Year 1 Biology Review

Define and give an example of emergent property

Emergence occurs when an entity is observed to have properties its parts do not have on their own. These properties or behaviors emerge only when the parts interact in a wider whole.

Tissue

A tissue is a group of cells that specialize in the same way and perform the same function.

Define differentiation and cell specialisation

Differentiation is the development of specialized structures and functions in cells. ​

Explain how gene expression leads to differentiation

Different genes in DNA are expressed while others are repressed by certain proteins. This leads to the creation of specialised cells.

Define zygote and embryo

The zygote is the fertilized sperm and egg which has a complete set of DNA (46 Chromosomes \= 23 From Male Sperm + 23 From Female Egg) An embryo results from the zygote's cell division and replication.

Totipotent Stem Cells

Can become any body cell, including placenta cells in mammals.

Pluripotent Stem Cells

Can become any body cell. (not including placenta)

Multipotent Stem Cells

Stem Cells that have partially specialised/differentiated already, and can only become a certain type of related body cells.

State the two essential characteristics of stem cells

1. Indefinite division to create more stem cells
2. Can differentiate to become a specialized cell type in multicellular organisms.

Advantages/disadvantages of embryonic, umbilical cord and adult stem cells

- Using multipotent adult tissue may be effective for certain conditions, but is limited in its scope of application
Stem cells derived from umbilical cord blood need to be stored and preserved at cost, raising issues of availability and access
The greatest yield of pluripotent stem cells comes from embryos, but requires the destruction of a potential living organism

Embryonic Stem Cells (Inner Cell Mass Stem Cells)

Embryonic stem cells are cell removed from the inner cell mass (ICM) of a blastocyst at a developmental stage before the time that implantation would normally occur in the uterus. If the ICM cells are cultured under appropriate conditions, they can continue to proliferate and replicate themselves indefinitely and still maintain the developmental potential to form any cell type of the body (pluripotent).

Cons of Embryonic Stem Cells (Inner Cell Mass Stem Cells)

- Technically considered the destruction of a human embryo, and therefore is the murder of a human who already has rights and personhood.
- There is danger of embryonic stem cells developing into tumour cells (and/or other harmful effects of the cells are not yet known)

Pros of Embryonic Stem Cells (Inner Cell Mass Stem Cells)

- Can divide indefinitely
- Support Research
- Provide material for testing
- Unlimited amount of tissue for transplantation

Umbilical Cord Stem Cells

The umbilical cord attaches the placenta to the fetus. The umbilical cord is made up of three blood vessels: two smaller arteries which carry blood to the placenta and a larger vein which returns blood to the fetus. With the consent of the parents, blood can be collected from the umbilical cord of a newborn baby shortly after birth.

Pros of Umbilical Cord Stem Cells

The umbilical blood is a rich source of the multipotent hematopoietic stem cells that can be used in research and by doctors to treat diseases of the blood and immune system.
- hematopoietic stem cells turn into any of the three blood types (Red Blood Cells, White Blood Cells, Platelets)

Cons of Umbilical Cord Stem Cells

- Umbilical cord stem cells will not continue to grow and divide in culture (the cells must be frozen).
- Are multipotent and can only differentiate to a limited number of cell types.

Adult Stem Cells (somatic stem cells)

Adult stem cells have been found in the brain, bone marrow, blood vessels, skeletal muscle, skin, teeth, heart, gut, liver, and other (although not all) organs and tissues.

Cons of Adult Stem Cells

- Are multipotent and can only differentiate to a limited number of cell types.
- Some types of adult stem cells are rare and hard to obtain from the tissue.

Pros of Adult Stem Cells

- No ethical issues
- Awareness and potential growing
- obtained from self, and therefore no risk of incompaitibility (no immune issues)
- lab culture possible

Describe how stem cells are used to treat Stargardt's disease

- Stargardt's disease is a type of debilitating eye disease that can lead to blindness in both eyes.
- It is caused by a recessive gene mutation, which means it can only come from the offspring of two carriers of the mutated gene
- As the patient ages, their eyesight deteriorates
- Stem Cells can be implanted back into the retina and will restore normal vision

Compare sexual and asexual production of clones

Asexual Reproduction: No genetic variation in offspring, cells divides by mitosis, can mass produce identical organisms.

