Cell theory
Cells are the smallest possible units of life
Living organisms are made of cells
All cells come from pre-existing cells
Exceptions to cell theory
Skeletal muscle - made up of muscle fibers that are enclosed inside a membrane (like a cell), but are larger than most cells and have 100s of nuclei
Giant algae - can grow to the length of 100 mm (so expected to have many small cells), but contain a single nucleus
Aseptate fungi - made of thread-like structures called hyphae that are not divided into sub-units containing a single nucleus, but many nuclei
Functions of life
Nutrition
Growth (increases in size and dry mass)
Response (reacts to stimuli)
Excretion (expels waste products of metabolism)
Metabolism (carries out chemical reactions in cytoplasm)
Homeostasis (keeps internal conditions within limits)
Reproduction
Emergent properties
Properties that arise from the interaction of the component parts of a complex structure.
e.g. each cell in a tiger is a unit of life with distinctive properties (such as sensitivity to light in retinal cells), but all cells combined to give additional properties (such as ability to hunt and kill)
Differentiation
A cell uses only the genes that it needs to follow its pathway of development, leaving other genes unused.
e.g. genes for making hemoglobin are only expressed in developing RBCs. Once a pathway of development has begun, it's fixed, or "committed."
Stem cells
Cells that have the capacity to divide and to differentiate along different pathways.
Embryos are entirely stem cells in their early stages, but gradually the cells commit themselves to differentiation. Small numbers persist in the adult body, usually in human tissues like bone marrow, skin, and liver, giving tissues powers of regeneration and repair. Other tissues like the brain, kidney, and heart don't have stem cells so can't repair themselves.
Examples of therapeutic stem cell use
Stargardt's macular dystrophy:
Develops in children 6-12
Due to recessive mutation of ABCA4 gene, causing a membrane protein used for active transport in retina cells to malfunction, so photoreceptive cells degenerate and vision worsens.
Embryonic stem cells injected into eyes attach to the retina and remain there, and vision improved
Leukemia:
Type of cancer in which abnormally large numbers of WBCs are produced in the bone marrow
A large needle is inserted into a large bone (usually pelvis) to remove fluid from the marrow
Stem cells are extracted from this fluid and stored by freezing them (since adult, only have potential for producing more blood cells)
High dose of chemotherapy is given to kill all the cancer cells in the marrow, so it loses its ability to produce blood cells
Stem cells are returned to the body, where they re-establish themselves in the marrow, multiply, and begins to produce RBCs and WBCs
Magnification calculation
size of image / size of specimen
(make sure in same units)
Size of specimen calculation
size of image / magnification
(make sure in same units)
Resolution
The ability of the microscope to show 2 close objects separately in the image. Depends on the wavelength of the rays used to form the image (shorter wavelength, higher resolution; electrons have shorter wavelength than light, so electron microscopes have higher resolution than light)
Transmission electron microscope
Used to view ultra-thin sections
Scanning electron microscope
Produce an image of the surface of structures
*know structure
Surface area to volume ratio
As a cell grows larger, it decreases.
