Final Exam Part 2 Flashcards
1
Q
Mitochondria structure
A
- mitochondria are the powerhouse of the cell turn fuel into ATP through respiration
- has a compartment with a high concentraiton of hydrogen ions which drives some processes in the organelles.
- has a double membrane - two lipid bilayers
- cristae - the infoldings of the inner membrane.
- two internal compartments: intermembrane space (used for respiration) and the matric where you find DNA and ribosomes
- they are small
- they are dynamic - they change shape, fuse and divide. form a branched tubular network.
2
Q
Mitochondria function
A
- Respiration
- Pyruvate and fatty acids passed across the lipid bilayers which are fed into the matrix where the citric acid cycle occurs.
- This drives oxidative phosphorylation where these proteins are sitting in the folds in the inner mitochondrial membrane – which produces a hydrogen ion gradient – acid space in the intermembrane space.
- Goes back into he matrix to drive ATP synthase. To produce ATP which goes out of the mitochondria to be used for different processes.
- The intermembrane space is where the hydrogen gradietn forms.
- The inner membrane is where the electron transport chain is
- Inside the mitochondria is where the citric acid cycle occurs.
3
Q
Plastids
A
- Plastids are only found in plants and algae.
- they are sites of manufacture and storage of important chemical compounds used by the plant cell.
4
Q
Evolutinary origin of plastids
A
- plastids share evolutionary origin.
- Proplastid - ancestor plastid - will differentiate into a specific cell type
- there are two types of plastid families - coloured and non-coloured plastids
5
Q
Coloured plastids
chloroplasts and chromoplasts
A
- coloured plastids give plants their colour - carotenes or xanthophylls - for communication to animals
- chloroplasts contain chlorophyll - harvest light energy, found in leaves - carry out photosynthesis.
- chromoplasts - contain beta carotenes and xanthophylls
- found in fruit, flowers
- provide colours
- differentiate parts of the plant so that it stands out.
- fruit and flowers to attract organisms - doesn’t carry out photosynthesis
6
Q
Uncoloured plastids
A
- uncoloured plastids are used for storing different molecules in the cell
- called leucoplasts - involved in storage and biosyntehsis
- amyloplasts (store starch), proteinoplasts (store proteins in seeds), elaioplasts (store and metabolise lipids).
7
Q
Uncoloured plastid: amyloplasts
A
- amyloplasts store and synthesis starch
- found in roots
- involved in gravitropism - gravity sensing.
- starch filled amyloplastas are more dense than cytoplasm and will sediment in the cell. auxin inhibits cell growth
- Full of starch because they are dense so end up at the bottom of the cell. Root responds to gravity by growing down.
- Uses the amyloplasts to sense the direction of gravity. So the amyloplasts fall to the bottom of the cell and triggers a reaction to re organise transporters in the membrane – for auxin.
- The auxin transporters will end up close to the bottom of the cell close to where the amyloplasts end up.
- Transported through vessels in the middle and then through the cells at the tip and sent up through the sides. When the auxin transporters are rearranged the auxin is sent down the bottom of the cell - very little coming out the top.
- Inhibits cell growth. If there’s lots of auxin at the bottom of the root the cells will stop growing and remain small whereas the cells at the top of the root will elongate and that will lead to the bending away from gravity towards the centre of the earth. How plants sense gravity.
8
Q
Plastid interconversion
A
- plastids are related and can interconvert between the different kinds.
- The chloroplast can change into chromoplasts – fruit or vegetables are green when they aren’t ripe – to not stand out and then when they are ripe the chloroplasts change into chromoplasts – breakdown the thylakoids breakdown the photosynthetic machinery synthesise new pigments to change into a chromoplasts.
- Amyloplasts and chloroplasts interconverting – potato – if the potato is exposed on the surface that will cause that part of the potato to turn green. The amyloplasts changing to start photosynthesising.
9
Q
Chloroplasts
A
- specialised plastids that carry out photosynthesis
- contains pigment chlorophyll responsible for plants green colour
- has a double membrane
- Also has an intermembrane space – not used
- Third set of membranes called the thylakoid membrane – stacked to form the granum.
- Contain chlorophyll to give plants the green colour.
- Stroma – outside the thylakoids.
- Inside the thylakoids is the thylakoid space.
10
Q
Thylakoids
A
- Where photosynthesis occurs - light harvesting and ATP synthesis
- Where photosynthesis occurs. Thylakoid membrane – the hydrogen ion space – acidic concentration is the thylakoid space.
