highschool/Grade 10/Science/SNC2DZ/Unit 2: Biology.md

Unit 2: Biology

A person contains roughly 100 trillion cells - Cells are roughly 20 μm (micrometre, 10^-6 m), around 250 cells / cm

Cell Theory

1. All living things are composed of cells
2. Cells are the basic units of living organisms
3. All cells came from pre-existing cells

Eukaryotic versus Prokaryotic Cells

Prokaryotic cell: Meaning before/lacking nucleus

Eukaryotic cell: Means complete nucleus

Factors	Prokaryotic	Eukaryotic
DNA	In nucleoid region	Usually in membrane-bound nucleus
Size	Usually smaller	Usually larger
Organelles	Not membrane-bound, smaller	Membrane-bound, more complex
Organization	Usually singlecelled	Often form multicellular organisms
Metabolism	May not need oxygen	Usually need oxygen

Organelles

Cell Membrane

• Controls what substances enter/leave the cell selectively via various receptors/osmosis
  • Allows nutrients to enter
  • Allows waste products to leave (removal of waste)
• Surrounds and holds other organelles in cell
• Interact with outside chemicals (e.g., hormones)
• Transports food and nutrients into the cell

Nucleus

• Is the control center of the cell
• Holds deoxyribonucleic acid (DNA) in form of chromatin
  • DNA is a double helix containing genes
    • Genes: any section of DNA that contains a full set of instructions to make either RNA or a protein, found in nucleus
  • Chromatin: is DNA wrapped tightly in protein
• Chromosomes: are even more tightly wrapped chromatin used in cell division only, formed when DNA condenses in mitosis
• Surrounded by a double membrane
• Substances enter and exit the nucleus via nuclear pores. Nuclear pores are holes in the membrane that allow proteins and nucleic acids into the cytoplasm
• Messenger RNA (mRNA) is encoded from DNA and sent to ribosomes to produce proteins
• Humans have ~2 meters of genes per cell per nucleus tightly wrapped

Nucleolus

• Dense region of DNA located in the nucleus
• This area of DNA is specially for ribosomal DNA (rDNA), or DNA used to code ribosomes, enzymes that assemble proteins
• Produce “large” and “small” subunits of ribosomes, which either form complete ribosomes in cytosol or mix with endoplasmic reticulum, forming rough endoplasmic reticulum (RER)

Cytoplasm & Cytosol

• Cytosol is the fluid cells contain
• All organelles are suspended in cytosol
• Cytoplasm is the cytosol along with everything in a cell, excluding the nucleus

Endoplasmic Reticulum

• The endoplasmic reticulum is a network of tubules and flattened sacs with a rough appearance because of the presence of ribosomes on the surface
• Network of tubules and flattened sacs
• Transports proteins via cytoskeleton in vesicles

Specific to Rough ER

• Appears “rough” due to the ribosomes attached to its outer surface
• Located directly adjacent and attached to nucleus
• Located next to Golgi apparatus
• Ribosomes in rough ER synthesize proteins
  • Transports synthesized proteins to Golgi apparatus for packaging and distribution
  • About half the cell’s proteins are produced here
• Folds, fixes and modifies both newly-created and pre-existing proteins somewhat like proof-reading

Specific to Smooth ER

• Does not synthesize proteins
• Appears “smooth” due to lack of ribosomes
• Located directly adjacent and attached to nucleus
• Synthesizes lipids (fats, e.g., cholesterol)
• Metabolises carbohydrates

Golgi Apparatus

• Also known as Golgi body, Golgi complex, etc.
• Receives, modifies and transports proteins that were produced by the rough ER
• Packages proteins into vesicles and sends them cell membrane for export

Lysosome

• Spherical vesicle that containing enzymes
• Digests and kills foreign matter which is then excreted
  • E.g., white blood cells use lysosomes to kill bacteria then spit it out
• Digests and breaks down old and unused material/non-functional organelles as needed
• If lysosome ruptures everything dies, hence they are known as “suicude sacs”

Mitochondria

• Singular form is “mitochondrion”
• Contains an inner and outer membrane
• Processes glucose + oxygen gas to form carbon dioxide + adenosine triphosphate (ATP)
  • ATP allows proteins to do things (e.g., spend 1 ATP break 1 molecule)
  • ATP cannot be stored
  • ATP is needed for daily function of the cell

Cytoskeleton

• Made of protein filaments
• Maintains and changes cell structure, much like a human skeleton + muscular system
  • Moves cells
  • Modifies and adjusts cell structure as needed
• Chemicals can travel along cytoskeleton, e.g., organelles, vesicles, etc.

