Module 1 Flashcards
Define cell
The simplest collection of matter that can be alive
How many species be classified into groups
Based on structure and DNA sequence
Highest level of classification
Domain: Bacteria, Archaea, Eukarya
Name the 4 Kingdoms
Plantae, Fungi, Animalia, Protist
Size of plant and animal cells
10-100µm in diameter
What is the size of a bacteria cell?
1-5 µm in diameter
Why are cells limited to a certain size?
SA proportional to diameter squared, but vol proportional to diameter cubed.
- thus a small cell has a greater SA:vol ratio
3 important parameters in microscopy
Magnification, resolution, contrast
Define magnification
Ratio of image size to real size
Define resolution
Clarity of the image
- the minimum distance that can separate two points that still remain identifiable as separate points when viewed through a microscope.
Contrast
The difference between light and dark areas of the image
What can you do to contrast?
Enhance, by staining
Magnification of light microscopy
1000x
What limits greater magnification of light microscopy
Resolution
What is the limit for resolution for light microscopy
0.2µm
How is the power of light microscopy enhanced
Staining and imaging techniques
Advantage of light microscopy over SEM and TEM
Light microscopy allows samples to be living
Difference between EM and LM
EM focuses electrons rather than light on a specimen
What is the relationship between resolution and wavelength
Resolution is inversely proportional to wavelength
Why do electrons allow higher resolutions
Because of their shorter wavelengths
- Shorter wavelengths of electrons increase resolution such that intracellular structures may be “seen”
How many times fold is the improvement of EM on LM
100x
What is the process of SEM
Scans the surface of the specimen which has been coated in a thin film of gold.
Electrons excite the gold atoms to generate a 3-D image of the surface of a specimen.
Something common between EM and SEM
Images are grayscale, but can be coloured artificially.
What is TEM used for
To examine the cell’s internal structure
What is the process of TEM
Electron beam passes through a thin section of a specimen that has been stained with heavy metals. The scattered electrons are focused by electromagnets to generate an image
What cells can SEM and TEM be used on
Processed dead cells.
Structures of animal cell (8)
- nucleus
- ER (rough and smooth)
- cytoskeleton: microfilaments, intermediate filaments, microtubules
- microvilli
- mitochondrion
- golgi
- ribosome
- plasma membrane
Structures of a plant cell (8)
- nucleus
- ER (rough and smooth)
- mitochondrion
- chloroplast
- central vacuole
- golgi
- plasmodesmata
How did the complex structure of the eukaryotic cell evolve?(5)
- mitochondria resemble bacteria
- prokaryotic cells were engulfed by early eukaryotic cells
- established a stable relationship of benefit to both parties
- engulfed prokaryotes evolved into mitochondria
- similar proposal for chloroplasts airing from photosynthetic prokaryotes.
Draw the endosymbiont theory diagram and label
.
Composition of a typical prokaryotic cell
Water 70% Protein 15% Nucleic acids 7% Carbohydrates 3% Lipids 2% Other small molecules 1% Inorganic ions 1%
Major atomic constituents of biological macromolecules
O>C>H>N
Building blocks -> higher order of structures
Aa - proteins
nucleobases - nucleic acids (RNA, DNA)
Simple carbohydrates - Complex carbohydrates
Lipids
Supramolecular assmeblies
- membranes
- ribosomes
- chromatin
Organelles
- nucleus
- mitochondria
- golgi
- ER
Difference between carbon chain and rings
- more stable and soluble than linear structures
4 macromolecules
- Polysaccharides (complex carbohydrates)
- Nucleic acids (DNA and RNA)
- proteins
- Lipids
4 levels of carbohydrates
- Monosaccharides
- Disaccharides
- Oligosaccharides
- Polysaccharides
Hexose monosaccharides
Building blocks of higher order carbohydrates
- 6 carbons
Pentose monosaccharides
Usually part of larger molecules eg nucleic acids
- 5 carbons
What are Disaccharides
Two monosaccharides joined together
What makes up sucrose
Glucose + fructose
What makes lactose
Galactose + glucose
What makes up Maltose
Glucose + glucose
What are oligosaccharides
3 to approx 10 linked monosaccharides
How long are polysaccharides
Approx >10 linked monosaccharides
What is amylose made of
Alpha glucose linearly linked
- forms spiral
What is amylopectin
Alpha glucose linked in chains, but with branches
- like amylose with branches
What bonds are between glucose monomers in amylose and amylopectin and glycogen
Alpha1,4 glycosidic bonds
Alpha1,6 glycosidic bonds at branch-points
Compare amylopectin to glycogen
Glycogen is more branched
What is cellulose made of
beta glucose linked with beta1,4 glycosidic bonds
What two forms can glucose be in
Linear and ring
Different between alpha and beta glucose
OH on C1 is below on Alpha
Above on Beta
2 forms of starch
Amylose and amylopectin
What does the glucose chain look like in cellulose
OH alternating between up and down
Functions of carbohydrates (3)
- Cell recognition
- Energy (energy storage as polysaccharide)
- Structure
Why can’t cellulose be used as an energy source
Can only break alpha1,4 bonds in our body. Can’t break Beta1,4 bonds = can’t digest
What is the structure of cellulose
Chains of beta glucose monomers linked by beta1,4 bonds.
H bonding between the glucose chains
3 characteristics of lipids
- not polymers
- heterogeneous
- hydrophobic
4 types of lipids
- triacylglycerol
- steroids (sterols)
- phospholipids
- fat soluble vitamins
Functions of lipids (3)
- Structural
- Regulatory
- Energy
2 structural lipids
Cholesterol and phospholipids in the cell membrane
What type of lipid is cholesterol
A steroid
How do phospholipids differ from triacyglycerol
Phospholipids have 2 chains of fatty acids and a phosphate head. Triacyglycerol have 3.
3 Steroids
Cholesterol
Testosterone
Oestrogen
Why do lipids make much more energy than fat
more carbons
3 components of nucleic acid
phosphate, (de)oxyribose sugar, nitrogenous base
Difference between deoxyribose and oxyribose
OH on C2 in RNA, H on C2 in DNA
What are proteins
Molecules by which cells perform their functions in the whole organism
1 gene codes for 1 protein
.
one gene can code for many proteins
the proteins are slightly different.
Functions of proteins
- structural
- regulatory
- contractile
- transport
- storage
- protective
- catalytic
- toxic
Example of structural protein
Collagen - skin and bones
Eg of regulatory protein
Insulin - a peptide hormone
Eg of contractile protein
Actin, myosin - muscle proteins
eg of transport protein
Hb - carries O2 around body
Eg of storage protein
egg white (albumin), seed proteins
eg of protective protein
Antibodies - immune proteins
eg of catalytic protein
amylase, RNA polymerase - enzymes
eg of toxic protein
Botulinum toxin, diphtheria toxin.
Size of bacterial cell
1µm^3
Old view of prokaryotes
- homogenous static structures
- undifferentiated - no behaviour
- sacs of jumbled enzymes/proteins
- small size, lack of organelles
Limiting factors for bacteria reproduction
- nutrients
- competition
- space
- build up of toxins
New view of bacterial cell biology
- highly ordered and dynamic
- capable of polarising and differentiation into cell types
- intracellular organisation - protein localisation, DNA and lipids
- signal each other to coordinate multicellular actions (3 languages: gram pos to gram pos, gram neg to gram neg, universal)
- exhibit learning behaviour - anticipate changes in their environment (Pavolonian conditioning)
Structures in Bacteria
- fimbriae
- nucleoid
- ribosomes
- plasma membrane
- cell wall
- capsule
- flagella
Width of bacteria
0.5µm
What is the cell wall of bacteria made of
Peptidoglycan
Function of cell wall of bacteria
- Structure: Rigid macromolecular layer that provides strength to cell
- Protection: Protects cells from osmotic lysis and confers cell shape.
What do antibiotics target?
The cell wall.
Structure of bacterial cell wall
NAG NAM (carbohydrate backbone with peptide side chains) linked up by peptide cross bridge
Difference in structure between gram positive and gram neg cell wall
Gram positive bacteria have a thicker peptidoglycan layer (20-80nm). Gram neg bacteria have a thin layer of peptidoglycan (5-10nm).
Gram neg have a thin layer of peptidoglycan between inner and outer membranes
Thickness of Gram-positive bacterial cell wall
20-80nm
Test observations for gram-pos vs gram-neg
For gram pos, Peptidoglycan traps crystal violet, which masks the safranin dye.
- so much peptidoglycan that can’t wash away with alc
- when iodine enters, an iodine-crystal violet copmlex forms.
- too large to pass through thick cell wall -> not removed by
- no effect of safranin
For gram neg, crystal violet is easily rinsed away, revealing the red safranin dye.
- thin layer of peptidoglycan -> take up crystal violet
- washed away with ethanol
- cells take up safranin
Thickness of gram neg cell wall
5-10nm
What constitutes the cell wall of gram neg bacteria
A thin peptidoglycan layer under an outer membrane
- outer membrane contains lipopolysaccharides
What is the outer membrane of gram-negative bacteria made of
Lipopolysaccharide (LPS)
colour of gram neg and gram pos
Gram pos = purple
Gram neg = red
Process of gram staining
- Application of crystal violet (purple dye)
- Application of iodine (mordant)
- alcohol wash (decolorisation)
- application of safranin (counterstain)
4 Unique structure found only in prokaryotes
- bacterial flagella
- Cell surface layers: capsules and slime layers
- Bacterial endospores
- Fimbriae
- peptidoglycan (only in prok)
Structure of flagella
- MOTILE bacteria produce flagella
= long flexible appendage resembling “tails” - made of protein
10 - 20nm in diameter
5 - 10/cell - number of flagella and location on cell surface varies
- act like a propeller: cell rotates them to move through a liquid medium
- attached to cytoplasmic membrane.
What allows bacteria to move in LIQUID MEDIUM
flagella
How wide are flagella
10-20nm
What are the 3 major sections of flagella
- Long filament
- Hook
- Basal body
Describe the long filament of flagella
- extends into the surrounding medium.
- rigid
- 50kDA
- 4.5µm in diameter
- composed of subunits (flagellin) - 20000 per filament
What are the subunits of flagella filament
Flagellin
How wide are flagella
10-20nm in diameter
How many subunits are in flagella
20000
Describe the hook of the bacterial flagella
- Curved section connecting the filament to the cell surface
- flexible
- motor. Drives rotation.
- couples motor to filament
- apply torque -> flagellum rotates
- couples torque
- couples rigid pendulum to motor
Describe the basal body of flagella
Anchors the flagella into the cell membrane of the bacterium by special disc-shaped structures called rings or plates
- bacteria can rotate flagellum into clockwise or counterclockwise direction
- direction depends on what they do in liquid medium.