Sexual Reproduction: Genetic variation in offspring, cells divide by meiosis, promote diversity among offspring

Describe embryo splitting

Results in two genetically identical twins and is a form of natural cloning. However, there is also artificial cloning that involves embryo splitting: Artificially splitting a single embryo at a very early stage of development. putting these split embryos (new cells) into surrogate parents, and then developing them into cloned organisms

Describe the steps of somatic cell nuclear transfer

Step 1: Obtain nucleus from donor somatic cell (diploid)
Step 2: Obtain unfertilised egg cell (no nucleus)
Step 3: Fuse donor nucleus and egg cell (via electric shock)
Step 4: Embryo creation (divides normally and becomes embryo)
Step 5: (of Artificial Reproductive Cloning) Embryo placed in the womb/uterus of a surrogate mother --\> Lamb Normally Born
Step 5: (Therapeutic Cloning) Embryonic cells can be induced to differentiate to create specific tissues or organs for transplantation

Outline the difference between reproductive cloning and therapeutic cloning

Reproductive Cloning:
Embryo placed into uterus of surrogate mother and cloned organism grown and given birth to.

Therapeutic cloning:
- Embryo split and stem cells cultivated (grown) in a petri dish
- Stem cells then differentiated into different cell types
- Or embryos used in research

Describe the structure of eukaryotic DNA

Linear and Associated with a histone protein (usually in loose chromatin as the cell is in Interphase most of the time)

Outline the structure of a nucleosome

The DNA is complexed with eight histone proteins (an octamer) to form a complex called a nucleosome

(beads on a string)

Describe the structure of a replicated chromosome

It is made of two sister chromatids with a centromere in the middle (supercoiled/condensed DNA)

Define the cell cycle

the process of steps by which a cell grows and prepares to divide.

Summarise the two main stages of cell cycle

Interphase: Where the cell carries out it's usual functions

Mitosis: (PMAT) Where the cell splits the nucleus

Outline the phases of interphase (state name and what happens in it)

Gap 1 (G1) - The cell carries out its usual specialized function, in animal cells duplicating mitochondria and in plant cells duplicating the chloroplasts as well. The cell also produces necessary proteins required for DNA replication/synthesis in the next phase

Synthesis (S) - The cell replicates its DNA in preparation for mitosis

Gap 2 (G2) - The finishes its preparation for division by finalizing its growth.

State the difference between mitosis and cytokinesis

Mitosis is the splitting of the nucleus while cytokinesis is the splitting of the cytoplasm of the cell, physically creating a second cell.

Outline the phases of mitosis (explain in words and with diagrams)

Prophase - The DNA that is in chromatin form condenses into Chromosomes, the mitotic spindle starts to form, and the nuclear membrane starts to disappear

Metaphase - The chromosomes align at the equator of the cell/in the middle of the cell.

Anaphase - The Sister Chromatids are split apart by receding mitotic spindles and move to the poles of the cell, creating complete sets of chromosomes for the two future cells.

Telophase - The nuclear membrane starts to re-form, and the cell begins to create a cleavage furrow via the formation of a microtubule filament ring surrounding the equator of the cell.

Describe the structure of DNA during interphase, metaphase and anaphase

Interphase - DNA is in chromatin form and is replicated once to prepare for cell division. However, it is still in an uncoiled chromatin form.

Metaphase - DNA is now in a supercoiled chromosome form that consists of two sister chromatids. However, it is considered one chromosome as it is the same genetic material, but just another copy.

Anaphase - DNA is still in supercoiled chromosome form, but it is now only one chromatid as the other has been pulled to the other side. HOWEVER, they are still considered to be one chromosome.

Outline cytokinesis in plant and animal cells

Plant Cells - The golgi body releases pectin containing vesicles which align at the center of the cell in order to form a cell wall to divide the two cytoplasms.

Animal Cells - A microtubule filaments ring surrounds the cell, creating a cleavage furrow in the center that allows for the pinching in of the plasma membrane and eventual separation into two distinct cells.