Organelles specific to animal cells

1. Centrioles and centrosomes
2. Lysosomes

Centrosomes

• Made of same protein as cytoskeleton
• Crucial to mitosis in animal cells
• Create and manipulate spindle fibres during mitosis in animal cells

Lysosomes

• Explained before.

Organelles specific to plant cells

1. Cell wall
2. Chloroplast
3. Central Vacuole

Cell wall

• Provides structure and prevents cell rupture
• A more stronger, thicker, rigit version of the cell membrane
• Made of cellulose (type of sugar)
• Also present in most bacteria, fungi, and protists
• The antibotic penicillin works by destroying the cell walls of bacteria, killing it

Chloroplast

• The solar panel of the plant cell
• Conducts photosynthesis
• All chlorophyll is located in chloroplasts
• Looks green
• Parts of the plant that do not photosynthesize do not have chloroplasts

Central Vacuole

• Extremely large, may take up to 90% of volume in cell
• Contains water
• Maintains turgor pressure against cell wall (pushes against cell wall in all directions)
• Maintains cell shape and resistance
  • Plant cells that lack turgor pressure (e.g., celery left in fridge) become flaccid

Cell Division

Purpose

1. Reproduction

• Single-cellular organisms reproduce via division asexually
• Multicellular organisms reproduce via combining two germ cells (“sex cells”) that contain half the DNA each of two organisms
  • This is sexual

2. Growth

• Cells have maximum size before transportation of substances within cell becomes inefficient, due to larger cells decreasing efficiency of diffusion
• Cells transport chemicals (e.g., nutrients) via diffusion, this limits cell size
• The only way to maintain proper function and get bigger is to add more cells

3. Repair

• Organisms need to repair cells to stay alive and maintain proper health
• Millions of cells are replaced everyday
• Cells naturally die and need to be replaced
  • e.g., red blood cells, hair cells, skin, injuries, broken bones

Cell cycle

• Interphase
  • Large majority of a cell’s time is spent in interphase
  • G1: (normal growth and function),
  • Prepare for cell divison
  • S: Replication of DNA
  • G2: Replication of organelles
  • Checkpoints
    • Cells check various things before progressing through various stages in interphase
    • Causes of stopping via checkpoints include damaged DNA, not replicated DNA, lack of nutrients for cell growth, and/or signals from other cells
• Mitosis
  • Occurs only in eukaryotic cells
  • P-MAT: Prophase, Metaphase, Anaphase, Telophase
  • Division of the nucleus
• Cytokinesis
  • cell division
  • The parent cell splits into two daughter cells
• G0
  • Cell no longer divides (“cell cycle arrest”)
  • Outside of cell cycle

Mitosis

• Chromatid: Supercoiled DNA, only visible during mitosis, cannot be read without unwinding, similar to compressed zip file
• Chromosome: Two identical “sister chromatids” held together in centre by centromere, or one sister chromatid after anaphase
• Centromere: Proteins sticking sister chromatids
• PMAT (prophase, metaphase, anaphase, telophase)
• Division of the nucleus

Phase	Diagram	Description
Prophase		- Chromatin condenses into two identical sister chromatids which condense into chromosomes - Happens to 23 pairs of chromosomes - Nuclear membrane dissolves - Centrosomes move to opposite ends (poles) of cell, creating spindle fibres that begin to attach to centromeres in animal cells
Metaphase		- Chromosomes line up in centre of cell to ensure they divide evenly - Everything in prophase has completed (e.g., nuclear membrane has dissolved completely)
Anaphase		- Centromeres split, separating sister chromatids - Sister chromatids are pulled towards opposite sides of cell via shortening spindle fibres - Sister chromatids are now called daughter chromomsomes
Telophase		- Effectively opposite of prophase - Nuclear membranes form across each of the two new nuclei - Daughter chromosomes unwind into chromatin and are no longer visible - Nucleolus forms in each nucleus - Spindle fibres break apart - Cytokinesis usually begins in telophase - Cells starts to cleave (cell centre starts to pinch itself)

