IB Biology

All definitions from IB biology

Cell theory

1. Cells are the smallest possible units of life
2. Living organisms are made of cells
3. All cells come from pre-existing cells

Exceptions to cell theory

1. 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

2. Giant algae - can grow to the length of 100 mm (so expected to have many small cells), but contain a single nucleus

3. 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

1. Bacterial chromosome is replicated so there are 2 identical copies
2. Copies move to opposite ends of the cell
3. 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:
1. Chemical analysis of membranes showed that they were composed of phospholipids and proteins
2. 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
3. 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:
1. Freeze-fracture electron micrographs show globular proteins present in the center of the phospholipid bilayer
2. 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)
3. 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

1. 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
2. Cut potato tissue into samples of equal size and shape
3. Find the mass of each sample, using an electronic balance
4. Bathe tissue samples in each of the range of solutions for long enough to get measurable mass changes, usually between 10 and 60 minutes
6. Calculate percentage mass change using the formula:
((final mass - initial mass) / initial mass) x 100
7. Plot the results on a graph
8. 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:
1. Particle enters the pump from the side with a LOWER concentration
2. Particle binds to a specific site. Other types of particles can't bind
3. Energy from ATP is used to change the shape of the pump
4. 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

1. Placed samples of broth in flasks with long swan necks and melted the glass of the necks to bend them into different shapes
2. Boiled the broth in some of the flasks to kill any organisms present, and left others unboiled (controls)
3. Fungi and other organisms appeared in the unboiled flasks but not the boiled ones (even after a long time)
4. 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
5. Snapped necks of some of the flasks to leave a shorter vertical neck, and organisms were soon apparent and decomposed the broth
6. 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:
1. 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
2. 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