What are the special disc -shaped structures in basal body of flagella called
Rings or plates
Describe chemotaxis in bacteria
movement of bacteria along a concentration gradient towards a chemical attractant or away from a a chemical repellent
What is the default state of motor
CCW
= run
Peritrichous
having flagella (tail like projections) all over its surface.
What does CW rotation of flagella result in
Tumble - flagella of peritrichous bacterium are pushed apart
How are the flagella in peritrichous bacteria arranged in CCW rotation
bundled together = run
How fast can bacteria “run”
10 bodylengths/sec
Do bacterium operate in a coordinated bundle?
No
Nature of movement of bacteria
Random
- tumbles promote random rotational turns during swimming.
Describe the mechanism of chemotaxis
Bacteria sense the change in chemical conc outside the cell over TIME -> temporal gradients
- thus respond to the change in conc as the cell moves.
Why can’t bacteria sense spatial gradient?
Because they are too small
How do they sense the chemical concentration over time?
Arrays of chemoreceptors
- hexagonal arrangement.
How large are fimbriae?
2-8nm in diameter
1µm in length
100-1000/cell
Describe the structure of fimbriae
Adhesins = bind to SPECIFIC receptors on the surface of cells.
- mediate attachment.
- vary adhesion to exploit different environments
Fimbrins = protein subunits helically wound with pore down centre polymerise to form fibres.
What is adhesin on fimbriae?
Allows bind to specific receptors on the surface of cells. Mediate attachment.
- vary adhesin to exploit different environments
What are fimbrins?
protein subunits helically wound with pore down centre polymerise to form fibres in fimbriae.
What are capsules and slime layers made of?
Glycocalyx
What is glycocalyx?
A gelatinous polysaccharide and/or polypeptide outer covering
- forms a sticky meshwork of fibers
What is a capsule?
Glycocalyx organised into a defined structure attached firmly to cell wall
What is slime layer?
Glycocalyx disorganised without cell shape, attached loosely to cell wall.
What functions do capsules serve? (4)
- Virulence factors: protect bacteria from phagocytosis and engulfment by immune cells
- slippery capsule makes it difficult for a phagocyte to establish contact with invading bacterium - Adhere to cell surfaces -> colonisation
- Source of nutrients and energy to microbes
- eg strep doc mutans colonise teeth: ferments suga in the capsule and acid byproducts contribute to tooth decay. - prevent cell from drying out (desiccation)
How does the capsule protect bacteria from phagocytosis and engulfment by immune cells?
Slippery capsule makes it difficult for a phagocyte to establish contact with invading bacterium
Why is adherence to cell surfaces important for bacteria?
Important first step in colonisation and sometimes leads to disease.
- eg structures such as medical implants, catheters and so on
Example of capsules being a source of nutrient and energy to microbes
Streptococcus mutans = colonise teeth, ferments the sugar in the capsule and acid byproducts contribute to tooth decay.
What are bacterial endospores
highly differentiated cells resistant to heat, harsh chemicals, antibiotics/disinfectants and radiation: “dormant” stage of bacterial life cycle.
What type of bacteria can form endospores?
Some gram-positive: members of genus Bacillus and Clostridium
When do endospores form and germinate
Formed during unfavourable growth conditions
Germinate under favourable conditions.
What is the function of endospores
protect cell from stress. Wait for more favourable conditions to germinate
is bacterial endospores transmissible?
Highly transmissible
Types of bacterial endospores
- Terminal spores
- subterminal spores
- central spores
Life cycle of an endospore- forming bacterium
- Vegetative cell
- Developing spore form on one end of cell (asymmetric cell division)
- Chromosome replication.
- Spore matures.
- mature spore is very different from vegetative, but genetically identical. Highly differentiated.
- mature spore is very resistant to temp, chemical etc
- mature spore is very different from vegetative, but genetically identical. Highly differentiated.
- vegetative cell dies.
Structure of Bacterial endospore
- Exosporium
- spore coat
- core wall
- cortex - has peptidoglycan- cell wall
- DNA
4 important properties of spores
- Heat and radiation resistant
- Water content low (10-25%)
- High in Ca2+ and dipicolinic acid
- Low metabolic activity/dormant ( good for dispersal and protect genome).
What make the endospore heat resistant?
- Low water content
2. Dipicolinic acid.
Size of prokaryotic cells and eukaryotic cells
Pro = <5mm Euka = >10mm
Difference between pork and euka cells
- No cytoskeleton in prokaryotes. Always have cytoskeleton in eukaryotic cells.
- Ribosomes in prokaryotes are small, ribosomes in eukaryotic are large.
- Prok are always unicellular. eukaryotic are often multicellular.
- Prok does not have nucleus or any membrane-bound organelle, eg mitochondria
- Prok DNA is circular, without proteins. Euka DNA is linear and associated with proteins to form chromatin.
- Prok have motility by rigid rotating flagellum made of flagellin. Euka cells have motility by flexible waving undulipodium, made of tubular.
- Prok cell division = binary fission. Asexual reproduction. Euka = mitosis/meiosis. Reproduction is asexual or sexual.
- Prok have a huge variety of metabolic pathways. Euka have common metabolic pathways.
How was the Tabacco Moisaic Virus discovered?
- Filter sap (bacterial-proof filter)
- Apply sap to healthy plant
- Agent multiplied only in cells that were dividing = virus
- Plant becomes infected.
What are viruses?
Acellular microorganisms that cannot survive without a host: no metabolic abilities of their own.
- rely completely on biosynthetic machinery of infected cell to multiply.
- hijack to use ribosome and polymerases to make protein and DNA and assemble to make more viruses
What types of cells can viruses infect?
All types (animal, plant, bacterial) - obligate intracellular parasites.
How many viruses on are Earth?
10^31
Size of viruses
10 - 400nm
Virus can have different shapes
Diagram.
Virion
when viruses exist in the form of independent particles.
Parts of a virion (2-3)
- genetic material made from either DNA or RNA
- a protein coat - capsid- which surrounds and protects the genetic material
- in some cases, an envelope of lipids that surrounds the protein coat when they are outside a cell.
- envelope may have glycoproteins on the outside.
What is a nucleocapsid
Nucleic acid genome (RNA or DNA) surrounded by a protein coat (capsid)
What are capsids made of
Multiple units of the same building block known as PROTOMERS
3 types of symmetry promoters could be arranged in
- helical eg TMV
- icosahedral eg Adenovirus
- complex eg bacteriophage
Describe the structure of icosahedral capsid
20 faced polyhedron. Each face = equilateral triangle.
- each triangle has 3 subunits: capsomers
- each capsomer has 5 (pentagon) protomer
Describe the viral genome
- RNA or DNA
- linear, circular, or segmented.
All four possible forms of RNA and DNA are found in viruses: single and double stranded RNA and DNA
Massive number of variation in number of nucleotides in viral genome
4000 to >1 million nucleotides.
What do viruses infect?
- all cell types: Euka and proka
- infect all forms of life i.e. animals, plants, bacteria, fungi, algae.
Define host organism:
An organism a virus infects.
- specific receptors recognised by virus
Define host cell
A cell a virus multiplies in
Basic viral life cycle in a host cell
- Attachment of vision to host cell.
- lock and key
- specific receptors - Entry of nucleocapsid to host cell
- Synthesis of viral components i.e. genome and proteins
- new capsid protein
- replicate genome
using host machinery, in cytoplasm. - assembly of viral components into progeny
- release of progeny visions from host cell.
Another word for lytic
Virulent cycle
Another word for lysogenic
Latent/temperate
2 types of infections from prokaryotic cells
- lytic/virulent
2. lysogenic/temperate.
Draw the lytic cycle of phage infection
- Attachment
- Entry of phage DNA and degradation of host DNA
- capsid does not enter cell
- DNA injected into cell
- viral DNA degraded by viral DNA = no replication of bacterial DNA - Synthesis of viral genomes and proteins
- no host DNA = viral DNA replicated - Self-assembly (of head, tail and tail fibres)
- release
- burst size (100-200 virions)
- viral makes lysosome and holisons punch hole in membrane
Define lysogeny
the relationship between the temperate phage and host bacterium
Define prophage
the form of phage harboured in lysogen, which is simply the phage genome.
Compare the virulent life cycle of a bacteriophage and the latent life cycle of bacteriophage
.
Where is the prophage?
Either integrated into lysogen’s genome or remains free in the cytoplasm.
Draw the lysogenic cycle of infection.
- Phage DNA integrates into bacterial chromosome
- Bacterium reproduces normally, copying the prophage and transmitting it to daughter cells.
- every time the bacteria DNA
- due to integration, viral genome = silent. No transcription of viral genes. = stable lysogen - Daughter cell with prophage
- Prophage exits the chromosome.
How is the lysogenic cycle induced to a lytic cycle?
- change in culture conditions
- UV irradiation
What happens when the prophage is induced to become a virulent phage?
- DNA becomes circularised
- lytic cycle commences
Draw diagram of lytic and lysogenic cycle
.
Outline Replication cycles of naked virus (no cell envelope)
- Entry and uncoating
- recognise specific receptors on host cell surface
- endosome or vesicle
- enters by endocytosis
- uncoats once in cell
- end up with viral DNA and proteins. - Replication
- Host machinery replicates viral DNA = more viral DNA to make more virus - Transcription and manufacture of capsid proteins.
- DNA turned into mRNA
- use mRNA to make capsid proteins.
- mRNA made by host enzymes. - Self-assembly of new virus particles and their exit from the cell.
- probably by cell lysis
Outline replication cycle of RNA enveloped virus (eg HIV)
- Glycoproteins on the viral envelope bind to specific receptor molecules on the host cell, promoting viral uptake by the cell.
- fuse with host cell membrane
- not endocytosis
- recognise receptor
- some envelope viruses enter the host cell by fusion of the envelope with the cell’s plasma membrane; others enter by endocytosis.
- for all enveloped RNA viruses, formation of new envelopes for progeny viruses occurs by the process below: - The capsid and viral genome enter the cell. Digestion of the capsid by cellular enzymes releases the viral genome.
- release of RNA and proteins - The viral genome functions as a template for synthesis of complementary RNA strands by a viral RNA polymerase
- the single-stranded RNA genome that functions as a template for synthesis of mRNA
- reverse transcriptase makes DNA from RNA
- number of cycles depend on how many RNA molecules (eg 2 RNA molecules for HIV) - New copies of viral genome RNA are made using the complementary RNA strands as templates.
- DNA inserted into chromosome for life
- never leave the host genome -> PROVIRUS - Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER and Golgi apparatus).