Cytokinesis

• Cell division
• Cell splits completely to two daughter cells
• In animal cells: Cell membrane pulled inward by cytoskeleton
• “Pinches in” along equator of cell, forming “cleavage furrow”
• In plant cells: Golgi apparatus produces and sends vesicles to centre of plant cell “cell plate” to make new cell wall and membrane between daughter cells

Cell Specialization

• Zygote: A single-celled organism formed from the fertilization of an egg by a sperm cell, is a totipotent stem cell
• A cell’s position in the gastrula (outer, middle, inner layer) will determine the fate of the cell, or its potiental.
• Chemical signals from other cells will also determine activated genes that lead to specialisation
• (LOCATION LOCATION LOCATION!)
• Specialisation is determined by reading only certain genes

Stem Cells

• Unspecialized cells with the potential to become one of several types of cells.
• Can either divide to two stem cells or one stem cell and one specialised cell
• Specialised cells generally do not divide

Type of Stem Cell	Obtaining	Potential	Pros	Cons
Totipotent	Morula (16-cell ball) 3-4 days after lab-fertilised zygote	Unlimited	Unlimited potential, does not initiate immune response	Ethical concerns of destroying fertilized embryos
Pluripotent	Blastocyst (200-300 cell ball) 4-7 days after fertilisation	Nearly unlimited	Nearly unlimited potential, no need to create new embryo as most are taken from discarded in vitro fertilisation	Ethical concerns of destroying embryos, greater chance of initiating immune response
Multipotent	Adult stem cells	Limited to cells of their group/organ/location (e.g., blood stem cells to red blood cells, white blood cells, etc.)	Easy to harvest, easy to find	Immune response, limited potential
Induced pluripotent	Multipotent stem cells	Reprogramming multipotent stem cells using embryonic genes using a virus	Same as pluripotent	Does not require new embryos, immune response not expected, high potential

Potential uses of stem cells

• Studying cell growth and function
• Testing drugs on specific target cells
• Lab-grown meat for vegetarian purposes
• Regenerative medicine to replace tissues (e.g., blindness, bone marrow transplant, cancers, limb regrowth)

Telomeres

Cancer

• Group of diseases that involve out-of-control cell division which may spread throughout the body
• Tumour: Uncontrolled lump of cells that do not perform normal cellular functions
• Benign: Describing a tumour that does not metastasise or interfere with normal cell function (harmless, non-cancerous)
• Malignant: Describing a tumour that does interfere with normal cell activity and metastasise
• Carcinoma: Cancerous/cancer
• Metastasis: Primary (original) tumour spreading throughout the body to create secondary tumours
• Carcinogens: Anything that can cause cancer, e.g., chemicals, radiation/energy, some viruses
• Neoplasm: A solid or fluid-filled sac that is formed by uncontrolled cell growth (e.g., tumours)
• Random mutations can also lead to a cancer cell due to irregular DNA replication
• Generally, multiple mutations in several key genes are required for a cell to become cancerous
• Cancer is not contagious, neither can it be inherited
  • A genetic predisposition to cancer can be inherited
• By the time cancer is detected, it can contain millions of cells that have been growing for years

Cancer screening

• PAP smear for cervical cancer
• Mammogram for breast cancer
• Colonoscopy for colorectal cancer
• PSA blood test for prostate cancer

Cancer diagnosis

• Endoscopy (using a flexible camera with tissue extractor to search for cancers of the respiratory and/or digestive systems)
• X-rays
• Ultrasounds for soft tissues
• CAT/CT scan (more x-rays)
• MRI scan (uses radio waves and magnetic fields)

Cancer treatments

• Surgery
  • Physically removing tumour with stabby things
  • Ineffective if cancer has metastasised
  • If even one cell escapes the stabby cancer can regrow
• Radiation therapy
  • Blasting radiation at tumours so that their DNA becomes so damaged that DNA replication, and, as a result, cell division is impossible
  • Can harm neighbouring cells
  • Ineffective if cancer has metastasised
• Chemotherapy
  • Blasting drugs that kill dividing cells
  • Does not feel very good for the patient
  • Fast-growing cells may die off (e.g., hair, skin cells)
• Biophonics
  • Using light beams to detect and treat cancer