- Photosystems are where the chloroplasts are where photosynthesis occurs.
- The hydrogen ion gradients drives ATP synthase generating ATP in the stroma. This can be used in the Calvin cycle.
11
Q
Chloroplast distribution - movement
A
- Large discrete units they don’t tend to fuse and divide constantly – static. But move around the cell during the day depending on the light conditions. If there is bright light on a leaf the photosystem can get damaged by the UV light – so they move the chloroplasts to the edge of the cell to minimise the amount of light damage/light radiation that they receive.
- If its dusk or its cloudy – not enough light the chloroplasts will move to the top of the cell. And try to absorb as much light as possible.
- Under UV radiation they are florescent red.
12
Q
How did mitochondria and plastids evolve?
A
- they both have unusual features - DNA, ribosomes (protein synthesis), double membranes
- Defining feature of the nucleus - the nucleus evolved through infolding of the plasma membrane. evidence for this? the nuclear envelope has a double membrane.
- Some bacteria come to the cell and the cell wanted to get rid of it so it did endocytosis and wrapped its plasma membrane around the bacterium and then that should of fused with the lysosome and got degraded but somehow the bacterium survived and must have given the cell some evolutionary advantage. Two membranes – one from the bacterial membrane and one form the plasma membrane of the cell.
- A photosynthetic bacterium did the same which could harvest light energy and turned into a plastid. Plasma membrane infolding encloses a photosynthetic prokaryote which evolves into the chloroplast - evidence? plastids have a doubel membrane.
13
Q
Endosymbiotic theory - what is the edivdence that mitochondria and plastids were once free living organisms?
A
- their double membranes
- their chromosomes - organelles contained DNA - bacterial chromosomes are circular, Eukaryotes nuclear DNA is linear. The DNA in the mitochondria are circular.
- their biochemistry resembles bacterial biochemistry - proteins passive channels - not specific
- they divide like bacteria and cannot be synthesised.
- their ribosomes are more similar to bacterial than eukaryotic.
14
Q
Mitochondrial genetics
A
- mitochondria contain a small circular chromosome
- in humans, encodes only 13 different proteins, codes for 22 tRNAs and rRNAs.
- replication, transcription and translation all occur in the mitochondrial matrix.
- The way that DNA is replicated inside the mitochondria is similar to how its done in a prokaryote.
15
Q
Plastid genetics
A
- the plastid genomes is much larger than the mitochondiral genome - 130 genes
- no.s of genes in mitchondria or plastids is far fewer than in bacteria.
- Plastids contain DNA. Must have lost genes.
- most mitochondrial and chloroplast proteins are syntehsised from nuclear genes.
16
Q
How did mitochondrial and plastid genes arise in the nucleus?
A
- Post-translational translocation
- Allowing proteins getting into the mitochondria or plastids. The proteins are translated in the cytoplasm by the ribosomes and sent out into the cytoplasm, signal peptides are recognised by the mitochondria or the plastid which bind to the proteins and allows them to pass into those organelles. How the proteins get into those organelles.
17
Q
endosymbiotic theory definition
A
the theory that mitochondria and plastids evolved through symbiosis from formerly free- living prokaryotes.
18
Q
What is an extracellular matrix?
A
- 3D network of extracellular macromolecules that provide structural support. made of proteins and carboydrates.
- structural support to the overall organism
- cell wall - a layer outside the plasma membrane providing structural support and protection.
19
Q
Who has a cell wall?
- animals?
- plants?
- fungi?
- protists?
- bacteria?
- archaea?
A
- Animal – no cell wall, does have an ECM
- Plants – cell wall
- Fungi – cell wall
- Protists – depends on the protist whether there is a cell wall or not, most no cell wall
- Bacteria – cell wall
- Archaea – cell wall
20
Q
ECM as a composite material
A
- composite materials are structuarlly strong and combine the good properties of the individual materials.
- they contain long, ridgid fibres embedded in the matrix - like resin or cement.
- the ECM is a composite material.
- two materials with good properties to get the good properties out of each.
21
Q
The extracellular matrix in animals
A
- long rigid fibres - glycoproteins such as collagen and elastin
- collagen - imbedded in the matrix - gel like substance sets the fibres together to make it strong.
- embedding materials - proteoglycans
- in animals the ECM is strong and elsatic - animals have a motile lifestyle rewuiring flexibility in the ECM.
- Polypeptide chains making up the elastin get crosslinked to each other so you get a network, when they relax they curl up a bit and when they relax the chains stretch out.