- Vesicles transport envelope glycoproteins to the plasma membrane
- A capsid assembles around each viral genome molecule
- Each new virus buds from the cell, its envelope studded with viral glycoproteins embedded in membrane derived from the host cell.
- budding means host cell not killed
Difference between provirus and prophage
Provirus -> DNA integrated into host genome. Unlike prophage, it remains FOREVER. Whereas prophage can become virulent.
What type of virus is HIV?
Retrovirus
- because they are RNA viruses, so must undergo retrostep.
Must convert RNA to DNA to mRNA
Describe the term viral latency in relation to the replication of bacterial and mammalian viruses
Viral latency = dormant, but can be activated.
Herpes simplex
- acute and latent infection
- DNA in nerve ganglion as a lysogenic virus - immune system can’t see
- acute phase results in blister formation
- virus retreats to nerve cells during latency
stressful stimuli (fever, trauma, emotional stress) and hormonal changes can reactivate the virus -> triggers reproduction.
Chickenpox (acute and latent)
- acute disease in childhood, begins as a rash progressing to vesicles (blisters)
- the virus remains latent in the body, can get activated and cause shingles during childhood.
- carry DNA for life.
Is shingles transmissible
- can’t transfer shingles to another person who has had chickenpox before. But if get shingles, can infect a person who hasn’t had chickenpox and give them chickenpox (not shingles).
Replicative cycle of HIV
- the envelope glycoproteins enable the virus to bind to specific receptors on certain white blood cells
- the virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA.
- reverse transcriptase catalyses the synthesis of a DNA strand complementary to the viral DNA
- reverse transcriptase catalyses the synthesis of a second DNA strand complementary to the first
- the double-stranded DNA is incorporated as a provirus into the cell’s DNA
- unique to retroviruses. - Proviral genes are transcribed into RNA molecules, which serve as genomes for progeny viruses and as mRNAs for translation into viral protein (capsid and envelope)
- the viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER)
- Vesicles transport the glycoproteins to the cell’s plasma membrane
- capsids are assembled around viral genomes and reverse transcriptase molecules
- new viruses, with viral envelope glycoproteins, bud from the host cell. (fuse with membrane)
What is the role of a membrane
To provide social conditions within the cell and keep them different to what’s outside
What must a cell do?
- manufacture cellular materials (biological macromolecules)
- obtain raw materials ( to make biomolecules)
- remove wastes generated from production
- generate the required energy to remove waste and build molecules
- control all of the above
Why need organelles?
A cell must carry out many different processes that
- require different conditions (eg catabolic vs anabolic) that
- need separate compartments
- called organelles
Functions of organelles
- Provide special conditions for specific processes
- keep incompatible processes apart
- allow high concentrations of substances
- form concentration gradients (some things only happen due to diffusion gradients)
- package for transport or export
3 membranes
- plasma membrane
- mitochondrial membranes
- nuclear envelope
Function of membranes
- provide a semi-permeable barrier, so control movement of substances.
2 major components of phospholipids
Hydrophilic phosphate heads and hydrophobic fatty acid chain tails
What is membrane fluidity affected by
The composition of fatty acids
What makes a membrane viscous
Saturated tails pack tightly together
What makes a membrane fluid
Unsaturated tails prevent packing due to kinking due to double bonds.
How does cholesterol affect membrane fluidity
Cholesterol reduces membrane fluidity at moderate temperatures but increases fluidity at low temperatures
- regulate fluidity.
Therefore, at body temperatures, membrane fluidity is reduced by the presence of cholesterol
What are peripheral proteins
A kind of protein that is attached to the plasma membrane but not span all the way through it
What are membrane associated proteins
Proteins that span from one side all the way through the membrane to inside of the cell
Which substances move across membrane by diffusion
- membrane permeable to lipid soluble (hydrophobic molecules) eg steroid hormones, gasses.
- movement down conc grad.
- eg O2, CO2, steroid hormones
Which substances move across membrane by facilitated diffusion
- movement of hydrophilic molecules require membrane proteins
- movement of specific substances down their conc grad
- involves channeled or carrier proteins
- no E input - passive.
eg water, glucose, ions
3 types membrane channels
- ungated
- voltage-gated
- ligand-gated
eg of Ungated membrane channels
A few types of ion channels are ungated, meaning they are open all the time. For instance, some K+ and some Cl- channels are ungated. By contrast, Ca++ and Na+ ion channels are NEVER ungated.
Voltage-gated channels
Voltage-gated ion channels open or close in response to changes in membrane potential. Voltage-gated ion channels are key in the generation of electrical signals in nerve, muscle, and cardiac cells. See the web page describing an important example, the voltage-gated Na+ channel.
- allow ion fluxes
eg of ligand-gated channels
Ligand-gated ion channels are opened when regulatory molecules bind to the channel protein. Many neurotransmitter receptors are ligand gated ion channels. An example is the nicotinic acetylcholine receptor. This is the receptor that is found at the neuromuscular junction on skeletal muscle cells, and also at synapses in autonomic ganglia.
- open in response to an extracellular signal
- bind to open eg hormones, neurotransmitters
Define active transport
The movement of specific substances against their conc gradient, requiring E input in the form of ATP and involving pumps
Types of active transport
- may be direct or indirect
- uniport, co-transport, antiport
Describe uniporter
A transporter than only transport one type of molecule at a time
Describe symporter/co-transport
Move two or more types of molecule in the same direction through a membrane.
- sucrose moved against conc grad
- H+ and sucrose bind to protein at the same time
Describe antiporters
Transporters that move two different types of molecule in opposite directions at the same time.
Primary and secondary active transport
Somtimes, AT of one type of solute crates a cow grad that drives the passive transport of another solute.
Disease for defect in K+ channel
Epilepsy
- neutrons get too excited
Defect in tyrosine transporter
Albinism (type 2)
Defect in Cu2+ and Ag+ transporter
Wilson’s disease
Defect in Cl- channel
Cystic fibrosis
What are the two roles of membrane proteins
- transporters
- give the cell its character
Functions of membrane proteins (6)
- transport
- enzymatic activity
- signal transduction
- cell-cell recognition
- intercellular joining
- attachment to (linking of) the cytoskeleton and extracellular matrix (ECM)
Describe the transport function of membrane proteins
- a protein that spans the membrane may provide a hydrophilic channel across the membrane that is selective for a particular solute
- other transport proteins shuttle a substance from one side to the other by changing shape. Some of these proteins hydrolyse ATP as an energy source to actively pump substances across the membrane.
Describe the enzymatic activity function of membrane proteins
A protein built into the membrane may be an enzyme with its active site exposed to substances in the adjacent solution.
- in some cases, several enzymes in a membrane are organised as a team that carries out sequential steps of a metabolic pathway
Describe the signal transduction function of membrane proteins
A membrane protein may have a binding site with a specific shape that fits the shape of a chemical messenger, such as a hormone.
- the external messenger may cause the protein to change shape, allowing it to relay the message to the inside of the cell, usually by binding to a cytoplasmic protein
Describe the cell-cell recognition function of membrane proteins
Some glycoproteins serve as ID tags that are specifically recognised by membrane proteins of other cells.
- this type of cell-cell binding is usually short-lived compared to intercellular joining
Describe the intercellular joining function of membrane proteins
Membrane proteins of adjacent cells may hook together in various kinds of junctions, such as gap junctions or tight junctions.
- this type of binding is more long-lasting than that for cell-cell recognition.
Describe the attachment to the cytoskeleton and extracellular matrix function of membrane proteins
Microfilaments or other elements of the cytoskeleton may be non-covalently bound to membrane proteins, a function that helps maintain cell shape and stabilise the location of certain membrane proteins.
= proteins that can bind to ECM molecules can coordinate extracellular and intracellular changes.
Describe the structure of tight junctions
At tight junctions, the plasma membranes of neighbouring cells are very tightly pressed against each other bound together by specific proteins.
- forming continuous seals around the cells, tight junctions establish a barrier that prevents leakage of extracellular fluid across a layer of epithelial cells.
- eg tight junctions between skin cells make us watertight.
Describe the structure of desmosomes
Desmosomes function like rivets, fastening cells together into strong sheets.
- Intermediate filaments made of sturdy keratin proteins anchor desmosomes in the cytoplasm.
Desmosomes attach muscle cells to each other in a muscle
Describe the structure of gap junctions
Gap junctions provide cytoplasmic channels from one cell to an adjacent cell and in this way are similar in their function to the plasmodesmata in plants.
- gap junctions consist of membrane proteins that surround a pore through which ions, sugar, amino acids and other small molecules may pass.
Gap junctions are necessary for communication between cells in many types of tissues, such as heart muscle, and in animal embryos.
What is the endomembrane system
- nucleus
- sER
- rER
- Golgi
- lysosome
- Plants cells do not have lysosomes. Instead, they have another type of organelle called the vacuole. The large central vacuole stores water and wastes wastes, isolates hazardous materials, and has enzymes that can break down macromolecules and cellular components, like those of a lysosome. Plant vacuoles also function in water balance and may be used to store compounds such as toxins and pigments (colored particles).
- cell membrane
- vesicles
Functions of smooth ER (4)
- metabolism of carbohydrates
- lipid synthesis for membranes
- detox of drugs and poisons (anything not part of nutrient intake eg red pigment in tomato)
- storage of Ca2+ (which can be released in response to signals)
How sER can change
- extensive sER in cells active in the processes that the sER carries out eg liver: intake. Digestive system goes through liver. i.e. cells are not alike
- the amount of sER can be increased or decreased to meet demand.
- eg ER grows in response to more drugs, meaning that take more drugs = break down drugs to a lesser amount, meaning have to take more drugs to get same effect
Functions of rER
- involved in protein synthesis (proteins that are released from cells or for membranes)
- secreted and membrane-bound proteins enter the lumen (interior) or the rER
- processed via the endomembrane system.
Why is rER rough in appearance
Due to ribosomes
Where dos the synthesis of cytoplasmic proteins (proteins that stay in the cell) occur
On free ribosomes
What is a vesicle
A bubble of phospholipid membrane
Properties of the Golgi complex
- series of membrane sacs and associated vesicles
- has polarity: cis and trans
- vesicles from Er arrive at the cis face
- processed vesicles leave at the trans face.
Roles of golgi
- GLYCOSYLATION of protein (add sugar to protein (to proteins that end up on cell surface) )
- addition or modification of carbohydrates to proteins (eg proteins on cell surface: the sugar on them interact with water)
- important for cell surface proteins.