Organ systems

Business model for organ/organ systems

Business thing	Corresponding organ/organ system
Management	Central nervous system (brain)
Messaging	Endocrine + peripheral nervous systems
Workplace	Body
Transport	Circulatory, digestive, urinary systems (internal, import, export, respectively)
Storage	Fats
Cash flow	Digestive + respiratory systems
Security	Immune + integumentary (skin) systems
Workers	Cells + muscular system

Tissues

• Tissues: Different cell types grouped together performing the same task
• Organisms have a hierarchical organisation
• Basic tissues: Connective, muscle, nervous, and epithelial tissues
• Epithelial tissue
  • Tightly packed cells that line body surfaces, e.g., skin
• Connective tissue
  • Produces collagen fibres that support organ structures and bone, e.g., ligaments (bone -> bone), tendons (muscle -> bone)
• Muscle tissue
  • Fibrous tissue that can be subdivided into cardiac (heart), smooth (digestive), and skeletal (voluntary) muscle tissues
  • They contract
• Nervous tissue
  • Responds to external/internal stimuli, e.g., brain, nerves

Digestive system

• Two types of digestive systems
• Bag digestive system
  • One way in, same way out (e.g., coral, jellyfish)
• Tube digestive system
  • One way in, another way out (e.g., worms, humans)
  • Mouth -> esophagus -> stomach -> small intestine -> large intestine -> rectum -> anus all part of the tube
  • Gallbladder, liver, salivary glands, and pancreas produce digestive enzymes/juices in humans
  • Process of eating food: Ingestion (eat) -> digestion (physical and chemical breakdown) -> absorption (of nutrients to bloodstream) -> egestion (poo)
  • Flies digest before ingesting
  • Jujunum: Centre of small intestine
  • Duodenum: Beginning of small intestine
  • Ileum: End of small intestine
  • Rectum: Holds waste to be excreted voluntarily
  • Anus: Controls waste to be defecated voluntarily
  • Appendix: Used to be used to digest plant matter, now virtually useless in humans
  • Gallbladder: Stores and secretes bile as buffer between liver and small intestine that helps break down fats (lipids)
  • Ruminants: Herbivores that digest food using a chambered tube
    • Chew -> Reticulum and rumen (first and second stomachs) -> regurgitate and rechew -> Omasum (third stomach) -> Abomasum (fourth stomach) -> small intestine -> large intestine -> waste
  • Eoprophagy: Consumption of feces

Human digestive system

• Mouth ingests food
• Teeth, tongue, and salivary glands work to begin digestion
• Esophagus squeezes food down in waves (peristalsis) down its smooth muscle tube
• Stomach
  • Mixes hydrochloric acid with digestive enzymes to break down food
    • Hydrochloric acid is diluted and does not break down the food itself much, enzymes are more effective at a lower pH
  • Liquifies food and kills bacteria
  • Goblet cells produce mucous, which lubricates the stomach and intestines, protecting the stomach
  • Made of smooth muscle to churn food, somewhat like cooking with enzymes or a washing machine
• Intestines
  • Pancreas makes most digestive enzymes and pumps them in the duodenum
  • Absorbs nutrients and water to bloodstream
  • Forms and excretes feces
  • Contains smooth muscle to continue peristalsis
  • Contains plenty of blood vessels for faster nutrient absorption
  • Intestinal epithelium
    • Optimised for surface area
    • Folds contain villi (singular, “villus”)
    • Villi contain capillaries and absorbing and goblet cells
    • Absorbing cells caintain microvilli, which absorb nutrients via diffusion