22
Q
Collagen
A
- 40% of your body is collagen
- found in connective tissue of animals - cartilage, ligaments and tendons. also in bones and skin
- contains two unusual amino acids - hydroxyproline and hydroxylysine. produced with proline and lysine with extra modifications – hydroxyl groups.
23
Q
Proteoglycans
A
- the embedding matrix is made up of proteoglycans.
- polysaccharide chains covalently linked to protein. polysaccharides branching off.
- combination of protein, sugars and carbs. main carb is glycosaminoglycans (GAGS)
- GAGs are hydrophillic molecules forming a hydrated gel like substance.
- Forms a gel raound the collagen fibres to set them to make the ECM substance
24
Q
A
25
Glycoproteins and proteoglycans
Where would we produce these molecules?
* glycoproteins:
* proteins with covalently bonded carbs usually short chain sugars.
* proteins will a little bit of sugars, little bit of carbs.
* proteoglycans
* small core protein with many carbohydrate chains attached, making up to 95% of the molecule
* Proteoglycans: carbohydrates which a little bit of protein.
* Where would we produce these molecules?
Glycoproteins and proteoglycans start in the ER and then further modified in the Golgi.
26
Production of animal extracellular matrix
example: collagen
1. translation of collagen proteins
2. hydroxylation of proline and lysine
3. glycosylation of hydroxylysine
4. more glycolysation
5. cross-linking and packaging into fibres.
Starts as a gene in the nucleus. Is transcribed to mRNA which goes out of the nucleus to a ribosome and will start translating that protein. The ribosome goes to the ER and the protein is going to be translated into the lumen of the endoplasmic reticulum. All proteins sent out of the cell are translated into the er. Once its in the er it gets modifications – amino acids – hydroxyproline, hydroxylysine this happens in the ER. Some sugars are added to the hydroxylysine. Then it is sent by vesicular transport to the Golgi apparatus where the sugars are further modified. Then it is sent out of the cell by exocytosis. The vesicle fuses with the plasma membrane and the collagen components are sent out of the cell and there will get modified by other enzymes out of the cell to crosslinks the collagen proteins together to bundle them into fibres.
27
Where do the steps of animal ECM production occur?
1. translation of collagen proteins - **ER**
2. hydroxylation of proline and lysine - **ER**
3. glycosylation of hydroxylysine - **ER**
4. more glycolysation - **GOLGI**
5. cross-linking and packaging into fibres. - **OUTSIDE THE CELL (membrane bound enzymes)**
28
the ECM in plants - plant cell wall
* long rigid fibres - cellulose (a polysaccharide)
* embedding material - pectin, hemicellulose, proteins.
* cellulose - primary component of plant cell walls.
* Cellulose – carb/polysaccharide that is made up of glucose sugar molecules joined together in a single chain and multiple chains will come together and hydrogen bond with each other to from cellulose chains which get bundled into a microfibril. The fibrils are laid down in perpendicular arrangements. Makes up majority of a plant cell wall.
* cellulose is made of glucose monomers. Glucose is joined alternating the direction of the glucose monomers where as starches monomers are in the same direction.
* We can digest cellulose but we can't starch – why? No enzymes to degrade cellulose but we do for starch. We would need lots of enzymes to breakdown all the components in the cell wall. Bacteria in the stomach breakdown cellulose in other organisms and then they steal the nutrients form the bacteria.
* Pectin - embedding material in the plant cell wall - a complex set of polysaccharides that helps bind cells together.
* In plant cell walls the ECM is rigid and stationary - consistent with plants non-motile life-cycle. They need to protect their cells.
29
Production of plant cell walls
* cellulose is synthesisde directly at the plasma membrane
* the enzyme cellulose synthase resides in the plasma membrane
* other cell wall components are synthesised in the golgi apparatus and secreted by exocytosis.
* Cellulose – carb
* A protein sits in the plasma membrane called cellulose synthase and it takes sucrose, chops off the glucose and makes It into these polysaccharide chains coming out of the cells. Then the enzymes on the outside help to bundle that together to package it together to make the cellulose fibrils.
* The pectin are produced in the Golgi, and secreted by exocytosis.
30
Vitamin C and the ECM
* collagen contains amino acids - hydroxyproline and hydroxylysine
* animals require vitamin C to make hydroxyproline
Enzymes in the er that modify the amino acids to make the hydroxy versions. The enzyme that makes hydroxyproline requires a cofactor – need another molecule to help them to protein. Vitamin c is needed to modify collagen to make hydroxyproline.
