APS138 Cell And Molecular Biology - Leegood Flashcards
What is a glycosome?
A peroxisome involved in glycogen storage and metabolism
What is the volume and total membrane area of a hepatocyte?
5000 micrometres^3
110,000 micrometers^2
What percentage of the volume of the cytosol is protein?
20-30% (200mg.ml^1)
In choloroplasts the protein concentration is even higher (280mg.ml^1)
Why are cells so small?
Metabolism needs fuel from outside and produces waste products
Exchange is limited by surface area to volume ratios
Small cells are easier to turnover than large cells
How long does a protein take to traverse e.coli cytoplasm vs the cytoplasm of a mammalian cell?
~10ms vs
~10s
How are some cells specialised for high material exchange?
Surface area increased by microvilli and mitochondria abundant
What feature do Sarum canadense roots have for material exchange?
Mycorrhizal arbiscules
What adaptions may very large cells such as bubble algae have?
Coenocytic structure with multiple nuclei and chloroplasts and a large central vacuole
What do membranes allow within cells?
Compartmentalisation
Why do cells and organelles have compartments?
Different environments (pH for example)
Metabolic regulation by keeping enzymes, substrates and regulators in separate locations
Locally high metabolite concentrations
Sequestration of toxic substances
What pH do compartments of choloroplasts and mitochondria have and why?
Acidic pH to drive ATP synthesis
What is the nucleus for?
Genome, DNA replication, transcription, RNA processing
Compartmenting the genome from the cytoplasm allows regulation of gene expression (e.g. post-transcriptional processing, such as alternative splicing)
What is the cytoskeleton made up of?
Motor proteins and protein filaments
Protein filaments form a 3D mesh for rigidity shape and structure.
Motor proteins form trackways for movement
In muscle cells, how much of the total cell protein is comprised by actin?
10%
What are microtubules?
Cylindrical tubes (20-25nm diameter) of Tubulin. Highly dynamic
What are microfilaments and what are they for?
Actin fibres (3-6nm diameter)
For gliding, contraction and cell cleavage. With myosin are responsible for muscle contraction
What are microtubules for?
Determining cell shape, provide a trackway for movement of cell organelles and vesicles. Form spindle fibres in mitosis. Found inside cilia and flagella.
What are intermediate filaments?
Anchor and position nucleus and give cell flexibility (8-12nm diameter)
What are movers (motor proteins) powered by?
Include Kinesin, Dynein, myosin (muscle)
ATP
In which direction does kinesin travel in?
Towards ‘plus’ end away from the nucleus
Which direction does dynein travel in?
Towards ‘minus’ end towards the nucleus
What are melanocytes?
Cells used by fish, amphibians, crustaceans, cephalopods and reptiles to change colour
Motor proteins transport pigments in melanosomes along microtubule/actin tracts
How do microtubules aid cell wall synthesis in plants?
Cortical microtubules form a template for the deposition of cellulose in bands
Turgid driven growth is constrained along the axis of elongation
Cells produce molecules that have to be delivered to other places inside the cell, or exported out of the cell, at exactly the right moment. Where are these molecules parcelled within?
Vesicles
What does the RER do?
Synthesises proteins and packages them in vesicles
What does the SER do?
Synthesises lipids
What do transport vesicles do?
Takes proteins and lipids to Golgi apparatus
What does the Golgi apparatus do?
Modified lipids and proteins, sorts and packages them in vesicles
What vesicles travel to the cell surface membrane and expel materials?
Secretory vesicles
What do lysosomes do?
Contain digestive enzymes that break down cell parts or substances entering by vesicles
What proportion of genes code for proteins that enter the ER?
1/3
What must happen to proteins before they are transpired to targets?
They must be folded and modified correctly in the ER
Where does protein translocation occur in the ER membranes?
Translocation pores
What is removed while the nascent polypeptide is emerging into the ER lumen?
N-terminal signal peptide
What does nascent mean?
Emerging/ forming
What is the ER lumen specialised for?
Folding, assembly, modification, quality control and recycling of proteins
Name 2 examples of processes used to enhance protein stability before secretion in the ER
Disulphide bond formation and glycosylation
What is ER movement dependent on in plants vs animals?