Respiratory system

• Exchanges oxygen gas and carbon dioxide gas between red blood cells and the surrounding air, which is required for cellular respiration
• Diaphragm contracts to lower itself, causing the rib cage to rise, which increases lung volume, which subsequently causes pressure to decrease and air to rush in to the lungs
  • Diaphragm relaxes to return everything to its normal position
• Air is warmed and moisted while passing through nasal cavity blood vessels
• Trachea and bronchi are made of rigid cartilage rings
  • Prevents airways from closing, similar to a vacuum hose
• Respiratory epithelium
  • Contains goblet and ciliated cells
  • Cilia: Singular “cilius”, sweep mucous out of the lungs and throat
  • Nose hairs and mucous trap debris which is swept out by cilia
• Alveoli (singular “alveolus”) epithelial tissue is one cell thick
  • Surrounded with capillaries which exchange gases via diffusion
• Trachea -> 2 bronchi -> bronchioles -> alveoli
• Gas exchange
  • Swapping of carbon dioxide and oxygen gas between the bloodstream and the environment (e.g., red blood cells and alveoli)
  • A large surface area, thin membrane, and moisture are all required for optimal gas exchange
  • Alternate gas exchange systems include
    • Fish using a constant water flow forcing dissolved oxygen through their gills
    • Gills stick together out of water, resulting in suffocation
    • Frogs use lungs on land, but can also perform gas exchange underwater using their skin

Circulatory system

• Interacts with literally every other system
• Carries oxygen and nutrients to cells, carries carbon dioxide and waste away

Components

• Composed of heart, arteries, veins, and capillaries
• Arteries flow away from the heart
  • Made of thick muscle layers and elastic connective tissue
  • Muscle layers must withstand and maintain higher blood pressure throughout body due to proximity to heart
  • May vasoconstrict or vasodilate to increase or restrict blood flow, for example, to blush or to pale, respectively
• Veins flow to the heart
  • Made of thin muscle layers and elastic connective tissue
  • Carries low pressure blood with valves to ensure one-way flow
  • Blood moves by movement of skeletal muscles pushing blood
• Capillaries are one cell thick
  • They transition between arteries and veins
  • Blood cells are forced to go in single file
  • Present, amongst other places, in alveoli and villi
• The heart pumps blood throughout the body
  • Has one-way valves
  • Has four chambers, two atria (sing. atrium) and two ventricles
    • Blood is returned to atria which push them to ventricles which push them out of the heart
  • Right side of heart receives and sends deoxygenated blood to lungs
  • Left side of heart receives and sends oxygenated blood from lungs
• Invertebrate circulatory systems are either open or closed (douse everything with blood then collect or use vessels like we do, respectively)
• Most invertebrates have an open circulatory system

Myocardial infarction

• Also known as heart attack
• When atherosclerosis occurs in coronary arteries (when fatty plaque deposits build up in arteries feeding the heart)
• If clots break open a larger clot forms over it
• This repeats until the artery is completely blocked, leading to death of cardiac muscle cells
• Caused by lifestyle choices, although predisposition can be increased due to genes

Blood

• Composed of red blood cells, white blood cells, platelets, and plasma
• Red blood cells: Biconcave discs carrying oxygen and carbon dioxide to and from cells, respectively, using hemoglobin
  • Denucleated, instead packing as much hemoglobin as possible inside
  • Hemoglobin and oxygen give them their colour
• White blood cells: Part of the immune system, they neutralise and remove foreign threats
  • Can make antibodies
  • Can engulf and kill pathogens
  • 700:1 ratio of red blood cells to white blood cells
• Plasma: Clear fluid made of 90% water filled with proteins and dissolved nutrients
• Platelets: Irregular colourless “bodies” that form fibrous clots

Immune system

• Pathogens: anything that cause disease
  • Pathogen waste can be toxic which cause symptoms of disease
• Passive defense
  • Skin - physical barrier
  • Sweat/tears - lysozymes kill bacteria
  • Stomach acid - it’s acid dangit acid kills things
  • Beneficial bacteria overpopulate surfaces to prevent harmful bacteria from settling
• Adaptive defense
  • White blood cells: For the sake of G10, divided into two subtypes:
    • Cells that engulf and consume bodies (phagocytes, e.g., macrophages)
    • Cells that produce antibodies (plasma B cells, i.e., plasma B cells)
  • Antibodies: Secreted proteins that stick to a specific molecule found on pathogens
    • Clumps pathogens together for simple cleanup and prevents them from spreading
    • Covers and prevents toxins from reacting
    • Acts as a flag for phagocytes to destroy marked pathogen or toxin
• Acquired immunity
  • After initial immune response, antibodies are still produced for that type of pathogen
  • Once pathogen is detected again, “memory cells” reactivate and kill things faster
  • Much faster than initial response, typically resulting in no symptoms
  • This is why you generally can never be sick from the same pathogen twice
  • Pathogens mutate (e.g., influenza) so that they are no longer recognisable by antibodies
• Vaccination: Injecting a small amount of a dead/weakened version of pathogen giving acquired immunity without actually getting disease
  • There may be mild side effects
  • Boosters are required for some vaccines as “memory” fades over time (e.g., tetanus)
  • Herd immunity: When enough of the population (90% in general) is immune to a disease, drastically reducing rate of disease even amongst those not immune
    • Those who cannot be vaccinated for whatever reason are protected due to a far lower chance of encountering the disease itself
  • Prevention (vaccine) > cure (treatment)
  • Chance of disease from the vaccine are far lower than chance of death or serious infection from a pathogen
  • Vaccines do not cause autism or seizures, but may act as a trigger for the latter due to genetics