- take carbohydrates made on the sER and modify them
- important for cell surface proteins
- SORTING proteins
- adds molecular markers to direct proteins to the correct vesicles
- eg a special phosphorylated sugar (mannose 6-phosphate) identifies lysosomal enzymes
- selective proteins
- Direct vesicle trafficking
- adds molecular tags to direct vesicles to the correct target compartment (on outside of vesicle)
- such tags are often short proteins exposed on the vesicle surface
- have specific amino acid sequences
What is the phosphorylated sugar that identifies lysosomal enzymes
mannose 6-phosphate
Important flow of direction of vesicles
- retrieval tag
- direct proteins BACK to ER or previous Golgi cistern
- important to maintain compartment integrity and function.
What’s the important of tags that direct to secretory pathways
Important for release and surface expression (expression of proteins on surface)
Describe exocytosis
- transports material out of the cell
- delivers material to the cell surface
Two pathways for exocytosis
- constitutive pathway: ongoing, uncontrolled. Cells are releasing things constantly (eg proteins that make up ECF)
- regulated exocytosis: very controlled. For hormones and neurotransmitters (which have to be released at exactly the right time)
Mechanism of exocytosis
- vesicle fuses with membrane.
- things on the vesicle membrane ends up on the cell surface.
3 roles of Golgi
- Glycoslyation
- sorting proteins
- direct vesicle trafficking
3 types of endocytosis
- phagocytosis
- pinocytosis
- receptor-mediated endocytosis
Describe phagocytosis
- uptake of food particles
- forms a phagocytic vacuole which is digested (using lysosomes)
Describe pinocytosis
- non-selective uptake of solutes.
- drinking of ECM and any particles in it.
- molecules dissolved in liquid
Describe receptor-mediated endocytosis
- collects and concentrates specific molecules (that may be at a low concentration) eg Low density lipoprotein (LDL)
- eg cell wants triangles
- build receptors that fit triangles
- pulled into cell
- far larger number of triangles than non-selective uptake
- but still takes up some unwanted solutes
- receptor that can hold onto wanted particles -> pull into cell.
- more specific compared to non-selective.
- would get a higher concentration of desired solute than non-selective
eg Low density lipoprotein (LDL) particles
Describe the endosome-lysosome pathway
When lysosome is first formed, it doesn’t function. However, when it fuses with the vesicle, it matures.
Lysosomes digest cellular materials, as they contain HYDROLYTIC enzymes.
They degrade proteins, lipids, carbohydrates and nucleic acids
What enzyme do lysosomes contain
Hydrolytic
What can lysosomes degrade
Proteins, lipids, carbohydrates, nucleic acids.
- break down into constituent components.
- eg amino acids make new proteins.
Two variations of endosome-lysosome pathways
- digest unwanted intracellular materials (eg nonfunctional organelles)
- digest endocytosed material
What is endosome-lysosome pathways important for
- Cell health eg stop taking drug, so ER broken down -> surplus for requirements - break parts down and build new ones. - important in programmed cell death - whole cell destruction or autophagy)
Tay-Sachs disease
- mental and physical deterioration
- motor/ cognitive and “speech” defects
- blindness, deafness and paralysis
- enzyme missing in lysosome, meaning can’t break down a certain material -> build up in cells. eg neurons.
Major components of the cytoskeleton
- microtubules
- intermediate filaments
- microfilaments
Function of cytoskeleton (5)
- gives mechanical support to cells and maintains, or changes, its shape
- Anchors or directs the movement of organelles and cytoplasm. Helps maintain position of organelles
- controls movement of cilia, pseudopods or even contraction of muscle cells
- mechanically transmits signals from the cell’s surface to its interior
- interacts with motor molecules (proteins) that change shape to produce cellular movements.
- helps maintain cell shape
- unlike the body’s skeletal system the cytoskeleton rapidly disassembles and reassembles
- allows changes in cell structure
- the cytoskeleton is highly dynamic but still provides stability
How is the cytoskeleton unlike the body’s skeletal system
The cytoskeleton can rapidly disassemble and reassemble, thereby allowing changes in cell structure.
- the cytoskeleton is highly dynamic but still provides stability.
What are microtubules made of
Tubulin subunits
Function of microtubules
- resist compression
- provide cell motility: cilia or flagella
- chromosome movements in cell division
- organelle movements
Where does the microtubules originate
- may radiate out from an organising centre (centrosome)
How does microfilament undergo whole cell movement
Cilia: “rowing-like” motion perpendicular to the direction of movement.
- when cells are fixed in place, the beating of cilia can move fluid past the cells.
eg lungs -> cilia beat = rubbish gets pushed up
How do organelles move within the cell
The microtubules provides a path that the vesicles can move along
- ATP-powered motor proteins attached to organelles
- ATP for motor
- moved along by moto
- can thus transport vesicles to targets or damaged organelles from distant sites eg nerve terminals
eg to lysosomes to be broken down.
ATP -powered motor proteins can “walk” organelles along MT
- can thus transport vesicles to targets, or damaged organelles from distant sites eg nerve terminals eg to lysosome to be broken down.
What are microfilaments made of
Double chain of actin subunits
- twisted rope
Structure of microtubules
Hollow tube of tubular subunits
Structure of microfilaments
Twisted rope (double chain of actin subunits)
- forms linear strands and 3D networks (with the aid of branching proteins)
- linear actin microfilaments support movement
Role of microfilaments
- resist tension
- cortical network under plasma membrane helps maintain cell shape
- provide a gel-like consistency to outer cytoplasm.
- changes in cell shape
- muscle contraction
- cytoplasmic streaming in plant cells
cell motility (as in amoeboid movement) - division of animal cells
How are microfilaments arranged in muscle
In parallel with the motor protein myosin
How do microfilaments support movement of non-muscle cells
Pull on one and resist tension of microtubules, can achieve movement of non-muscle cells.
What are intermediate filaments made of
- various proteins including keratins, vimentins and lamins
What is the structure of intermediate filaments
Supercoiled into “cables”
- fibrous subunit (keratins coiled together)
How does IM compared to MT and MF
IM is less dynamic than MT or MF, which can build quickly and collapse quickly. IM is more stable, which is important for maintaining cell shape
- IM’s less dynamic nature is why its used for nuclear lamina
Function of IM
- maintain cell shape
- anchor organelles- nuclear lamina.
- anchors nucleus and certain other organelles
- formation of nuclear lamina.
- neuronal processes (neurofilaments)
- abundant in nucleus -> nuclear lamina
- neuronal processes -> neurofilmanets
What are the 3 types of cell junctions
- tight junctions
- desmosomes
- gap junctions
Describe tight junctions
- neighbouring cells tightly pressed together.
- may form a continuous seal
Purpose of tight junctions
Prevent movement of fluid across cell layers
eg don’t want all crap from small intestine into blood supply
- select what it needs
Describe desmosomes
- anchoring junction: holds cells tightly tog, anchoring them
- attachments between sheets of cells eg muscle
- eg pull on muscle -> ind muscle cells contract -> all cells need to move together to turn into movement of the arm
- lock together by desmosomes
- hold hold onto the next
Purpose of desmosomes
Act like rivets
- a torn muscle is a torn desmosome
- Pull on muscle = muscle cells contract -> all cells need to lock together-> locked by desmosomes -> cells hold onto next
What are the fibres extending from the desmosomes
intermediate filaments.
- connect desmosomes into the rest of the cell
Describe gap junctions
a point of cytoplasmic contact between cells
Function of gap junctions
- ions and molecules may pass from cell to cell
- allow rapid intercellular communication
What is ECM composed of
- material secreted by cells (fibroblasts) via constitutive exocytosis (constitutive type: ongoing and continuous). Fibroblasts are specialised to make ECM
- mainly glycoprotein (rER then Golgi)
- most abundant glycoprotein is collagen.
What is the most abundant glycoprotein
Collagen
Properties of collagen fibres in ECM
- great tensile strength
- cable-like
- approximately 50% of total body protein
- like other proteins, collagen is “turned over” and must be replaced.
How many % of total body protein is collagen
50%
Disease due to lack of vitamin C
Scurvy
What does a lack of vitamin C result in
A failure of collagen synthesis. (after collagen breaks down, it’s not replaced)
- hydroxyproline amino acids not formed
- collagen fibres cannot cross-link correctly.
What are proteoglycans
Proteins with extensive sugar additions
Where is collagen embedded in
A proteoglycan matrix
Why is proteoglycan important in ECM
- traps water, therefore:
- resists compression and retains shape.
How is there a pathway from outside of the cell to inside?
Other glycoproteins (fibronectins) attach cells to ECM
- membrane proteins (integrins) link ECM to cytoskeleton
- a communication link from ECM to the cell interior
How do microtubules allow whole cell movement
Microtubules make up the core of flagella and cilia. They are arranged so that motor proteins can move along the microtubules and cause the flagellum/cilium to bend and change shape, thus propelling the cell.
- If the cell is fixed in position, then the movement of the cilia can cause fluid to move like they do in the lining of the respiratory tract.
Why does a cell need energy?
To do work:
- make new materials (bio molecules - many polymers: nucleic acids, proteins etc)
- growth and replacement (need new materials) eg for cell division
- movement: whole body (muscle) and within cell (transport) - eg neutrophil -> cytoskeleton etc Trackways inside cell for vesicles
- pumping substances across membranes: accumulating materials (receptor-mediated endocytosis) and generates gradients (moving ions from one side to other. Pumped). Cotransport
What are the two types of movement possible for a cell
- whole body eg muscle
- within the cell (transport)
Why does a cell need to pump substances across membranes?
- to accumulate material (receptor-mediated endocytosis -> use E to generate vesicle)
- generate gradient: moving ions from one side to other
- cotransport
Example of co-transport
- active transport of H+ outside of membrane into a higher concentration
- as H+ diffuse back in, it picks up sucrose, which is co-transported
Where is the cell’s energy generated?
- cytosol: glycolysis
- mitochondria: citric acid cycle
- mitochondrial membranes (oxidative phosphorylation)
- Organelles are important as they allow different conditions for different reactions to occur.
How is the cell’s energy generated?
- cellular respiration
- releases the chemical energy stored in food
- converts this into small (useable units)
- carried by the energy transfer molecule ATP
How long is mitochondria?
1 - 10µm
How many mitochondria are there per cell?
1 - thousands
What does the number of mitochondria in a cell depend on
Energy demand due to cell type and function
Structure of mitochondria
- enclosed by two lipid bilayers
- membranes contain special proteins
- inner membrane highly folded -> cristae
- contains mitochondrial DNA and ribosomes
- produce some but not all mitochondrial proteins
- mobile within the cell: go where E is needed eg nerves (at cell body, where neurons need E)
- can change shape, fuse or divide
- may form branched interconnected networks in cell
Can the mitochondria produce proteins
Can produce some but not all
- contains mtDNA and ribosomes
Can the mitochondria change shape, fuse or divide
Yes
Is the mitochondria mobile within the cell
Yes
The mitochondria may form branched interconnected networks in the cell
Yes
What process happens in the cytosol (for respiration)?