Surface area: determines rate at which substances enter or leave a cell Volume: determines rate at which substances are used or produced by a cell
Prokaryotic cells
First cells to evolve
Not compartmentalized
Replicates by binary fission
No nucleus, mitochondria, or membrane-bound organelles within nucleus
Has:
Cytoplasm
Nucleoid (region containing naked DNA)
70S ribosomes
Cell wall
Plasma membrane
Pili
Flagellum
Binary fission
Division of prokaryotic cells into two
Sometimes can do this every 30 minutes
Bacterial chromosome is replicated so there are 2 identical copies
Copies move to opposite ends of the cell
Wall and plasma membrane pulled inwards so the cell pinches apart into 2 identical cells
Eukaryotic cells
Compartmentalized (allows enzymes and substrates in a process to be concentrated in a small area in the cell, with pH, other optimum conditions, and no other enzymes that might disrupt the process)
Membrane-bound organelles
Has: Organelles with single membrane:
Rough ER
Smooth ER
Golgi apparatus
Lysosomes
Vesicles and vacuoles
Organelles with double membrane:
Nucleus
Mitochondrion
Chloroplast
Davson-Danielli Model
Developed in 1930s
Bilayer of phospholipids with layers of protein on either side
Electron micrographs showed two dark lines separated by a lighter band
Proteins usually appear darker than phospholipids
Process of discovery:
Chemical analysis of membranes showed that they were composed of phospholipids and proteins
Evidence suggested that the plasma membrane of red blood cells has enough phospholipids in it to form an area twice as large as the area of the plasma membrane, suggesting a phospholipid bilayer
Experiments showed that the membranes form a barrier of passage of some substances, despite being very thin, and layers of protein could act as a barrier
Singer-Nicolson Model
Developed in 1950s and 1960s
Falsified by evidence
Polar amino acids:
On the surface of proteins, so make them water soluble
Create channels through which hydrophilic substances can diffuse; positively charged R groups allow negatively charged ions through and vice versa;
Cause parts of membrane proteins to protrude from the membrane (transmembrane stick out in 2 spots)
Non-polar amino acids:
In the center of water-soluble proteins, so stabilize their structure
Cause proteins to remain embedded in membranes
Process of discovery:
Freeze-fracture electron micrographs show globular proteins present in the center of the phospholipid bilayer
Analysis of membrane proteins showed that parts of their surfaces were hydrophobic (so they'd be positioned in the bilayer and sometimes stretch to both sides)
Fusion of cells with membrane proteins tagged with different colored fluorescent markers showed that these proteins can move within the membrane as the colors became mixed within a few minutes of cell fusion when they became 1 cell
Fluid Mosaic Model
Also by Singer and Nicolson (1966)
Made of a phospholipid bilayer and proteins in a range of positions in the membrane (integral proteins are embedded in the bilayer; peripheral proteins are attached to the outer surface; glycoproteins have sugar units attached to the outer surface of the membrane)
Phospholipid
Basic components of cell membrane
Amphipathic (part of the molecule is hydrophobic and part hydrophilic)
Phosphate head is hydrophilic and 2 fatty acids tails (composed of hydrocarbon chains) are hydrophobic
When mixed with water, they form bilayer, with hydrophilic heads facing out and making contact with water, and hydrophobic tails facing inward away from the water
The attraction between the hydrophobic tails in the center and between the hydrophilic heads and surrounding water makes them very stable
Amphipathic
Part of the molecule is hydrophobic and part hydrophilic e.g. phospholipids
Cholesterol
Component of animal cell membranes
Most of it is hydrophobic with one hydrophilic end, so fits between phospholipids in the membrane
Restricts the movement of phospholipid molecules, thus reducing fluidity and permeability of membrane to hydrophilic particles like Na and H ions
Integral proteins
Embedded in phospholipid bilayer
e.g. insulin receptor - hormone receptor that protrudes off both ends
e.g. cytochrome oxidase - immobilized enzyme embedded in membrane to which cytochrome c binds on the outside
e.g. calcium pump - active transport of calcium ions
e.g. nicotinic acetylcholine receptor - receptor for neurotransmitter and channel for facilitated diffusion of Na ions
Peripheral proteins
Attached to outer surface of the membrane
e.g. cytochrome c (electron transport) that binds to the outside of cytochrome oxidase
Glycoproteins
Sugar units attached on the outer surface of the membrane
Used for cell-to-cell communication
Diffusion
Passive process
When particles are unevenly spread (higher concentration in one region than another), this occurs