Give the formula for mitotic index

Explain what mitotic index is and how it can be used in diagnosis and treatment

Mitotic index is a number between 0 and 1 which indicates the proportion of cells in a tissue that are in mitosis.

Diagnosis - This number can be used to determine whether a tissue is cancerous or not, as the closer it is to 1, the more likely it is that the tissue is cancerous.

Treatment - After surgery has been conducted for a cancer patient, the mitotic index is used to see whether they now have clear margins in the tissue, meaning that the mitotic index is at a level that is safe and not cancer concerning.

Define cyclins

Cyclins are a family of proteins that are involved in the regulation of the cell cycle.

State the purpose of cyclins

They are used to ensure that the correct tasks of the cell cycle are being conducted at the correct times and that the cell only moves on to the next phase when appropriate.

Explain how cyclins control the cell cycle

Cyclins are used to activate Cyclin-Dependent-Kinases, which in turn are able to phosphorylate target proteins in order to achieve a certain criteria of the cell cycle. After the event occurs, the CDK is degraded and rendered inactive once more.

State the role of each of the cyclins and what phase of the cell cycle they have the highest concentration

Cyclin D - Synthesized at the beginning of G1, but does not reach its peak till S phase. It phosphorylates the target protein that is the tumor-suppressor, turning it off and allowing the cell to move from G1 to S phase.

Cyclin E - Synthesized midway through G1, phosphorylating its target protein which prepares DNA for replication, also allowing the cell to move from G1 into S phase.

Cyclin A - *Regulates multiple stages of the cell cycle*
- In S phase, the A-CDK Complex initiates DNA replication and ensures that is it only replicated once per cycle.
- In G2 phase, the A-CDK complex prepares the centrosome (pair of centrioles that are used in the creation of the mitotic spindle) for mitosis.


Cyclin B - It is the trigger into prophase as it phosphorylates a target protein that is essential in the creation of the mitotic spindle.
- Degradation of this cyclin is necessary for the cell to begin anaphase.

Outline the difference between mutagens and carcinogens

Mutagens are environmental factors that cause mutations in DNA. Carcinogens are mutagens that lead to cancer.

Outline the difference between tumour and cancer

A tumour is simply a growth due to uncontrolled cell division, while cancer can occur if tumours metastasize and spread throughout the body, causing abnormalities in the normal functions of organs. Cancerous tumours have the ability to spread to or invade other parts of the body.

Outline the general cause of cancer

Cancer is caused by accumulation of genetic mutations that lead to abnormal cell division and the growth of tumours with the potential to metastasize.

Explain the relationship between oncogenes, tumor suppressor genes and cancer

Proto-oncogenes - Genes that push the cell through the cell cycle. "Code for proteins that stimulate the cell cycle" - If a mutation occurs in this gene, abnormal and excessive cell division will occur, causing the growth of a tumour, which may result in cancer.

Tumor Suppressor - This is a protein which keeps the cell from moving through the cell cycle and dividing when it should not be. "(Tumour-Suppressing genes) code for proteins which stop the cell cycle if a damaged DNA is replicated." - If a mutation occurs, then the cell will divide with this damaged DNA when it should not be, and can lead to a lack of control of the cell cycle, and therefore possibly cancerous tumour growth.

Summarise the development of primary and secondary tumours

Primary tumours occur at the initial site where the abnormal cell growth started. Secondary tumours may happen if cancerous cells from the primary tumour break off and circulate around the body via the bloodstream or penetrating the wall of lymph, thereby entering the lymphatic system. These cancerous cells may invade other tissues and initiate growth at those new sites. This phenonenon, known as metastasis, is what causes the growth of secondary tumours to occur.

Outline the relationship between smoking and cancer

Smoking has been linked with many types of cancer, but the most prevalent of which is lung cancer; There is a strong positive correlation between the level of smoking a person does and the likelihood of them developing lung cancer in the future. There are many chemical compounds in a cigarette, of which more than 60 are known to be carcinogenic. (About 90% of lung cancer patients can attribute their condition to smoking, including second-hand/passive smoking)

Explain the relationship between vitamin D, calcium and rickets/cancer

Vitamin D is essential for the absorption of calcium and phosphorous into the body, two elements which are important for the creation of strong and healthy bones. Rickets and Osteomalacia (two conditions that cause the weakening of bones) may occur if a person does not have enough Vitamin D, and this can be due to a lack of exposure to sunlight.