If you don't have vitamin c you get scurvy. Affects on the skin because collagen cant be built up properly.
* problem for sailors.
* . In the 1700 the scottish doctor he conducted trial to see if he could find the component of diet that causes curvy. Gave the sailors a supplement in their diet. They found that the sailors given organs or lemons recovered quickly from scurvy.
31
the roles of extracellular matrix and cell walls
* protecting cells
* providing support and rigidity
* providing elasticity to tissues
* gluing cells together.
Form a barrier against invading pathogens.
In animals and plants the ECM helps to glue cells together.
In plants the cell wall helps to keep the cells together.
32
What is the cytoskeleton?
* the cytoskeleton is a complex system of protein filaments that fucntions in shape and mechanical support and motility - movement of things within cells and cells within their environment.
* The cytoskeleton is constantly growing and changing - can be built up or taken down.
* motor proteins use the cytoskeleton as tracks to trasnport cargo around the cell.
33
Three components of the eukaryotic cytoskeleton
* microtubules - growing around the centrosome.
* actin microfilaments
* intermediate filaments
34
Structure of microtubules
* hollow tube - 25 micrometres wide - diamter
* subunits - alphas tubulin and beta tubulin forming heterodimers.
* Dimer – two polypeptide chains that bind to each other and work together. Can be the same two proteins or different ones that bind together. Function together
* Bigger molecules – trimers, tetramers. If we have lots we call that a polymer.
* Tubulin are formed together as a dimer. If the cell wants to form microtubules the dimers will form together to make a polymer. They spiral around to make a tubular shape – hollow through the middle. Largest filaments of the cytoskeleton filaments. The polymer has two ends – at one end the alpha tubulin is exposed and at the other end the beta tubulin is exposed. Has polarity.
35
Microtubule polymerisation
* + end where dimers add on more easily. The minus end is we depolymerisation happens more easily where dimers fall off the end. Very dynamic, balance of those two processes determine the length of the microtubule.
* Don't tend to form on the cytoplasm on their own, they Need an organising centre to grow out of to organism the organise the microtubules and start their polymerisation. This organising centre is called the centrosome – two perpendicular cylinders where the microtubules grow out. Minus end towards the centrosome and the plus end growing out.
* Found somewhere in the centre of the cell in the nucleus. Grow out towards the plasma membrane.
36
Motor proteins of microtubules.
* microtubules are train tracks that material can move along.
* Two different motor proteins – dynein and kinesin.
* The motor proteins are driven by the hydrolysis of ATP. Can hydrolyse ATP to ADP which allows them to walk along the microtubule.
* The cargo might be things like vesicles, organelles, cytoskeleton components.
* The different between them is that they have a direction. Kinesis moves cargo out towards the plus end and dynein moves cargo in to the minus end.
37
Microtubule functions
* Mictrotubules function in controlling
* cell shape
* cell motility/migration
* cell division
* We will conside two different systems in which microtubules are used to generate cell motility
* the mitotic spindle
* cilia and flagella.
38
Mitotic spindle - in chromosome segregation and cell division
* A cell about two divide makes two copies of everything, it has already copied its DNA. The microtubules during mitosis will attach to the chromosomes, when the cell divides the chromosomes get pulled apart by the action of motor protons on the microtubules pulling the DNA towards each end so two new cells forms around those chromosomes.
* mitotic spindle - an array of microtubules with associated proteins, included the motor proteins kinesis and dynein.
* it functions to seperate chromosomes during mitosis
39
Eukaryotic cilia
* in protists - function in locomotion and food collection
* in multicellular organisms - move them environemnt past the cell.
* small and numerous little fibre bits on the outside of the cell.
* Uses it to find food and swim around. Finds food and pushes it up to the top where it will get taken into the cell by phagocytosis.
40
Eukaryotic flagella
* drives cell movement
* function in locomotion of some unicellualr eukaryotes and in sperm cells of animals, algae and some plants and fungi.
* large and only one to a few per cell
* prokaryotes also have flagella but they are unrelated to eukaryotic flagella *and not made of microtubules*.
41
Eukaryotic flagella and cilia
* common strutcure - 9 microtubules in the doublets in ring, 2 single microtubules in the middle
* sheated on extension of plasma membrane
* Both made of microtubules and both function in the same way on a molecular function.
* Two microtubules in the middle and then nine microtubules on the outside. Surrounded by the plasma membrane. Walk along microtubules with a microtubule as their cargo.
42
What drives the movement of cilia and flagella?