Passive movement of particles FROM a region of HIGHER concentration to a region of LOWER concentration (as result of random motion of particles)
Can occur across membranes if there is a concentration gradient and membrane is permeable to the particle
e.g. membranes are permeable to 02, so lower concentration of 02 inside than outside, so diffuses into the cell
e.g. not permeable to cellulose, so it does not diffuse across
Membrane
Partially permeable (allow some substances to diffuse through but not others)
Simple diffusion
Some substances move between phospholipids molecules in the membrane
Facilitated diffusion
Passive process
When substances are unable to pass between the phospholipids
Use channel proteins
Only one type of substance can pass through
Cells control whether substances pass through their membranes by the types of channel proteins inserted in their membranes
FROM region of HIGHER concentration to region of LOWER concentration
e.g. chloride channels only allow chloride ions through e.g. sodium and potassium channel proteins in the membranes of neurons open and close depending on voltage across membrane to transmit nerve impulse
Channel proteins
Control what substances pass through cell membrane
Only one type of substance can pass through
FROM region of HIGHER concentration to region of LOWER concentration
e.g. chloride channels only allow chloride ions through e.g. sodium and potassium channel proteins in the membranes of neurons open and close depending on voltage across membrane to transmit nerve impulse
Potassium channels
On the axons of neurons
Used during action potential
Closed when the axon is polarized, but open in response to depolarization of axon membrane
Allow K+ ions to exit by facilitated diffusion, which repolarizes the axon
Only remain open for short time before globular sub-units block the pore and closes again
Osmosis
Passive movement of water FROM region of LOWER solute concentration to HIGHER solute concentration
Different from diffusion because water is a solvent
Moves due to concentration of solutes, not water
Attractions between solute particles and water molecules are reason for water moving to regions with HIGHER solute concentration
Can cause cells in human tissues or organs to swell up and burst, or to shrink due to gain or loss of water
Solvent
Liquid in which particles dissolve
Solute
Dissolved particles
EXPERIMENT Estimating Osmolarity
Prepare series of solutions with a suitable range of solute concentrations, like 0.0, 0.1, 0.2, 0.3, 0.4, and 0.5 moles/liter
Cut potato tissue into samples of equal size and shape
Find the mass of each sample, using an electronic balance
Bathe tissue samples in each of the range of solutions for long enough to get measurable mass changes, usually between 10 and 60 minutes
Calculate percentage mass change using the formula: ((final mass - initial mass) / initial mass) x 100
Plot the results on a graph
Read off the solute concentration which would give no mass change, which means that the osmolarities are the same
Accuracy:
the volume of the water used for making solutions should be measured with a volumetric flask
the initial and final mass of tissue samples should be measured with the same electronic balance that is accurate to 0.01 grams (10 mg)
Osmolarity
Number of moles of solute particles per unit volume of solution
Greater concentration of solutes, then higher osmolarity
If two solutions with different osmolarity are separated by a semi-permeable membrane, water will move by osmosis FROM solution with LOWER osmolarity to HIGHER osmolarity
Can be hypotonic, hypertonic, or isotonic
Pure water has osmolarity of 0
Hypotonic
Surrounding solution has lower solute concentration, and cell has higher solute concentration
HYPO in reference to surrounding concentration
Hypertonic
Surrounding solution has higher solute concentration, and cell has lower solute concentration
HYPER in reference to surrounding concentration
Isotonic
Surrounding solution and cell have same solute concentration
Avoiding osmosis in donor organs
Osmosis can cause cells in human tissues or organs to swell up and burst, or to shrink due to gain or loss of water
To prevent this, tissues of organs used in medical procedures such as kidney transplants must be bathed in a solution with same osmolarity as human cytoplasm
A solution of salts called isotonic saline is used for some procedures
Donor organs are surrounded by isotonic slush when they are being transported, with the low temperatures helping to keep them in a healthy state
Active transport
-Movement of substances against concentration gradient (FROM region of LOWER concentration to HIGHER concentration)
Active transport
-Can move substances against concentration gradient (FROM region of LOWER concentration to HIGHER concentration)
Use protein pumps
Transports only particular substances, so cells control what is absorbed and what is expelled