Musculoskeletal system

• Maintains structure
• Protects other systems and cells
• Enables movement
• Four types of connective tissues: Ligaments, tendons, bones, and cartilage

Bone	Information	Location
Clavicle	Collarbone	Collar
Humerus	Funny bone	Lower upper arm
Femur	Largest bone	Thigh
Tibia	One of two bones in lower leg	Front lower leg
Vertebrae	Enable spinal movement	Spine
Patella	Prevents leg overextension and protects knee join	Kneecap

Bones

• Hard and dense
• Bone cells produce minerals (e.g., phosphorus + calcuium) and collagen
  • Minerals for strength, collagen for flexibility
• Bone marrow produces blood cells
• Contain blood cells

Joints

• Anywhere where two bones meet
• Types of joints
  • Hinge joint (e.g., knee, elbow)
  • Ball and socket joint (e.g., Hip, shoulder)
  • Fixed (e.g., skull, pelvis)
• Ligaments connect bones across joints
• Cartilage cushions bone on each side of joint and allows for smooth motion

Skeletal Muscle

• Made of striated muscle fibres of long cells
• Voluntary muscles, receive signals from brain via nerves
• Always come in pairs as any muscle can only pull, not push
• Must be attached to two bones in order to move a bone

Nervous System

• Coordinates body activities
• Central nervous system: Brain + spinal cord
• Peripheral nervous system: All other nerves connecting everything to spinal cord/brain
• Neurons send electric signals down their singular long axon branch thing
  • They accept signals from dendrites on the main cell body
  • Schwann cells form the myelin sheath to insulate and nurture the axon, protecting it from interference
  • Neurotransmitters are chemical signals that transmit information between neurons
  • Electrical signals tell chemical signals to go to other neurons
• Nerves
  • Bundle of axons
  • Surrounded with blood vessels and connective tissue
  • Nerve signals are short-lived, fast, and targeted towards specific groups of cells

Disorders

• Parkinson’s disease
  • Loss of brain neurons that send neurotransmitters to muscles
  • Leads to muscular and mental decline
• Multiple sclerosis
  • Immune system attacks myelin sheath
  • Disruption of neurons’ electric signals due to lack of protection
  • Causes spasms and loss of muscular control
• Alzheimer’s disease
  • Protein deposits (plaque) build up in brain tissue
  • Leads to memory loss and total system failure

Endocrine System

• Coordinates organ functions
• Hormone chemical signals produced by endocrine glands that, compared to nerve signals, are long-lasting, slower, and general
• Specific hormones bind to specific receptors on specific cell membranes (e.g., mailing lists)
• Hormones travel through the bloodstream
• Hormones either encourage or discourage activity
• Can cause positive or negative feedback loops with glands

Endocrine organ	Purpose	Location
Pituitary gland	Controls growth and development	Brain
Pancreas	Secretes insulin to ensure sugar in bloodstream is taken in by cells	Attached to duodenum
Gonads (ovaries + testes)	Secretes the reproductive hormones testosterone and estrogen, respectively	Lower abdomen
Adrenal glands	Control stress response, secrete adrenaline (fight/flight response)	Above kidneys

Disorders

• Type 1 diabetes: The pancreas is unable to produce any insulin, resulting in high blood sugar
  • Generally caused by genetics
• Type 2 diabetes: The pancreas produces not enough insulin and/or cells are resistant to it, resulting in high blood sugar
  • Generally caused by lifestyle choices (e.g., diet)
• Growth disorders (dwarfism/gigantism)
  • Caused by poor pituitary and/or hypothalamus function or endocrine gland damage as an adult