Osteomalacia (Adults)

disease marked by softening of the bone caused by calcium and vitamin D deficiency

Rickets (Children)

Bones of children are inadequately mineralized causing softened, weakened bones
\= Bowed legs and deformities of the pelvis, skull, and rib cage are common
- Caused by insufficient calcium in the diet, or by vitamin D deficiency

Outline how skin cancer develops

Skin cancer is caused by excess exposure to the sun - While UV light in moderation is beneficial for vitamin D synthesis in the body, it is still a carcinogen which can lead to skin cancer in those who are over-exposed to sunlight.

Definition of hydrophilic and hydrophobic

Hydrophilic - ("water loving") head portions are exposed to water (inside and outside of cell)."

Hydrophobic - ("water fearing") tail portions of the phospholipid are oriented inside the bilayer.

Definition of amphipathic

A molecule that has both hydrophilic (heads) and hydrophobic (tails) regions

Definition of peripheral and Integral

Integral:
- Span the entire membrane (transmembrane proteins are examples)
- Permanently attached to the cell membrane.

Peripheral:
- Not embedded- attached to one surface of the membrane (sometimes attach to integral proteins)
- Attach only temporarily to the cell membrane.

Structure of a phospholipid, including phosphate, glycerol, fatty acid, head, tails, hydrophilic and hydrophobic

Membrane models proposed by Gorter and Grendel

Just a phospholipid bilayer

Membrane models proposed by Davson and Danielli (Sandwich)

It was discovered that the cell membrane is made of both phospholipids and proteins. The cell membrane's phospholipid bilayer is embedded between two layers of proteins.

Membrane models proposed by Singer and Nicolson

Fluid mosaic model, emphasized the dynamic nature of membranes in sharp contrast to the static Davson-Danielli model.

Experimental evidence for the fluid mosaic model of membrane structure, including how we know the membrane is a bilayer with a variety of proteins that can move and are either peripheral or integral

- Freeze Etch Micrographs showed that transmembrane proteins were not accounted for by the Davson Danielli Model of the cell membrane.
- (Structure of membrane proteins) Proteins were able to be extracted and found to be varied in size and shape & proteins were hydrophobic on at least part of that surface. This DID NOT MATCH with D&D's conclusion that proteins would be relatively uniform in shape and hydrophilic in nature.
- (Cell fusion) Red or green fluorescent markers were attached to antibodies that bind to membrane proteins. The membrane of some cells were tagged with red markers and the other cell with green markers. After 40 minutes, they had moved, showing that they had mixed and mingled with each other throughout the cell. IT SHOWED that protein molecules are not fixed in place and can move from one place to another place on the membrane.

Sketch of the cell membrane, including: phospholipid bilayer, integral proteins shown spanning the membrane, peripheral proteins on membrane surface, protein channels with a pore, glycoproteins with a carbohydrate side chain and cholesterol between phospholipids in the hydrophobic region

Primary Function of the Cell Membrane

A semi-permeable membrane that controls the movement of substances in and out of the cell.

Why is it called the FLUID Mosaic Model?

- The phospholipid bilayer is flexible, allows for cellular shape changes.
- Membrane lipids (and some protein) can drift laterally within the membrane
- Individual phospholipid molecules are not bonded to one another
- Proteins drift laterally
- Some membrane proteins are attached to the cytoskeleton and can't move far

Receptor Proteins (Integral or Peripheral)

Communicate signals between the cells internal and external environments.
- A specific molecule will bond and trigger a change inside the cell
EXAMPLE: Insulin receptor protein

Enzyme Proteins (Integral or Peripheral)

Promote chemical reactions that synthesize (create) or break apart biological molecules.
EXAMPLE: ATP Synthase

Adhesion Protein (Usually Integral)

Anchors the cell membrane to other cells (as well as the inner cytoskeleton or proteins outside the cell)
- Can be glycoproteins (proteins with an attached sugar molecule)
EXAMPLE: Cadherins
A type of transmembrane protein.
In the presence of calcium-binds cells within tissues together.

