 non-sister chromatids is cut at the same location. The DNA breaks are repaired, joininh ends from non-sister chromatids, the S complex dissolves metaphase 1 - homologous chromosomes are held together by chiasmata (crossover sites). Microtubule fibres attach to kinetochores

Question 34

adaption in sexual and asexual reproduction

Answer 34

sexual - faster adaptation asexual - adaption happens at mutation rate

Question 35

Evidence for cost of not having sex + cost of meisosis

Answer 35

asexual lineages go extinct more often potentially asexual organisms occasionally have sex each allele only has 50% chance of being passed on costly in terms of energy and chance of predation etc

Question 36

meiotic errors

Answer 36

chromosome nondisjunction - in meiosis 1 translocation and deletion gene dupplication -can lead to more genetic material not under selection pressure. sub or neofunctionalism of a gene can lead to new gene function

Question 37

cell cycle regulation in cancer

Answer 37

density dependent inhibition - cells stop dividing when they are surrounded by cells anchorage dependent inhibition - cells will only divide if attached to a surface proto-oncogenes normally promote cell division when growth factors are present tumour suppressor genes normally stop cell cycle if errors occur

Question 38

control of cell division in plants + evolution of multicellularity

Answer 38

plant cell walls prevent migration after division orientation of cell division plane is important for lateral root development gonium and volox have modified Rb gene (tumour supressor gene which controls cell cycle Transformation of chlamydomonas with Rb leads to colony formation

Question 39

life cycle of cerevisiae and bryophytes

Answer 39

yeast - unicellular, haploid for most of life cycle haploid cells form diploid zygote if types match diploid zygote undergoes meiosis to make 4 haploid spores eg mosses - multicellular, haploid for most of life cycle spores germinate and grow protonema (filamentous tissue), where gamentophytes develop Male and female gametes (haploid) are produced by mitosis Then diploid sporophyte develops, which undergoes meiosis to make haploid spores

Question 40

action of rifampicin and ampicillin

Answer 40

binds to rna pol active site so disrupts transcription. mutations in the binding site on rna pol cause resistance ampicillin inhibits synthesis of bacterial cell walls. Bacteria are resistant when they have the Bla gene/beta-lactamase. It breaks down the beta-lactam ring in the antibiotic

Question 41

action of miniprep buffer and lysis mix in gene cloning practical + potassium acetate, isopropanol and ethaol

Answer 41

Both dissolve cell membrane miniprep: contains tris = pH buffer, EDTA = deactivates enzymes and weakens cell membrane. lysis: contains NaOH= makes DNA single stranded, and SDS. potassium acetate and isopropanol precipitates and coagulates DNA. ethanol acts as a wash to remove salts + detergent.

Question 42

how to calculate frequency of mutants

Answer 42

number of colonies on the plate/ number of cells plated. Supercoiled DNA runs faster through electrophoresis gel than linearised plasmid