Work in a specific direction (only enter on one side and exit on the other)
Process:
Particle enters the pump from the side with a LOWER concentration
Particle binds to a specific site. Other types of particles can't bind
Energy from ATP is used to change the shape of the pump
Particle is released on the side with a HIGHER concentration and the pump then returns to its original shape
Antiporter
Pumps substances in opposite directions across membrane
Sodium-Potassium Pumps
Energy required for active transport/pumping is obtained by converting ATP to ADP and phosphate, so it an ATPase (Na+/K+-ATPase)
One ATP provides enough energy to pump 2 K+ ions in and 3 Na+ ions out
Pump an antiporter because pumps substances in opposite directions across membranes
In the center of the pump there are 2 binding sites for K+ and 3 for Na+. The pump has 2 alternate states: there's access to the binding sites from the outer of side of the membrane and a stronger attraction to K+ (so Na+ discharged from cell); and there's access to the binding sites from the inside and a stronger attraction to Na+ (so K+ discharged into the cell)
Concentration gradient created by this transport is needed for transmission of nerve impulses in axons
Vesicles
Fluidity of the membrane allows parts of it to be pinched off to create a vesicle containing some material from outside the cell (endocytosis)
Can fuse with plasma membrane and release contents outside the cell (exocytosis)
Move materials from one part of the cell to another (move proteins from rough ER to Golgi apparatus)
Endocytosis
Fluidity of the membrane allows small pieces of it to be pinched off to create a vesicle containing some material from the outside
Exocytosis
Vesicles move to the plasma membrane and fuse with it, releasing the contents of it outside the cell
Spontaneous generation
19th-century belief that life could appear in non-living material
No evidence today that shows that living cells can be formed by anything except division of pre-existing cells
Origins of the first cell
Before cells today, there was only non-living material on Earth
64 codons of genetic code have same meanings in all cells of all organisms, apart from minor variations, which suggests that life evolved from the same original cells
Pasteur's experiment
Verified principle that cells can only come from pre-existing cells
Placed samples of broth in flasks with long swan necks and melted the glass of the necks to bend them into different shapes
Boiled the broth in some of the flasks to kill any organisms present, and left others unboiled (controls)
Fungi and other organisms appeared in the unboiled flasks but not the boiled ones (even after a long time)
The broth in the flasks was in contact with air (which had been suggested was needed for spontaneous generation), but that didn't occur, so disproved it
Snapped necks of some of the flasks to leave a shorter vertical neck, and organisms were soon apparent and decomposed the broth
Concluded that the swan necks prevented organisms from the air getting into the flasks and that no organisms appeared spontaneously
Symbiosis
Two organisms living together
Endosymbiosis
A larger cell takes in a smaller cell by endocytosis, so the smaller cell is inside a vesicle in the cytoplasm of the larger cell
Instead of being digested, smaller cell is kept alive to perform a function for the larger cell
Smaller cell divides as often as the larger cell so that one or more of them are inside vesicles in the new larger cells
Happened at least twice during the origin of eukaryotes:
A cell that respired anaerobically took in a bacterium that respired aerobically, supplying both itself and the larger cell with energy as ATP. It gave the larger cell a competitive advantage because aerobic respiration is more efficient than anaerobic. The aerobic bacterium gradually evolved into mitochondria and the larger cell evolved into heterotrophic eukaryotes like animals
A heterotrophic cell took in a smaller photosynthetic bacterium, which supplied it with organic compounds, making it an autotroph. The photosynthetic prokaryote evolved into chloroplasts and the larger cell evolved in photosynthetic eukaryotes like plants
Explains characters of mitochondria and chloroplasts:
grow and divide like cells
have naked loop of SNA, like prokaryotes
synthesize some of their own proteins using 70S ribosomes, like prokaryotes
have double membranes (as expected when cells are taken into a vesicle by endocytosis)
Chromosomes
DNA molecules with proteins attached to them
Term for them once sister chromatids are separated during mitosis
Condensation
When chromosomes become shorter and fatter during mitosis
Makes them visible with a light microscope
Supercoiling
Complex process of coiling that causes condensation (when chromosomes become shorter and fatter during mitosis) of chromosomes