Recognition Proteins (Can be Integral or Peripheral)

- Serve as identification tags on the surface of a cell.
- Often these are glycoproteins (proteins with an attached sugar molecule
EXAMPLE: Major Histocompatibility Complex (MHC) Proteins:

Channel Proteins

- Used for passive (no energy required) transport of large/hydrophilic molecules into and out of cell
- Usually shaped like pores/tunnels
EXAMPLE: Glucose channel protein

Pump Proteins (Only Integral)

- Used for active (energy required) transport of large/hydrophilic molecules into and out of cell
- Usually shaped like pores/tunnels
EXAMPLE: Sodium/Potassium Pump

State function of cholesterol within the cell membrane

A lipid that regulates membrane fluidity by making the membrane less fluid in warm temps & more fluid in cold temperatures.
- It does this by preventing rips and holding together the membrane in hot temps, and spaces the phosphate molecules in cold temps.

In High Temps Cholesterol...

...Holds the Phospholipids together

In Low Temps Cholesterol...

... Acts as a spacer between the phospholipid molecules

Explain why SA:V limits cell size

It needs to stay high so that metabolic/chemical reactions can occur more efficiently. This means that nutrients can be taken in more effectively.

List three adaptations of cells that maximise SA:V ratio

Neurons - Long extensions that increase surface area without a large increase in volume
Red Blood Cells - Having a thin, flat cell shape without large increase in volume.
Microvilli - Projections out of the cell that increases surface area without large increase in volume.

Compare passive and active transport

Passive Transport: Does NOT require energy - goes along along the concentration gradient (high to low --\> equilibrium)

Active Transport: DOES require energy - goes AGAINST the concentration gradient (low to high)

Describe simple diffusion (include the types of particles transported in each)

Over time, the solute will move down its concentration gradient across the cell membrane without using energy.

Describe facilitated diffusion (include the types of particles transported in each)

Facilitated diffusion is the diffusion of an ion through a channel protein, down its concentration gradient, without energy use. Used for small charged molecules (ions).

Describe osmosis (include the types of particles transported in each)

Movement of water from an area of low solute concentration to an area of high solute concentration over time without the use of energy (until equilibrium is reached)

Describe active transport (include the types of particles transported in each)

Particles move against their gradient across the membrane using a protein pump & energy in the form of ATP. Used for large charged molecules.

Define Osmolarity

Osmolarity: The concentration of water in a solution

Define isotonic

Isotonic: Same solute concentration, no net movement.

Define hypotonic and hypertonic

Hypotonic Solution has Low solute concentration, higher water concentration --\> CELL BECOMES HYPERTONIC AND EXPANDS (more water on outside, water wants to move inside)

Hypertonic Solution has Higher solute concentration & lower water concentration --\> CELL BECOMES HYPOTONIC AND SHRINKS (water will want to move outside)

Explain why tissues/organs need to be placed in isotonic solutions

Normal saline is a solution of water and salt ions that is isotonic to human blood. Because the solution is isotonic to body cells, the cells will not shrink or swell when exposed to the solution.

Describe the fluid properties of membranes

1) There is weak to no bonding between phospholipid tails
2) Kinks in the phospholipid tails prevent close packing
3) Cholesterol keeps phospholipids from packing too close or drifting too far apart.

Describe endocytosis (include an example of each)

Process by which cells take in molecules such as proteins by engulfing them.
EXAMPLE: Phagocytosis - white blood cells engulf bacteria during an infection.

Describe exocytosis (include an example of each)

A cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space. An example would be the secretion of neurotransmitter proteins to send signals between neurons.

Structure of an atom (proton, neutron, electron)

An atom is the smallest unit of matter that is unique to a particular element. They are usually electrically neutral because they have equal protons (+) and electrons (-). The neutrons are part of the atomic nucleus, they are neutral. The protons are part of the atomic nucleus and have a positive charge. The electons move around the nucleus in a cloud and have a negative charge.