Glycolysis
What is glycolysis
- reduces glucose into smaller units (pyruvate) (by the time take to get to cells, converted into glucose)
- releases some energy (2ATP/glucose)
- transfers electrons to the electron carrier NAD (which becomes NADH)
What are mitochondrial compartments important for?
Energy generation
What process takes place in the matrix of the mitochondria?
Kreb’s Cycle
Describe the Kreb’s cycle
- processes pyruvate
- releases more energy (2 ATP/glucose)
- transfers more electron to NAD and FAD
Why have organelles (for respiration)?
Concentrate enzymes and substrates
to generate a concentration gradient and use this to power ATP formation
What does NAD and FAD turn into once they receive electrons?
NADH and FADH2
What process happens in the inter membrane space?
Oxidative phosphorylation ( electron transport and chemiosmosis) - releases more energy (26-28 ATP/glucose)
Describe the process in the ETC
ETC:
- proteins in the inner membrane pump out protons
- pump didn’t use all the Energy. Some left.
- electron is passed to next pump.
- next protein pumps H+
- Next pump pumps out H+
- H+ pump created a gradient.
- electron is combined with O2 (H2O produced)
Chemiosmosis:
- As H+ flow back into the matrix, it goes down the ATP synthase channel
- turn the rotor around using the energy of flowing down concentration gradient.
- ATP is produced (from attaching P to ADP).
Where is the high concentration of H+ in mitochondria?
Intermembrane space
Where is the high concentration of H+ in chloroplasts?
Thylakoid
Why does a cell need energy?
To do work:
- chemical, transport or mechanical work (movement of cell or whole organism)
How is work achieved in the cell
Through E coupling
What are exergonic reactions
Release E -> heat, light
What are endergonic reactions
Absorb E eg building biological molecules/polymers
What is energy coupling
When an exergonic reaction drives an endergonic reaction
What provides the Energy coupling mechanism
ATP
- captures E from exergonic reaction
- transfer E to drive endergonic reaction.
What is ATP involved in (3)
- E transfer
- RNA synthesis: build nucleotides
- Neurotransmission: neurons send ATP messages to other neurons. ATP released from one neutron goes across synapse and communicates.
How does ATP transfer E
- 3 phosphates in a row.
- neg charge on phosphate don’t like being pushed together
- need to put lot of E to put 3rd O in
- break down -> get E back
- put a lot of E to make, break -> get lot of E back
What type of reaction is ATP hydrolysis
Exergonic
- most E released when end phosphate breaks off -> ADP
Are P-P-P bonds relatively large
yes
What type of E does ATP mainly generate
Heat
eg shiver -> muscle contract. Lost ATP -> Heat E released.
What does ATP hydrolysis require
Water
- when ATP hydrolyses, it releases E
- high E bond
How is coupling achieved
Through the transfer of phosphate: coupling speeds up.
- forms a phosphorylated intermediate from donating a P from ATP.
- the intermediate may be more reactive and therefore will react with the other reactant.
How does the phosphorylated intermediate speed up a reaction
eg Glutamic acid and NH3
- if just put with NH3, nothing happens
- ATP makes it happen by transferring phosphates
- creates a more reactive intermediate -> allows reaction to proceed.
- the phosphorylated intermediate has more E (is unstable) than Glutamic acid and therefore are more likely to react with NH3.
When ATP binds to a protein, what can it do?
ATP forms a phosphorylated intermediate which may change the shape of the molecule, therefore:
- allows active transport of molecules
- allows molecular movement to occurr
- ATP puts PO43- on protein -> causes a change in shape.
- eg one end open -> other end. Molecule move from one end to the other.
- eg motor protein walk along MT, carrying a vesicle.
PO43- on motor protein = change shape, moves one part of the molecule forward. Shuffles forward. Keep putting more on = another part shuffles forward = walking.
How many ATP molecules does a single muscle cell use
10^6
Is ADP + P -> ATP an endergonic or exergonic reaction
Endergonic
Where does the energy to ADP + P -> ATP come from?
Cellular respiration
2 ways cells get E out of food
- fermentation: catabolism without O2
- aerobic respiration: catabolism with O2: last stage of ETC: tale e-.
- some prokaryotes substitute for O2 (with S)
How may electrons move in a redox reaction
Movement of electrons within a molecule
- eg if electron move away from C = CH4 has been oxidised
- eg if electrons move closer to O, O has been reduced
Energy involved in electron movement in redox
- E is required to pull electron away from the positive atomic nucleus: E used to keep away electron away from positive charge
- during reduction, electron move nearer to the O2 molecules therefore releasing E (from bonds) (E no longer needed)
- This is the energy the cell captures and puts to work
How does cellular respiration harvest E
Respiration harvests E in C-H bonds in food molecules by transferring the electron to O2 -> closer to nucleus = E released as the energy is lower.
- repositioning of electron in bonds
Which bond does respiration harvest energy from
C-H
Why do we respire rather than combust food
Simple combustion generates too much heat.
What’s the process of respiration oxidation like
A series of controlled steps
- electron stripped from glucose and transferred to NAD
Which enzyme reduces NAD+
Dehydrogenase
What does the dehydrogenase enzyme do?
removes 2 H atoms from glucose
- transfers 2 electrons plus 1 H+ to NAD+ forming NADH (electron carrier)
- NADH used to power ETC
How many electrons and H+ are transferred to NAD+ by dehydrogenase?
2 electrons plus 1H+
What is NADH used for?
to power ETC
Which two processes does oxidative phosphorylation encompass?
- ETC
- Chemiosmosis
Draw ATP synthase
.
Components of ATP synthase
- half channel
- rotor
- Stator
- internal rod
- catalytic knob
What is ATP described as
Ion pump in reverse
Pathway of H+ in ATP synthase
- H+ ions flow into a half channel
- H+ bind to the root and change its shape. The change in shape causes the rotor to turn (eg one notch around)
- Rotor spins
- After one turn of the rotor, H+ exit to the mitochondrial matrix
- rotor turns the rod which activates catalytic sites to produce ATP.
Why can’t H and O2 just react in one step
too much energy
- explosive release of heat and light energy
- 2H (from food via NADH)
- 2 H -> 2H+ + 2e-
- electrons go through electron transport chain
- each protein pump produces some energy
2H+ + 2e- + O2 recombine to make H2O = controlled release of energy for synthesis of ATP
How is NAD reduced
NAD + 2H (which is broken down to 2e- + 2H+)
- NAD + 2e- + H+ -> NADH
Most prominent organelle in the cell
Nucleus
How big is the nucleus
5-10um
How many nucleus per cell in most cases
1
- except RBC and muscle
Does the nucleus contain all of the cell’s genes
No. It contains most but there are some in mitochondria
What does the nucleus store
Serves as a repository of genetic information
Describe the structure of the nucleus
Surrounded by nuclear envelope
- composed of TWO membrane, each membrane is a phospholipid bilayer
Inner surface of nuclear envelope lined by nuclear lamina -> protein
- composed of IF -> cable-like, tough, bit of flexibility, built to last
How many membranes are there in the nuclear envelope
2
What is the inner surface of the nuclear envelope lined by?
Nuclear lamina
What is the nuclear lamina composed of?
IF
- cable-like, tough, bit of flexibility, but to last
Function of nuclear lamina
- helps maintain shape of the nucleus
- organises the packing of DNA -> anchor points in which DNA is structured
What is the disease due to defective nuclear lamina
Hutchinson-Gilford Progeria syndrome
- cell nuclei have abnormal shape
- results in accelerated again
- can’t use DNA properly -> can’t cell div properly therefore can’t replace old cells that die off
What is transported out of nucleus
mRNA, rRNA, tRNA
- need to get info from nucleus to outside to make proteins
What is transported into the nucleus
Control signals from other cells
- eg growth factors, hormones
Energy and materials
- raw materials: nucleotides for making RNA -> Need ATP to make RNA etc
- proteins needed for transcription
- proteins needed for chromosome replication
What do nuclear pores act as
Regulated mechanisms -> gates
- so that repository of genetic information is protected
How long is DNA in human cell
2.5m
How must DNA be organised
- well packed
- but also ACCESSIBLE (to turn into mRNA etc)
What are chromatin fibers
After DNA double helix is combined with histone proteins
First step of DNA organisation
DNA double helix is combined with histone proteins to form chromatin fibres.
- chromatin fibres undergo multi-level packaging.
What is the structure called after DNA double helix is wound around histone proteins (bead)
Nucleosome
What is a nucleosome
After DNA has wound around histone protein (each bead)
Diameter of DNA double helix
2nm
Which histone proteins do the helix interact with first
H2, H3, H4
What is the diameter of nucleosome
10 - 11nm
Why does DNA wrap around histone proteins
to ensure accessibility by twisting around histone
2nd Step of DNA organisation around wrapping around H2-H4
Further interactions between DNA and H1
- causes 10nm fibre to coil to form 30nm fibre
Diameter of the fibre after interaction with H1
30nm
3rd stage of DNA organisation
30nm fibre loops to form 300nm fibre
- coiled in an organised way
Diameter of fibre after 3rd stage of DNA organisation
300nm
4th stage of DNA organisation (during metaphase)
During cell div, 300nm fibres coil to form metaphase chromosomes during METAPHASE
- pack into a transportable form so can send to one cell or another
Chromatin
Histone
Why is the DNA packed into chromosomes during cell div?
pack into a TRANSPORTABLE form so can send to one cell or another
Interphase
between cell divisions
Euchromatin
less dense
- appear light on EM
- often genetically active = DNA that the cell is using at that time
- genes for cell function are active
Heterochromatin
- dense
- genetically inactive
- certain genes “switched off”/not expressed
eg neutrophil vs neuron - neutrophil need components to phagocytose bacteria, whereas neurons need to turn on genes to make neurotransmitter
What happens to chromatin during interphase
Some regions of chromatin are more compact than others during interphase
- euchromatin
- heterochromatin
What type of relationship exist between euchromatin and heterochromatin?