Actin/myosin in plants
Microtubules in animals
What enables vesicles to dock and fuse with their target membranes precisely
A protein complex
In milk secretion what is the role of the Golgi apparatus?
Synthesis of lactose form Glc and UDP-Gal
Sorting and packaging
What is the main type of protein body used in plants, to store proteins and provide C, N and S for rapid growth?
Vacuoles
What type of plant contains ricin and what is ricin?
Castor bean seeds
A potent cytotoxin
What is ricin for and how does it work?
Anti-herbivory - inhibits protein synthesis by irreversibly inactivating eukaryotic ribosomes
Where in castor bean cells is ricin stored?
Protein bodies - when seed germinates, ricin is rapidly degraded
When is ricin not catalytically active until?
It is proteolytically cleaved within the protein bodies.
Plant thus avoids poisoning its own ribosomes
Demand for insulin will potentially double over the next 10 years. How much insulin is found in safflower and how many hectares would be required to meet the worldwide demand?
0.4kg.ha^-1
6,500 hectares
What happens to proteins that are incompletely or incorrectly folded (e.g. mutants)?
They are recognised and retained within the ER and targeted for degradation by lysosomes or proteasomes
What are chaperones?
Proteins that assist the correct intercellular folding and assembly of polypeptides
What does ERAD stand for?
Endoplasmic Reticulum-Associated protein Degradation
What is CFTR?
Cystic Fibrosis Transmembrane conductance Regulator - a chloride ABC transporter
In cystic fibrosis what do the epithelia lining sweat gland ducts fail to take up efficiently?
Cl from the lumen
What does lack of CFTR allow the accumulation of?
Mucus
- in the lungs, and in the pancreas, so digestive enzymes cannot get into the intestine
What does cystic fibrosis stop from happening during quality control?
The mutant protein from leaving the ER
Lack of Phe^508
70% of cystic fibrosis sufferers
In which types of organisms are vacuoles and lysosomes found?
Plant and fungal cells
Some protist, animal and bacterial cells
What are lysosomes for?
Autophagy, lysis and recycling misfolded proteins
What proportion of leaf epidermal cell volume is comprised by vacuoles and lysosomes?
99%
70% in leaf mesophyll cells
What are vacuoles for?
Storage of carbohydrates, organic acids, anthocyanins, seed storage proteins
Isolation of toxic substances
Anti-herbivory (eg cyanogenic glycosides)
Maintaining internal hydrostatic pressure (turgor)
How many species use cyanogenesis as a method of anti-herbivory?
3000 species
Including cassava - major source of calories for people in sub-Saharan Africa - chronic cyanide poisoning can occur
Sorghum leaves
Hydrolysis of dhurrin occurs only after tissue disruption (by herbivory)
A few species of insects are able to synthesise cyanogenic glycosides. E.g…
Larvae of the burnet moth sequester then from their food plants, storing them in viscous droplets in cuticular cavities.
Adult females release HCN as a pheromone to attract males. Makes give cyanogenic glycosides to females as gift during mating - helps females protect eggs
What is the theory of how chloroplasts and mitochondria came from aerobic and photosynthetic bacteria called?
Endosymbiotic theory
What are some similarities between prokaryotes and mitochondria and chloroplasts?
70S ribosomes
Binary fission
1 single circular chromosome containing DNA
Similar size (approx. 1-10micrometres)
Positive porins
Same initiating amino acid (N-formylmethionine)
What evidence for endosymbiosis can be found in arabidopsis?
Genes for Cyanobacteria peptidoglycan (cell wall) synthesis still present
Cardiolipin
What theory is suggested for why plastids often have many envelopes (membranes)
Secondary (Multiple) endosymbiosis
How do sea slugs display similarities to endosymbiosis?
Ingest chloroplasts and can use for photosynthesis and survive for months without eating, running in “solar power”
How many arabidopsis protein-coding genes were acquired from cyanobacteria?
~4,500 (18% of total)
Transfer of organelle DNA to nucleus, increasing nuclear complexity
What does mitochondrial DNA code for?
rRNAs, tRNAs, 13 our of ~85 components of oxidative phosphorylation system
What does chloroplast DNA encode?
About 80 genes: some rRNAs, tRNAs, ribosomal proteins, RNA polymerase subunits and some genes for photosynthesis
Why is mitochondrial DNA inherited maternally (from the mother)?