Sister chromatids
The two parts of the chromosome
Term for it before separated during mitosis
Centromere
Point at which sister chromatids are held together
Mitosis
Prophase Metaphase Anaphase Telophase
Prophase
Spindle microtubules grow
Chromosomes becoming shorter and fatter by supercoiling
Each chromosome now consists of two identical chromatids formed by DNA replication in interphase and held together by the centromere
Spindle microtubules extend from each pole toward the equator
Metaphase
Nuclear membrane is broken down
Chromosomes align at the equator
Spindle microtubules from both poles attach to each centromere from opposite sides
Anaphase
Centromeres divide, making chromatids now chromosomes
Spindle microtubules pull the genetically identical chromosomes to opposite poles
Telophase
All chromosomes have reached the poles
Nuclear membranes form around the chromosomes
Spindle microtubules break down
Chromosomes uncoil and are no longer individually visible
The cell divides (cytokinesis) to form 2 cells with genetically identical nuclei
Mitotic index
Ratio between the number of cells in mitosis in a tissue and the total number of observed cells
Used by doctors to predict how rapidly a tumor will grow and therefore what treatment is needed (high index indicates fast-growing tumor)
Cytokinesis
Division of the cytoplasm to form two cells
Occurs after mitosis
In plant cells:
A new cell wall forms across the equator
Plasma membrane is on both sides
This divides the cell into two
In animal cells:
The plasma membrane at equator pulled inwards until meets in the center of the cell
This divides the cell into two
Cell cycle
Sequence of events between one cell division and the next
2 phases: interphase and cell division
Interphase
Very active phase in the life of a cell when many metabolic reactions occur
e.g. DNA replication in nucleus; protein synthesis in cytoplasm (though some occur during mitosis, too; e.g. cell respiration)
Numbers of mitochondria increase as they grow and divide
3 phases:
G1 phase - synthesizes mRNA and proteins
S phase - cell replicates all genetic material (so after mitosis both new cells have complete genetic code)
G2 - growth and preparation for division
G1 phase (of interphase)
"Growth 1"
growth/increase in size
synthesizes mRNA and proteins and organelles
S phase (of interphase)
Synthesis
DNA replication
occurs in nucleus
G2 phase (of interphase)
"Growth 2"
growth and prepartion for division
lower SA:V ratio so that the cell can get bigger
Cyclins
A group of proteins used to ensure:
that tasks are performed at the correct time
that the cell only moves on to the next stage of the cycle when appropriate
Bind to enzymes called cyclin-dependent kinases, which become active and attach phosphate groups to other proteins in the cell, which triggers other proteins t be active and carry out tasks specific to one of the cell cycle phases
4 main types:
cyclin A, B, C, and D
unless they reach a threshold concentration, the cell does not progress to the next stage
Discovered serendipitously by Tim Hunt, who was doing research into protein synthesis in sea urchin eggs. He noticed a protein that increased and decreased in concentration repeatedly and also that those changes corresponded with particular cell cycle phases. He named them cyclins.
Serendipity
Making happy and unexpected discoveries by accident
e.g. Tim Hunt and cyclins in sea urchin eggs
Cyclin-dependent kinases
Enzymes that become active when cyclins bind to them and then attach phosphate groups to other proteins in a cell, which triggers other proteins to become active and carry out tasks specific to one of the cell cycle phases
Oncogenesis
Formation of tumors that starts with mutations in oncogenes (genes involved in the control of the cell cycle)
When control of cell cycle lost, cell divides uncontrollably to produce a mass of cells called a primary tumor
Mutations must occur in several oncogenes in the same cell for control to be lost (chance is very small, but body has billions of cells, so risk is high)
Anything that increases the chance of mutation will increase risk (e.g. mutagens)
Oncogenes
Genes involved in the control of the cell cycle
Mutagens
Chemical substances that increase the chance of mutations and thus the risk of tumor formation (oncogenesis)
Primary tumor
Mass of cells as the result of repeated uncontrolled divisions of cells with a mutation in an oncogene
Often benign because they go not grow rapidly and do not spread; but can become malignant if cells become detach and are carried else in the body, to become secondary tumors (called metastasis)
Secondary tumors
When cells detach from the primary tumor and are carried elsewhere in the body, no longer benign but now malignant (now called cancer)
(detachment called metastasis)
Metastasis
Spreading of cells to form tumors in a different part of the body