DYNAMIC
- eg during cell div, need genes that allow cell div
- after cell div, don’t need so get packed into heterochromatin until needed again, where it is then unfolded into euchromatin
Is the location of chromosome within the nucleus random
NO
- not random
- stay organised due to interaction/hooking onto with nuclear lamina
What happens to chromosomes in cancer cells
Loss control of chromosomes
- genes mixed up
- genes from different chromosomes on different chromosomes
2 parts of a plant cell
cell wall and protoplast
Main differences between animals and plants
Animals are heterotrophic
- rely on plants indirectly (Carnivore) or directly (herbivore) for food
- mobile
Plants are autotrophic
- immobile
- have to cope with the environment they are in
- make their own food
Function of cell wall
- protection -> against eg fungi
- structural support - enables leaves to present to maximise photosynthesise
One problem of having a cell wall
Communication
- solved by plasmodesmata
What is a vacuole
an organelle surrounded by a single membrane -> one phospholipid bilayer -> tonoplast
Tonoplast
membrane of vacuole
How many vacuoles do plant cells have
Mature plant cells typically have a single large vacuole
- young plant has many small vacuoles
How does the vacuole affect the position of organelles
Push all organelles to between the plasma membrane and tonoplast
- pushed against cell wall
Where is the tonoplast produced
by the golgi associated ER
- membrane broke off -> budding off of Golgi ass
3 functions of vacuoles
- storage
- breakdown of macromolecules
- regulation of cell turgor -> rigidity of plant cells
What are the two types of metabolites that the vacuole stores
Primary metabolites - growth associated
Secondary metabolites - not growth associated
Which type of metabolites are growth associated
Primary
Examples of primary metabolites
- inorganic ions (Ca2+, K+ eg cofactor for enzymes)
- organic acids
- sugars (glucose, polysaccharides, eg oligosaccharides)
- amino acids
- proteins
- lipids
Can different types of cells have different ratios of primary metabolites
yes.
- eg more lipids in seedlings as it is used as an energy source to drive germination
What type of membrane is tonoplast
SELECTIVE
- controls movement of substances into and out of the vacuole
- some molecules such as water can pass in and out freely (for turgour pressure)
How is the tonoplast selective
Proteins in membrane that transport certain substances
- regulate particular substances in and out
Example of a substance that can pass freely through the tonoplast
Tonoplast
- for turgour pressure
2 types of secondary metabolites
- molecules for defence
- molecules for signalling
- eg pollinators to disperse fruit
Where are secondary metabolites found
Secondary metabolites are specific to specific plants
- found in certain regions.
Example of molecules for defence
Rubber tree
Rubber = a carbohydrate consisting of high molecular weight chains of 1,4-polyisopene residues
- specialised cells have small latex containing vacuoles -> deterrent for insects
- latex move into mouthpart.
- becomes more viscous on contact with O2
- makes mouth stick together
2nd example of molecules for defense
Some specialised plaint cells have vacuoles containing raphides
- raphides are needle shaped crystals of calcium oxalate
- makes leaf less penetrable to silkmoth larvae
- if the insect ingest it, it damages their digestive tract -> prevent eating more
Group of nitrogen-containing bases
Alkaloids
What are most of the alkaloids produced from
amino acids
3rd type of molecules for defense
Alkaloids
What are alkaloids
Group of nitrogen-containing bases
Properties of alkaloids
- have a variety of toxic effects on animals
- eg humans -> target nervous systems
- sequestered in sufficient conc to be effective (big hit -> kill insect)
- found in vacuoles that the plant wants to protect the most eg cells of new tips
Where are alkaloids found
in vacuoles of cells that the plant wants to protect the most eg cells of new tips
How are vincristine and vinblastine produced commercially
Using cell cultures biotech
- undifferentiated plant cells
- when groups of undifferentiated cells grow together they are often leaky -> so secondary metabolites excreted into medium
Why is using cell cultures to make pigments (vinblastine and vincristine etc) more efficient than extracting from harvested material
- more efficient than extracting from harvested material as it degrades over time etc
- ecologically less damaging
What is nicotine used for
Insecticide. From tobacco plant
Example of pigments that is anticancer
Vincristine and vinblastine
Name of pigments (molecules for signalling)
Anthocyanins
What is anthocyanins used for
- attracting animals -> cross pollination -> genetic diversity. eg distribution of seeds when ripe
- attract pollinators and animals to disperse seeds. eg blackberries -> more palatable. More black = more anthocyanins -> insect move away long enough to excrete it out.
2nd function of vacuoles
Breakdown of organelles and macromolecules
- digestion of cytoplasmic constituents
How does the vacuole breakdown organelles and macromolecules
Vacuoles are acidic and contain hydrolytic enzymes similar to lysosomal enzymes of animal cells
Organelles and macromolecules that need to be broken down need to be transported into vacuole across tonoplast
Another reason why tonoplast is selective.
What types of enzymes does the vacuole contain
Hydrolytic
is the vacuole acidic or alkaline
Acidic -> for breakdown of substances
3rd function of Vacuoles
regulation of turgour
- provides structural support
How come the vacuole can regulate cell turgour
because they contain water and make up such a large portion of the protoplast, vacuoles can play a role in the regulation of cell turgor
Does the vacuole have a neg or pos osmotic potential
High concs of solute (as it is a place of storage) in vacuoles have a negative osmotic potential, resulting in water uptake
- expands
What is osmotic potential
The potential of water molecules to move from a hypotonic solution to a hypertonic solution across a semi-permeable membrane.
What structure enables plant cells to take up water without bursting
- plant cell wall
- pressure from cell wall prevents bursting
- plant cells build up a large internal pressure -> turgour pressure
What does turgour pressure contribute to
Rigidity and structure
When would the plant have a decreased turgour pressure
Loss of water from vacuoles
- if can’t move-> soil dry
What does loss of turgour pressure result in
Wilting (dec cell size)
loss of structural integrity
What happens to the cells when a plant loses turgour pressure/wilts
Dec cell size
- plasma membrane pulls away from cell wall.
- cell wall remains as before
What happens when a wilted plant rehydrates
go back to original state
What does wilting cause the leaves to be like?
Leaves turned away from light
- under water stress no photosynthesis -> damaging to capture high E light
Key points about vacuoles
- bounded by a single membrane - tonoplast
- multiple small vacuoles in young cells
- single larger vacuole in old cells
- originates from golgi associated ER (reflected in the function of degradation of macromolecules -> enzymatic function)
- 3 functions:
- storage of primary and secondary metabolites
- breakdown of organelles and macromolecules
- regulation of cell turgor.
Does the tonoplast have a single or double membrane
Single
How did the photosynthetic eukaryote come about
- Non-photosynthetic eukaryote
- engulfing of photosynthetic prokaryote. Bacteria maintained within rather than taking its carbohydrates. Internal source of energy -> mutualistic relationship
- chloroplast becomes a semi-autonomous organelle
- photosynthetic eukaryote
Chloroplast -> bacteria
What does semi-autonomous refer to
- divide independently of the cell but remain dependent on cell for most of their proteins
- has own genome (circular DNA, mRNA, tRNA and ribosomes) and produces some of its own proteins
- divide on their own in a sim way to binary fission
How is the chloroplast DNA arranged
Circular
Are all of the proteins that the chloroplast need encoded by chloroplast’s genes
Although ctDNA contains info for formation of many chloroplast proteins, some proteins (that are shuttled back in to the chloroplast) found in the chloroplast are encoded by genes present in the nucleus of the cell.
= reliant on host.
- some genes were transferred to host nucleus, so host has ultimate control.
What is ATP used for
- biosynthesis
- AT (accumulation of materials and generation of gradients)
- movement (whole body eg muscle, or movt of structures within cell)
- bioluminescence
- electrical work
- growth (inc cell size) and repair
- inc cell number (cell div)
- differentiation (egg to ind)
- to maintain order
Not every cell need chloroplasts
in a multicellular organism
4 types of plastids
- chloroplasts
- chromoplasts
- leucoplasts
- proplastids
Function of chloroplasts
Ps
Function of chromoplasts
synthesise and storage of coloured pigments (NOT anthocyanins)
Where are anthocyanins
IN VACUOLE NOT CHROMOPLASTS
Function of leucoplasts
storage of assimilates (starch)
- C compounds: carbohydrates
Function of proplastids
precursors to other plastids
- undifferentiated
- can form any of the other plastids depending on cell its in.
Features that the chloroplast has in common with mt
- bounded by 2 membranes
- contain nucleic acids
- outer membrane highly permeable
- inner membrane more selective -> needed for subcellular organisation
How many membranes does a chloroplast have
2
- 2 phospholipid bilayers
What is the unique feature of chloroplasts
- 3rd membrane system -> light harvesting
- lipid bilayer
- grana and thylakoids
- increased SA for capturing light
Examples of large SA:vol ratio in plant
Leaf itself
thylakoid.
Functions of chloroplasts
- capture light energy (big SA) and convert it to chemical E
- light reactions -> thylakoid membranes
- Calvin cycle in storm
What does light reactions produce
- ATP and NADH
- energy as chemical E
Where do light reactions occur
On thylakoid membrane
Where do the Carbon fixation/dark reactions occur
in stroma
- What does the Calvin cycle use
ATP and NADH
- fixing CO2
Structure of chloroplasts
- thylakoid stacked -> light harvesting
- lumen (inside each pancake) -> space in thylakoid -> thylakoid space. Accumulation of H+ -> diffuse down conc grad
How big are chloroplasts
Plant chloroplasts are large organelles (5 to 10 μm long
What are the 3 membranes of chloroplasts
- inner
- outer
- thylakoid
What are the 3 compartments of chloroplasts
- stroma
- thylakoid space
- intermembrane space
These compartments and the membranes that separate them serve to isolate different aspects of photosynthesis
Reactions of Calvin Cycle
- Carbon fixation.
- reduction
- regeneration
How do deoxy and oxyribose differ
O on OH of C2
how do carbohydrate function as energy sourcae
E storage polysaccharides
- starch in plants (in starch granules) -> amylose and amylopectin
- glycogen in animals
- NOT cellulose
- E source need to break glycosidic bonds ti sep glucose. Can only break alpha 1-4 bonds in our body. Can’t break beta1-4 bonds = can’t digest.
How do carbohydrates function as structure
cellulose in plant
- cell wall -> cellulose microfibrils in plant cell wall
- long chain of glucose linked by beta1-4. H bonds between chains
- cellulose provides dietary fibre.
Mycoplasmas
Prokaryotes that lack cell walls
- live in isotonic environments and therefore not subject to osmotic pressure.
What are prokaryotes that lack cell walls called
Mysoplasmas
What does penicillan target/inhibit
Inhibits enzymes catalysing cross-linking of NAG NAM
- cross links not formed = cell wall weakened = cell lyses.
Structure of bacterial cell wall
Carbohydrate backbone NAM NAG linked by peptide cross-bridge
What does tumbling promote
Random rotational turns during swimming.