Simple dilution (egg contains 100,000 to 1,000,000 mtDNA molecules, sperm contains only 100 to 1000)
Degradation of sperm mtDNA in the fertilised egg
Failure of sperm mtDNA to enter the egg
How do proteins cross chloroplast membranes?
Most proteins are nuclear encoded. A signal peptide is a target sequence of amino acids that is recognised and cleaved by a signal peptidase at the chloroplast envelope
(2 signal sequences if also entering thylakoid membrane)
What size are the ribosomes used to synthesise the large subunits in rubisco?
70S (chloroplast plastid DNA)
Chaperones are required
80S ribosomes in the cytoplasm are used to translate the pre-SS polypeptide which then enters the chloroplast as the small subunits, and rubisco is formed (L8S8)
Name a plant without plastid genomes
Rafflesia lagascae
A parasite that has plastid-like structures but no intact genome
The freshwater alga polytomella has…
A plastid but no trace of a plastid genome
What are apicomplexa?
Parasitic single-celled eukaryotic organisms deriving from red algae, loss of plastids.
Malaria, toxoplasma, coccidiosis (loss to poultry industry worldwide)
Plasmodium in malaria - still retains its plastid genome. How many membranes do its apicoplasts have?
4
Suitable target for drug treatments
What has cryptosporidium lost?
Apicoplast
Expressing a large genome is expensive. What do mitochondria contain for efficient energy generation in eukaryotes?
A large area of internal membranes
What is an advantage of chloroplasts and mitochondria?
They expand and diversify the genome in eukaryotes
Mitochondria increased number of cel proteins by 4-6 orders of magnitude
List functions of proteins
Catalysis (enzymes)
Energy production (light harvesting, electron transport, rotary ATPases)
Host/pathogen interaction: antibodies, mucus
Structural: keratin, collagen
Motion: cytoskeleton, muscle, flagella
Organisation of DNA and regulation: histones
Regulation: kinases
Storage: seeds and eggs
Toxins and venoms
Transport: membrane proteins, haemoglobin
What do proteins consist of?
Chains of amino acids joined by peptide bonds
What does the polypeptide protein backbone have?
Amino acid side chains (may be polar or non polar)
How many amino acids with different side chains with different properties are there?
20
The polypeptide backbone is identical in all proteins
What do side chains determine?
How the polypeptide chains of the protein interact and how the protein is folded
How many levels of structural organisation are there in proteins?
4
What does the quarternary structure involve?
The association of two or more polypeptides into multi-subunit complexes
Rubisco has 16 subunits
Where are h bonds found in a helices?
Between side chains within the same polypeptide
Where are I bonds found in ß pleated sheets?
Between different polypeptide chains
Sulfide bonds can be interchain or intrachain
Yes they can joey well done!
What processes may proteins go through to increase their stability before secretion?
Sulfide bond formation and glycosylation
In the cytosol the gluthione reduction potential is…
Reducing
What is mucin?
A glycosylated protein used to produce mucus.
Large extracellular glycoproteins with hundreds of oligosaccharide chains linked to a protein backbone.
Either anchored or secreted
What does high glycosylation mean for mucin
It is resistant to acids (stomach acid), proteolysis, adds gel like properties found in mucosal barriers
What percentage of the amino acids in keratin are cysteine?
25%
What gives keratin polypeptide chains great stability?
Disulfide bridges (cross linkage of chains)
What is the major extracellular insoluble fibrous protein and most abundant protein in animals
Collagen
What is collagen for?
Helps tissues withstand stretching
What happens to collagen if there is an absence of vitamin c (ascot if acid)?
Helices cannot form, blood vessels, tendons and skin become fragile, leading to scurvy
What makes silk so strong in structure and tensile strength?
High glycine content, small non-polar side chains allowing for tight packing of the anti parallel ß sheets
What happens to silk when water is present?
It is stored as an emulsion as the C-terminus ensures solubility and the core is hydrophobic.
It can be spun into a thread when water is absent
What does gluten form (that traps CO2 bubbles)?
A matrix
Gluten proteins are linked by hydrogen bonds and disulphide bridges
What are enzymes?
Proteins folded into complex shapes that allow substrate molecules to fit into the active site
They do not change during reactions, they simply facilitate the interaction of reactants and speed up the rate of the reaction.