Smoking
Positive correlation between cigarette smoking and death rate due to cancer
Although does not by itself prove smoking causes cancer, there's evidence that chemicals in tobacco smoke are mutagenic and therefore carcinogenic
Carcinogen
Chemical substances that cause cancer
Theory of vitalism
Theory that living organisms were composed of organic chemicals that could only by produced in living organisms because a "vital force" was needed
Falsified by a series of discoveries, including the artificial synthesis of urea
Molecular biology
Explains living processes in terms of the chemical substances involved
Synthesis of urea
Urea was discovering in human urine in the 18th century
The theory of vitalism predicted that urea could only be made in living organisms because it was an organic compound, and thus needed a "vital force"
In 1828, Friedrich Wohler synthesized urea artificially using silver isocyanate and ammonium chloride, the first time that an organic compound had been synthesized artificially
Falsified theory of vitalism
Atom
A single particle of an element, consisting of a positively charged nucleus surrounded by a cloud of negatively charged electrons
Molecule
A group of two or more atoms held together by single, double, or triple covalent bonds
E.g. ethanol, CO2, hydrogen cyanide
Bonds: Hydrogen - 1 bonds Oxygen - 2 bonds Nitrogen - 3 bonds Carbon - 4 bonds
Intermolecular forces
Weak bonds between molecules
Metabolism
Web of all the enzyme-catalyzed reactions in a cell or organisms
Metabolic pathways consist of chains of reactions, but there are also some cycles
Metabolic pathways
Most often chains of reactions, but sometimes cycles of reactions
e.g. initial substrate --> intermediate substance --> intermediate substance --> intermediate substance --> intermediate substance --> end produce/substrate
Anabolism
Synthesis of complex molecules from simpler molecules (in living organisms, monomers --> macromolecules)
A form of condensation reactions (water is produced)`
Catabolism
Breakdown of complex molecules into simple molecules (in living organisms, macromolecules --> monomers)
A form of hydrolysis (water molecules are split)
Covalent bonds
Bond between two atoms sharing an electron
Polarity
In a covalent bond, when the nucleus of one atom is more attractive to the electrons than the other, electrons are not shared equally, thus one part of the molecules has a slight positive charge and another part has a slight negative charge
e,g, water molecules (hydrogen nuclei are less attractive to nuclei than oxygen nuclei, so 2 hydrogen atoms have slight positive charge and oxygen has slight negative charge (has two poles, so DIpolarity)
Dipolarity
Polarity only on two poles
e.g. water molecules
Water molecule
...
Water polarity
(Specifically dipolarity)
Hydrogen nuclei are less attractive to nuclei than oxygen nuclei, so 2 hydrogen atoms have slight positive charge and oxygen has slight negative charge
Hydrogen bond
An intermolecular bond that forms between the positive pole of one water molecule and the negative pole of another
Energy is released when the bond is made, and energy is used when the bond is broken
e.g. when a water molecule evaporates, hydrogen bonds between it and other molecules must be broken. Heat energy is used to do this, explaining the use of sweat as a coolant - evaporation of water from sweat removes heat from the body
Thermal properties (water vs. methane)
Melting point: Methane: -182 C Water: 0 C Explanation: ice melts at much higher temperatures - hydrogen bonds restrict the movement of water molecules and heat is needed to overcome this
Specific heat capacity: Methane: 2.2 J per g per C Water: 4.2 J per g per C Explanation: water's heat capacity is higher - hydrogen bonds restrict the movement of water molecules so more energy is stored by moving molecules of water than methane
Latent heat of vaporization: Methane: 760 J/g Water: 2257 J/g Explanation: water has a much higher heat of vaporization - much heat energy is needed to break hydrogen bonds and allow a water molecule to evaporate
Boiling point: Methane: -160 C Water: 100 C Explanation: water's boiling point is much higher - heat energy is needed to break hydrogen bonds and allow water to change from liquid to gas
Solubility in water
Ionic compounds and substances with POLAR molecules are HYDROPHILIC, and thus SOLUBE in water because their ions or molecules are more attracted to water than to each other
HYDROPHOBIC substances are not repelled by water, but water molecules are more attracted to each other than to the NON-POLAR molecules of the substances, thus they are INSOLUBLE
Hydrophilic
Substances that are more attractive to water and form intramolecular bonds with water molecules
Hydrophobic
Substances that, when placed in water, do not overcome the hydrogen bonds between water molecules, so they are insoluble