How are the chemoreceptors in cytoplasm arranged
Hexagonal array.
Parts of an endospore
- exosporium
- spore coat
- core wall
- cortex
- DNA
What’s the type of virus that can integrate the DNA synthesised from the viral RNA genome as a provirus into the host cell chromosomal DNA?
Retroviruses.
- a characteristic unique to retroviruses
What happens to Herpes simplex during the latent phase
Lysogenic/latent virus
- viral DNA sits in nerve ganglia -> dorsal ganglia
- immune system can’t see
= no symptoms
How is the Herpes Simplex virus reactivated
By stressful stimuli (fever, trauma, emotional stress)
- triggers replication of virus
What is the acute phase of Herpes simplex
blister formation
How do flagella work
The motor of a prokaryotic flagellum consists of a system of rings embedded in the cell wall and plasma membrane.
- the ETC pumps protons out of the cell
- the diffusion of protons back into the cell provides the force that turns a curved hook and thereby cases the attached filament to rotate and propel the cell.
Differences between attachment of glycoprotein and glycolipid
Glycoprotein attaches to membrane protein. Glycolipid attaches to phosphate head of phospholipids.
Integral protein
Penetrate the hydrophobic interior of lipid bilayer
Function of peripheral proteins
eg released into the cell as a secondary messenger when the integral protein its bonded to changes shape.
- also enzymatic.
Enzymatic activity of membrane proteins
A protein bult into the membrane may be an enzyme with its active site exposed to substances in the adjacent solution
- in some cases, several enzymes in a membrane are organised as a team that carries out sequential steps of a metabolic pathway.
Drug example of smooth ER function
- enzymes embedded in Er break up drugs eg liver eg painkillers
- drugs arrive in blood stream. Goes into cells of liver
- cells break down drug but still enough remaining to go to blood and then brain to dec pain
- if not enough drug, take more. Same amount of enzyme means ER can’t cope so more left into blood.
- ER grows in response. More enzymes. Take more drugs = break down into low levels = take more drug to deal with same pain to get same effect.
Where do the secreted and membrane-bound proteins go after being made on the rER
Lumen of rER
- go to gGolgi and then travel elsewhere
- in vesicle = bubble of phospholipid membrane
What are retrieval tags
- direct proteins back to ER or previous Golgi cisternae to maintain compartment integrity and function.
two types of tags for vesicles
- retrieval tags
- other tags direct to secretory pathways (important for release and surface expression of proteins on surface)
What is autophagy
Whole cell destruction
- important for programmed cell death.
Diameter of MT
25nm with 15nm lumen
Diameter of MF
7nm
Diameter of IF
8-12nm
Two things that the ATP-powered motor proteins can transport
Vesicles to targets
- damaged organelles from distant sites eg nerve terminals et to lysosome to be broken down.
What is a torn muscle
A torn desmosome
- pulled desmosomes out from one cell to other
Fibronectin
Fibronectin sometimes serves as a general cell adhesion molecule by anchoring cells to collagen or proteoglycan substrates
Fibronectin is a high-molecular weight (~440kDa) glycoprotein of the extracellular matrix that binds to membrane-spanning receptor proteins called integrins. Similar to integrins, fibronectin binds extracellular matrix components such as collagen, fibrin, and heparan sulfate proteoglycans (e.g. syndecans)
What is the glycoprotein that anchors cells to collagen or proteoglycan substrates
Fibronectin
How is collagen like other proteins?
Must be turned over and replaced
What amino acid is not formed in scurvy
Hydroxyproline
What do interns function as
a communication link from ECM to cell interior
Difference between intern and integral proteins
Integrins are receptors (a specific category) which are responsible for cellular adhesion and in some cases, cellular signalling too.
- However, integral proteins are a generalised category which includes all sorts of transmembrane proteins like receptors, enzymes, signalling cascades, transporters, cellular adhesion domains etc.
Which type of bacteria are fimbriae more commonly found on
Gram neg
Structure of gap junctions
Gap junctions are plasma membrane spatial microdomains constructed of assemblies of channel proteins called connexins in vertebrates and innexins in invertebrates.
Desmosome structure
.
What do proplastids develop in response to light
Chloroplast
Co-transport
Take H+ from inside and pump out -> requires E as moving up conc grad
- want to get back in -> diffuse (facilitated). E produced used to piggy back sucrose
- pick up sucrose
- drags sucrose with it
- can move in at same time.
Protein complexes in ETC
Protein complex I, III, IV
At which protein complex in mt ETC is water produced
Complex IV
At which complex in mt ETC is NADH oxide to NAD+
Complex I
What happens at complex I in respiration in ETC
NADH -> NAD+
What happens at complex IV in ETC in respiration
2H+ + 0.5O2 -> H2O
What happens at each of the protein complexes in ETC
H+ pumped into intermembrane space
What does oxidative phosphorylation compose of
ETC and Chemiosomosis
Which stage of respiration produces NADH
Glycolysis and Krebs cycle
In which stage is NADH oxidised
At protein complex 1 in ETC
What are the pumps in mt and ct powered by
mt - electrons from food
ct - light E
Darker layer between two plant cells
Middle lamella
What is the middle lamella made of
Predominantly pectin
What is pectin
A gel-like polysaccharide
- joins the cells together
Which cell wall is the furthest away from the interior of the cell
Primary cell wall
Whys is the primary cell wall the furthest from the interior of the cell
Because it is laid down first
- cell walls are laid down just outside plasma membrane
What is wood
Secondary cell wall
What makes cellulose highly ordered and strong
H bonds between glucose chains
Is cellulose a High E carbohydrate
Yes
What is the most abundant organic macromolecule on Earth
Cellulose
What do cellulose form
Microfibrils
What is the major component of primary and SECONDARY CELL WALL?
Cellulose
What cells produce the primary cell wall
Young cells
Properties of primary cell wall
Relatively thin and flexible
- therefore the cells can still grow
- push against cell wall- > rearrangement of cell wall as it expands
Composition of primary cell wall
Cellulose 25-30% Hemicellulose 15-25% Pectin (absorbs water and gel-like) 35% Protein 5-10% - predominantly extensin
What its the predominant protein in the primary cell wall
Extension
What is the composition of cell wall
Two phases plus a network of extensin
What is the crystalline microfibrillar phase made of
Cellulose
What is the noncrystalline matrix made of
Pectic polysaccharides
Hemicellulosic polysaccharides
What is hemicellulose
- polysaccharide
- heterogenous = different sugars
Difference between cellulose and hemicellulose
Cellulose just has glucose
Hemicellulose has other sugars
Structure of hemicellulose
One type of sugar forming backbone
- other sugars forming side chains
Cross linking between cellulose and hemicellulose
What is pectin’s structure
Zigzag
- branched
- negatively charged polysaccharides
- bind water and have gel-like properties
- gel-like properties also allows binding with cellulose
What is extensin primarily involved with
Extensibility
- ability for the primary cell wall to expand as it grows
How does extension affect extensibility
In a disorganised way when the cell wall is able to expand, eg phase of expansion. Push against microfibrils can slide against each other.
When stop growing/under stress conditions, cross-linking of protein with the cellulose
- causes dehydration of cell wall
- makes it much stronger and rigid.
- not expandable
- cells can’t grow in this stage.
What happens when the plant cells stop growing/under stress conditions
Cross-linking of protein with cellulose
- causes dehydration of cell wall
- makes it much stronger and rigid
- not expandable
- cells can’t grow in this stage.
How is the primary cell wall synthesised
- Cellulose microfibrils at plasma membrane
- excreted by plasma membrane - Polysaccharides (pectin and hemicellulose) in Golgi and transported to PM in vesicles.
- fuse with PM, contents released (to where cellulose is produced) - Cell wall proteins (extensions) from the rER
- vesicle through Golgi, vesicle to PM and released.
Therefore immediately outside the plasma membrane = producing cellulose and secreting pectin, semi and extensins
Where is cellulose synthesised
Plasma membrane
Steps to forming cellulose
Sucrose = disaccharide
- cleaved
- take glucose
Protein complex SPANS plasma membrane
- two enzymes
sucrose synthase
cellulose synthase
Cellulose synthase bind glucose together and form chains of cellulose
- secreted into cell wall.
Two enzymes in the plasma membrane complex for cellulose formation
- sucrose synthase
- cellulose synthase
Once cellulose is made, can the glucose be taken back
No.
Can’t degrade them.
What does the arrangement of cellulose affect?
- strength of the ell
- morphology of cell
What is cellulose synthase associated with
Microtubules
What affects where cellulose is laid down
Position of the microtubules
- MT = railway tracks that the cellulose synthase go across
- MT on the inner surface of cell
- Cellulose on outer
What is the middle lamella high in
Pectin
Three functions of cell wall
- Structural support and influences cell morphology.
- protection: from pathogen attack eg fungi and bacteria
- prevents excessive water uptake: regulation of turnout
What must the plant cell defend itself from (protected by cellulose)
Pathogen attack from fungi and bacteria.
How does the orientation of cellulose microfibrils influence cell morphology
Randomly oriented
- the cell will expand equally in all directions
- no pressure points, equal coverage
- expand equally in all direction
Right angles to the ultimate long axis of the cell
- the cell will expand longitudinally along that axis
What determines the shape of the cells
How the cellulose is laid down
How the cellulose is laid down is determined by the cytoskeleton
What must the position of the cellulose allow for guard cells?
Come together in certain circumstances
How does the cell wall serve its protective role
Cell wall acts as a protective barrier
- not just passive protection (but can be just passive)
Example of cell wall acting as an active protection
Sorghum plant responding to fungal infection
- red colour = response to infection
- produce inclusion bodies that contain fungicide
Neighbouring cells sense neighbour’s pathogen attack
- also produce fungicide
- secreted into cell wall
Sensing and responding
How does the cell wall regulate turgour pressure
The plant vacuole has a negative osmotic potential due to high conc of solutes
- water will enter the cell by osmosis into a higher osmotic potential
- no cell wall = water continues to enter
- presence of cell wall = pressure
- pressure of protoplast pushing against cell wall
- equal and opp forces so cell wall pushing against protoplast = no expand = no more water intake
= no burst of cell - turgour pressure = riding cells
- contributes to the structural support.
Do all plant cells have a secondary cell wall
No
When are secondary cell wall produced
After cell growth has stopped
how do secondary cell walls compare to the primary cell walls
- thicker and stronger than primary (no expansion)
- provides more structural support than primary eg wood is all secondary cell wall
Structure of secondary cell wall
- multiple layers (can lay down multiple layers of cellulose)
- eg three layers of secondary cell wall. Really thick.