Atom vs ion

Ions are atoms that are electrically charged because they gained or lost electrons.

Ionic, covalent and hydrogen bonds

Ionic Bond: An atom gives up 1 or more of its electrons to another atom --\> oppositely charged ions attracting to one another


Covalent Bond: Atoms sharing electrons (evenly or unevenly) - ALLOWS FOR HYDROGEN BONDS

Polar vs nonpolar covalent

Polar Covalent Bond: Atoms share electrons unequally, those atoms with greater positive nuclear charge pull move strongly on electrons in a covalent bond.

Structure of water molecule

Each water molecule has two positive ends (hydrogen) and one negative end (oxygen).

Bonding within a between water molecules

Partially positive hydrogen atoms of one water molecule are attracted to the partially negative oxygen atom of another molecule. The bonds are made and broken quickly as molecules move, however the large numbers of bonds contribute to the stability water.

Adhesion vs cohesion and benefit of each to living organisms

Cohesion is the ability of like molecules to stick together, dipolarity means that water will stick to other water molecules via H-BONDS. It explains how wwater molecules can form a chain in delivering moisture to the top of a tree of through the blood stream.

Thermal properties of water that are useful to living organisms (i.e. for habitat temperature regulation and homeostasis)

Ice Floats, Solvent, Cohesion/Adhesion, High Specific Heat, High Heat of Vaporization

Ice Floats

Ice floats and insulates the underlying water so many plants and animals are not frozen.
- Water is less dense as a solid than as a liquid (max density of water occurs at 4 degrees celsius

Water is a near Universal Solvent

Water is the main transport medium for dissolved nutrients. In animals, blood (mostly water) goes through all parts of the body, carrying nutrients. In plants, water carries nutrients up plants and through leaves.
- dipolarity allows water to dissolve molecules that are polar or charged

Cohesion/Adhesion

Cohesion and Adhesion explain how water molecules can form a chain in delivering moisture to the top of a tree or through the bloodstream.

Cohesion:
- Ability of like molecules to stick together
- Dipolarity means water will stick to other molecules via Hydrogen-bonds.

Adhesion:
- Ability of dissimilar molecules to stick together (water w/other molecules)

Cohesion + Adhesion \= Capillary Action, which allows water to flow in opposition of gravitational forces.

High Specific Heat

Contents of cells are unlikely to freeze. Aquatic environments are thermally stable. Organisms have stable internal temperatures when the external temperature is fluctuating.

High heat capacity: takes a large amount of energy to raise the temperature by 1 degree.
- At a cellular level,, water absorbs heat produced by cell processes, regukating the temperature of the cell --\> makes body temperature constant.

High Heat of Vaporization

Organisms rely on energy required for vaporization to remove body heat to remain cool. (evaporative cooling)
- Lots of energy is needed to break hydrogen-bonds.

As the water evaporates, the surface becomes cooler --\> allows organisms to cool through sweating.

Types of molecules that water will and won't dissolve

Water can dissolve any substance that contains charged particles (ions) or electronegative atoms (polarity)

Glucose (Hydrophilic): Due to its ability to dissolve in water, it WILL dissolve in blood plasma and CAN be transported to the cells of the body via the blood plasma.

Sodium Chloride AKA Salt (Hydrophilic): Sodium and Chlorine ions are FULLY SOLUBLE in water and ARE able to travel through the blood plasma throughout the body.
Amino Acids (Variable): They are SOLUBLE, and CAN be transported via the blood plasma.

Oxygen (Hydrophobic): Dissolves in water SPARINGLY (non-polar). and therefore most DOES NOT EASILY DISSOLVE in the blood plasma and needs to be transported via hemoglobin.

Cholesterol & Fat (Hydrophobic): Non-polar molecule that DO NOT dissolve in water, and therefore need to be transported using molecular 'sacs'.

Why solvency is important to life

It allows the blood to transport nutrients inside of the blood plasma.

(Also, most of the cytosol is water, and this is where the metabolic reactions necessary for the functions of life occur)

how to identify molecules as hydrophilic or hydrophobic

If it is facing away from water, it is hydrophobic. If it is touching water, it is hydrophilic.