They are the most powerful and selective catalysts known.
What do nucleases do?
Break down nucleic acids by hydrolysing bonds between nucleotides
What do synthases do?
Synthesise molecules by condensing two small molecules
What do isomerases do?
Rearrange bonds within a single molecule
What do kinases do?
Add phosphate to molecules (eg sugars or proteins)
What do phosphatases do?
Remove phosphate group
What is the total number of enzymes in a person?
Approx 75,000
What percentage of plant enzymes have unknown functions?
60%
How is enzyme protein abundance regulated?
Transcription and translation
How does the cell regulate the catalytic activity of enzymes?
Direct fine-tuned control of protein activity and kinetics by metabolites and regulators
Specific post-transcriptional modification
Transcription and translation regulation
How many types of post-translational modifications are there?
Over 300
What are the two types of repression for the tryptophan pathway?
Inhibit activity of the first enzyme in the pathway (rapid response)
Depress expression of the genes for all the enzymes needed for the pathway (longer-term)
Name some types of PTMs
Addition of functional groups - phosphorylation, glycosylation
Structural changes - reduction/oxidation
Changes to amino acids
Addition of proteins or peptides - ubiquitunation can increase protein lifespan and stability
Some PTMs are fixed for the life of the protein, while other changes are reversible
Many proteins have two or more different functions, for example…
Some crystalline, structural proteins in the lens of the vertebrate eye, are also metabolic enzymes. E.g. duck crystalline is lactate dehydrogenase.
Aconitase in man is both an enzyme of the Krebs cycle and involved in iron homeostasis
Called moonlighting proteins
Extended aerobic respiration required a regulated supply of…
Carbon from glycogen and lipids
How many glucose units in a glycogen granule around its core protein of glycogenin?
Approx 30,000
What advantages does branching give glycogen?
More soluble
Exposure of more C4 ends means that glycogen can be both synthesised and degraded more quickly than a single starch chain with the same number of residues
What percentage of the arabidopsis genome is protein kinases?
5.5%
Name 3 hormones controlling glycogen metabolism in mammals.
Insulin, glucagon, adrenaline
Why is glucagon and adrenaline action selective?
Only liver cells have receptors
What are glucagon and insulin used to do?
Maintain a constant concentration of blood glucose ~5mM
What is glycogen synthase b?
Phosphorylated (by protein kinase a) and inactive
What is protein kinase A activated by?
cAMP (formed by adenylyl Cyclades pathway)
Why is transport necessary in eukaryotic cells?
Metabolism needs fuel and produces waste products.
Organelles must be able to transport materials to and from the cytosol.
Proteins need to be seceted.
Signalling within and between cells
What are gap junctions?
Channel proteins (connexins in vertebrates, innexins in invertebrates) for the rapid exchange of ions and metabolites between cells
How many connexins are in the human genome?
~20
What are plasmodesmata?
Gaps in the cell walls of plants that allow trnasport of materials between cells (as cell walls are impermeable to most substances) - enable cytoplasmically interconnected fields of cells called symplasm.
There is also a tubule of ER that passes through plasmodesmata
Which types of molecules easily pass through the phospholipid bilayer?
Hydrophobic molecules, very small uncharged polar molecules (H2O)
What are aquaporins?
Membrane channels for transport of water, glycerol, CO2 etc.
An extremely hydrophobic protein
They facilitate the diffusion of small uncharged molecules (water, glycerol, urea, CO2)
Occurence correlates with high water fluxes (e.g. kidney)
Activity can be regulated by phosphorylation
what are the 3 ways of driving active transport?
- Coupled transporter
- ATP-driven pump
- Light-driven pump (e.g. halobacteria)
What do P-type pumps (P-ATPases) transport?
Specific ions e.g. H+, Na+, K+, Mg2+, Ca2+.
One or two polypeptides (less than rotary ATPases)
What do ATP-Binding Cassette (ABC) transporters transport?
lipids and sterols, ions and small molecules, drugs and large polypeptides
e.g. Cystic Fibrosis transmembrane conductance regulator (CFTR) is an ABC Cl- trnasporter
What do rotary ATPases transport and why?
H+ pumps with a role in energy conversion
Ion channels can be opened by different stimuli, including….
Voltage, temperature, pH, stretch, ligands