- lay down secondary cell wall
- undergo programmed cell death
= hollow tubes
= xylem cells. - microfibrils in each layer have different orientations
- this strengthens the secondary wall
How are the microfibrils oriented in the microfibrils in each layer f the secondary cell wall
microfibrils in each layer have different orientations
- this strengthens the secondary cell wall.
Secondary cell wall chemical structure
- More cellulose than primary
- less pectin
- 15-35% lignin
Number one thing that limits processing of cell wall
lignin
Second most abundant organic macromolecule
lignin
What is the function of lignin in secondary well wall
Confers
- strength
- rigidity
- hydrophobicity (innert, eg enzymes can’t activity as water can’t get in)
Do different plants have different lignin in their wall
Yes
Compromise between what tow factors? (cell wall)
A good enough cell wall that the plant can grow well and a cell wall thats easy to process
Reduced lignin = more susceptible to wind damage and not as strong and pathogen attack
How do plant cells communicate
Plasmodesmata
- plasma membrane is continuous between two cells
- small enough to prevent organelle movements
- allow the free exchange of small molecules.
Pit field
Aggregation of plasmodesmata
Properties of plasmodesmata
- plasma membrane is continuous between two cells (goes through the gaps)
- small enough to prevent organelle movements
- allow the free exchange of small molecule (Eg Water)
How are things stopped from being moved through plasmodesmata
They are quite small
Example of substance that can cross plasmodesmata freely
Water
What is another structure apart from the plasma membrane that goes from one cell into the other
Endoplasmic reticiulum
What are the two structures that go across from one cell into the other in plants
- Plasma membrane
- Endoplasmic reticulum
How do viruses take advantage of plasmodesmata
Alfalfa mosaic virus
- too big to go through plasmodesmata
Two components of viruses: protein coat and nucleic acid
- Leave coat in first cell, just move nucleic acid through plasmodesmata.
- with aid of gating (movement) proteins
- within genome, has a gene that encodes for the protein
Special protein that helps move through plasmodesmata in virus
Gating (movement) proteins
- attaches to viral nucleic acid and helps it move into the plasmodesmata
enables virus to spread rapidly throughout the leaves
Potato leafroll virus
Leaves roll up = reduced ps
Genetic engineering for viral infections in plants
Introduced into plant genome a gene that encodes for the transport protein
- put a mutant -> non functional protein
- mixed population of wild-type (work fine) and modified (mutant, non functional)
- both associated with the nucleic acid
- enough to stop the function of the proteins that do work
= don’t get movement through plasmodesmata
= infection localised and doesn’t spread.
What plastid does Proplastid develop in response to light
Chloroplast
Chromoplasts
- attract animals - give colour to many flowers and fruits
- increased carotenoids (pigments) and decreased thylakoid membranes (light reaction)
What do chromoplasts contain
Increased carotenoids and decreased thylakoid membranes
Conversion when a green tomato ripens
Chloroplasts in unripe break down and are converted to chromoplasts in ripe tomatoes
- signal to animals that this fruit is palatable and ready
- breakdown of chlorophyll, accumulation of carotenoids
What are leucoplasts
Storage:
- pigments
- protein
- lipids
- starch
eg starch in leucoplasts in potato
NO highly differentiated thylakoid membrane
Two types of photosynthesis
Oxygenic and an oxygenic
Flow of biological energy
Light E -> organic molecules and O2 -> respiration -> CO2 + H2O
Can food production match demands of a growing pop?
Predicted increase is smaller than the increase required to meet predicted demand (for maize, rice, wheat, soybean)
- maybe improving photosynthesis would improve crop production
- inc productivity
Two stages of ps
Light reactions and Calvin Cycle
Where does light reaction occur
Thylakoid membrane
- photolysis of water
- ATP and NADPH produced
Where does Calvin Cycle occur
Stroma
- carbon fixation
- ADP and NADP+
Maximising SA of plant
- Maximise leave
- chloroplast to outer edge of cells
- thylakoid membranes
How is light absorbed
by pigments
absorb photons
3 pigments in chloroplast
Chl a
Chl b
carotenoids
Which colour is the least absorbed
- green (of all three pigments)
- modify pigments that could absorb extra wavelengths to inc productivity of photosynthesis
Action spectrum
O2 evolution
- dip in green = no O2 when do ps due to no light absorbed
Engelmann’s expt
Took filament of algae
- use prism to divide light into diff wavelengths
- put aerobic bacteria
Aerobic bacteria does well where the algae is photosynthesising and producing O2
Two primary pigments in ps
chl a and chl b
How do chl a and chl b differ
CHO in chl b
CH3 in cola
Structure of chlorophyll
Hydrophobic tail - interacts with protein.
- anchors molecule into light harvesting complex
- porphyrin ring
- harvest light energy
- absorb photon
- wavelength depends on group
- Mg absorbs photon
Which part of the chlorophyll interact with protein
Hydrophobic tail
Which part of chlorophyll harvest light E
Porphyrin ring
How does the chlorophyll sit in membrane
Complicated group on a stick that’s embedded in a protein in membrane.
What are chlorophyll associated with
Photosystems
Structure of photosystem
Light harvesting complexes around the reaction centre
- reaction centre in middle
Process of light harvesting in photosystems
- Photon absorbed by chlorophyll molecule
- Light Energy from photo passes to chl. Transfer of E from one chl to another
- continues until transfer of E to chl in the reaction centre.
- chl in reaction center are called “special chl molecules”
- they are not different but have different protein environment in rh reaction centre - excitation of electron from special chl
- E transfer from chl to special chl, excitation of electron
- excited electrons leaves and transfers to another molecule -> primary electron acceptor = first molecule that takes the electron from the chl.
- charge sep -> movt of high E electron.
- light E -> CPE
What is the reaction centre made of
Pigment-protein complex
What happens to the electron released from chl
Move into the photosynthetic electron transport chain
Process of ps ETC
- Both Photosystems II and I absorb light E
- light go through light harvesting complex
- both have special chl in reaction centers
- excitation of electron and go to primary electron acceptor
- electrons leave the photosystem - electrons from PS II go to cytochrome complex (which doesn’t not absorb light E
- act as channel
- move through channel and go to PS I
- replace two e- that left PS I - movement of e- across thalloid membranes results in H+ pumping across thylakoid membrane from outside to inside.
- electrons that left PS I go to NADP+ reductase
- make NADP+ + H+ -> NADPH
- high E electrons in NADPH (E carrying molecule) (used in Carbon fixation) - Replace lost electrons from PS II from photolysis of water
- H2O -> 0.5O2 + 2H+ (Get two electrons)
- energetically unfavourable
- catalytic center allows two e- to be drawn from water.
- O2 as byproduct (O2 is the terminal electron acceptor in respiration)
- accumulation of H+ on inside - H+ go through ATP synthase, flow down conc grad to outside of thylakoid into stroma.
- ATP generated
ATP and NADPH go to Calvin Cycle
Smaller complexes in membrane
Mobile electron carriers that can move through thylakoid membrane carrying those electrons.
Compare and contrast high H+ conc in mt and ct
mt: intermembrane space
ct: thylakoid space
Important of organelles
both have ATP synthase
H+ flow through down conc grad.
- into stroma
- into matrix
Overall, what happens in the light reactions
- water split
- O2 produced
- ATP and NADPh produced
Overall, what happens in the Calvin Cycle
ATP and NADPH produced in the light reactions are used to fix CO2 and produce carbohydrate
- in stroma
- Fix 3CO2 into 1 high E 3C compound.
3 steps of Calvin Cycle
- Carbon fixation
- fix CO2 into carbohydrate - Reduction
- Regeneration of CO2 acceptor
Process of Calvin Cycle
- 3 x 5C
- 3 x CO2
- CARBON FIXATION uses Rubisco
- 6 x 3C
- need 6 ATP -> 6ADP
- need 6 NADPH -> 6NADP+ + 6Pi - REDUCTION. Makes 1 x 3C compound
- goes off to form glucose and other compounds - left with 5 x 3C
- REGENERATION OF CO2 ACCEPTOR uses 3ATP
- Back to 3 x 5C
Most abundant protein in plant
Rubisco (catalyses carbon fixation)
eg potato on windowsill
Leucoplast convert to chloroplast in response to light stimulus
- production of thylakoid membranes
What is
Undifferentiated organelle
- harvest light E
- convert into chemical E
Describe chloroplast development triggered by light
- Dispersion of prolamellar body within the primary layer of labelled
- formation of grana after 24 hours of continuous light exposure
- 48 hours later fully differentiated chloroplast
- refer to diagram
Two compounds of pigments in periwrinkles
Vinblastine and vincristine
- also anti-cancer
Similarities between E generation in A and P cells
Sim:
- ATP by chemiosmosis
- ETC pump H+ across membrane from low to high conc
- H+ diffsuse back in thru ATP synthase -> ATP synthesis
- electron carriers are sim
- ATO synthase are sim
Diff:
- flow of H+
- high energy electron from oxidation of organic molecules vs electron from H2O
- transfer CPE to ATP vs transform light E to CPE in ATP
- ATP production in matrix vs ATP produced in stroma
Where are the high energy electrons from in mt and ct
in mt: from oxidation of organic molecules
- in ct: from water.
Function of nucleolus
rRNA synthesised from DNA
- protein imported from cytoplasm are assembled with rRNA into large and small ribosomal subunits (these subunits then exit the nucleus through the nuclear pores to the cytoplasm, where a large and small subunit can assemble into a ribosome
Things that go out of nuclear pore
- rRNA
- mRNA
- tRNA
- ribosomal subunits
Things that go into the nucleus
- control signals eg growth factors, hormones
- E and materials eg ATP
- proteins needed for transcription
- protein needed for chromosome replication
- ribosomal proteins
Where are plastids found
actively dividing root and shoot tissue
What do light reactions produce
NADPH, ATP, O2
Function of plasmodesmata
Allow continuity of PM from 2 adjacent cells and cytoplasmic exchange between cells
Structure of plasmodesmata
narrow cylindrical desmotubule derived from ER, surrounded by a narrow ring of cytoplasm (annulus)
Which substances can cross plasmodesmata
H2O, glucose, even proteins and RNA
- plant viruses
- as viral RNA is too large to move freely through the channels, gating (movement) proteins bind to the viral nucleic acids and “thread” the RNA thru the plasmodesmata into an adjacent cell where replic take place
How do viruses pass through plasmodesmata
- as viral RNA is too large to move freely through the channels, gating (movement) proteins bind to the viral nucleic acids and “thread” the RNA thru the plasmodesmata into an adjacent cell where replic take place
Chemical structure of lignin
Complex phenolic polymer