* Dynein.
* ATP activates dyenin motor activity and causes microtubules to slide past one another.
* inside the cell microtubules are anchored which force them to bend rather than slide.
* Causes the microtubules to slide past each other.
* They have crosslinking proteins and the motor proteins are stopped by these proteins which don't allow them to walk further and this produces strain onto the microtubules causing them to bend.
* Stop giving ATP and relax and then add ATP again to bend.
43
Structure of actin microfilaments
* Actin microfilaments - thin solid rods composed of a twisted downle chain - 7 micrometres.
* subunit actin monomer
* small and made up of a monomer.
* no hollow gap in the middle
* polymerised and unpolymerised actin monomers exist in a dynamic equilibrium
* actin microfilaments have polarity
* Actin monomers like to add on one end more than the other - + and – end
44
What is the motor protein of actin microfilaments?
* myosin - uses ATP to walk along microfilaments towards the plus end
* cargo includes - vesicles and roganelles, other cytoskeleton components.
## Footnote
Motor proteins move cargo along the filaments – only one protein – myosin. Only movement towards the plus end.
Myosin – the legs swings off and swings around – walking along the filaments.
The domain that attaches to cargo – cargo domain. Hydrolyses ATP to do the work to move along the filaments.
The feet domains, also called head domains.
45
Actin microfilament function
* microfilaments function in
* cell shape
* cell motility
* organelle motility
* muscle motion
* systems in which actin microgfilaments and myosin generate cell motility - muscle movement, cytoplasmic streaming plant cells.
46
muscle movement in animal cells.
* in muscle cells myosin protein bundle together to form myosin think filaments
* Actin working with myosin. Myosin form bundles of lots of myosin proteins – myosin filament and out of the filament is sticking out the motor domain (feet) where they can contact the actin filaments.
* proteins are arranged in a Z line - Z line – the filaments anchor themselves to for their motion.
* Thin filaments of single actin microfilaments.
Thick filaments – lots of myosin bundled together.
Both overlap.
47
myosin and muscle contraction - how it works
* When relaxed there is not much overlap between the thin and think filaments. If we activate muscles – add ATP the motor domains grab on to the actin and walk along from both ends and that will slide the actin along and bring the z line anchors closer in to each other and the muscle contracts. Molecular explanation for how muscles contract.
48
Why do we use calcium to regulate muscle contraction
* A calcium trigger and ATP results in muscle contraction
* Needs atp which drives the work to contract the muscles. Calcium needs to trigger contraction in the muscle fibres. We need calcium because atp is always present and if we remove atp from the cell to stop the cells from caontracitng all the other processes stop so the we need the proess to be under control of a molecule that's usually not repsetn in a cell – calcium ions are at a low concentration – normally no Ca so no contraction.
* Calcium is relased from outside the cell or from another organelle stored in the cell in the ER, when the muscle fibres wan to contract they release the Ca and then they pump the Ca out of the cell or to the er when we don't want the muscle ot contract.
* Signalling processes need to switched on and of f and needs to be controlled by molecuels that can be added or removed form the cell.
49
Cytoplasmic streaming in plact cells
* cytoplasmic streaming is a process used to generate flow in especially large plant cells.
* myosin coated organelles move along microfilaments
* Cells are limited to a certain size because it would take too long if everything was too big. All the processes get slower and slower. Limitation.
* Getting cells bigger – by generating a flow within the cells. Helps to mix things up so that molecules can get to where they need to be quicker.
* Drag the chloroplast around the cells will drive motion.
* Using actin microfilaments and myosin.
* Some actin microfilaments are anchored onto the cell membrane and then the myosin motors are attached to actin microfilaments and holding cargo which in this case is a chloroplast.
* The myosin drag the chloroplasts along the actin microfilaments creating motion within the cell.
50
Prokaryotic flagella
* Half of all prokaryotes are capable of directional movement which usually uses flagella
* Prokaryotes don't have cytoskeleton, actin filaments, or microtubules.
* Do have same functions. Bacteria needs to move around to escape from toxins and find food.
* Done with flagella. Works differently to eukaryotic cells.
* filament composed of the protein falgellin
* movement is by the drive by basal apparatus which acts as a motor
* Flagellin proteins are not motors. Passively flopped around in the liquid by a protein machine at the base of the flagellum.
* Rotor protein that spins around and the spinning drives the movement of the flagellum. Driven by a proton gradient.
* Space between the two membranes – acidic space, high concentration of hydrogen ions that drives the movement of the rotor.
