BIOLOGY 1 - Biomolecules:

-Amino Acids Proteins

BIOLOGY -Monosaccharide Carbohydrates
– The study of LIFE -Fatty Acids  Lipids
Biological Applications: -Nucleotides  Nucleic Acid
- Medicine -Organismal Level:
- Food Production
- Natural Products
- Environmental Preservation
- Conservation
- Biological Warfare

LIFE *Ecological level – an organism is part of a

- The particular set of processes that result from
the organization of matter
- life can only be defined based on what living
things ARE, what they’re MADE UP of, what
they DO, and where they COME FROM.
- Can be recognized based on what living things
do
- No single definition
- The chemical building blocks of life:
-Tissue  Organ  Organ system  Organism
population
Organism  Population  Community 
Ecosystem  Biosphere
- The order exhibited in living things opposes the
force of entropy
- Life’s organizational hierarchy gives rise to
emergent properties
- Emergent Properties: Properties in higher levels
of organization that are absent among its
individual components
- Producing and maintaining order requires
energy

2.) Energy Processing

- Source(/s) of energy : Sunlight
- Organisms take in energy and transform it to do
work
- Life requires energy input for:
- Regulation
- Catabolic processes require energy - Growth
- Anabolic processes release energy - Movement
- - Excess energy goes into: reproduction
Properties of life (common to living things):
1.) Order - When there are scarce resources of energy,
- living things have a complex organization behaviour is limited to conserve energy for
-Life is highly organized growth and movement
- Cellular level:
3.) Regulation
- Energy utilization
- Requires internal control
*Homeostasis – any self-regulating process by
which biological systems tend to maintain
stability while adjusting to conditions that are
optimal for survival.
Ex. Optimal temperature
Regulated blood sugar level

Atom  Molecules  Biomolecules  Organelle  Cell 4.) Response and Movement

 - Living organisms respond to environmental - Uses specific observations to develop
stimuli (irritability lol) general conclusions
Ex. The Auxin Hormone in plants allows for stem
elongation (it’s why the plants get bendy) Scientific process:
- For self-preservation - Observation
- Of a process or phenomenon
5.) Reproduction - Hypothesis
- Organisms produce their own kind - Guess concerning observation
- Life can reproduce itself - May have multiple hypothesis
-Genes replicate - Prediction
-cells divide - Expected consequence of a hypothesis
*in the case of unicellular organisms, - Experiment
reproduction is by binary fission or - Test hypothesis
mitosis  Controlled Experiment: all the
variables are constant
6.) Growth and Development - Conclusion
- Growth is the increase in size - Drawing a conclusion from the results
- Increase in cell size and number - Reject or Fail
- Development involves differentiation and
specialization Theory
- Heritable programs or DNA direct pattern for - Set of hypotheses that have been thoroughly
growth and development tested over time
- Is generally accepted in the scientific
7.) Evolutionary Adaptation community
- Life varies and evolves - Acceptance is “provisional”
*Evolution: unifying concept in biology - Theory =/= hypothsis
Special creation  evolution
Theories on the origins of life
Physical entities with some of the characteristics of 1.) Abiogenesis or Spontaneous generation
Living Organisms: - Life was created spontaneously from
1.) Viruses nonliving or inorganic matter
- Obligate intracellular parasites - Aristotle- thought that some of the
- Made up of nucleic acid enclosed in a protein simpler invertebrates could arise from
coat abiogenesis
- Sometimes wrapped in membranous envelope - Ex. Maggots were thought to arise
2.) Viroids spontaneously but was refuted in
- Plant pathogens Francesco Redi’s experiment
- Composed of molecules of naked RNA only - Louis Pasteur conducted broth
several hundred nucleotides long experiments that refuted this theory
3.) Prions 2.) Biogenesis
- Infectious form of protein - Rudolf Virchow
- Increases by converting other protein into new - Simple or complex organisms can only
prions come from pre-existing organisms
- Doesn’t answer the question of where
Scientific Method life came from
3.) Special Creation
Ways of formulating a hypothesis: - Life on earth was created by some
- Deductive Reasoning supernatural force or being
- Examining individual cases by applying - Based on faith
accepted general principles - Cannot be tested in a lab or be
- General principles  Specific subjected to scientific inquiry
predictions 4.) Panspermia or Interplanetary (cozmoic)
- Inductive Reasoning theory
 - Life originated from a distant planetary
body
- Such an origin gives a greater timespan
for early evolution than has been
available on earth
- Applied to the possible dispersion of life
throughout the galaxy
- Directed Panspermia  deliberately
planted on earth
- Europa (Jupiter’s Moon)
- Mars
5.) Biogeochemical theory
- Life may have originated or evolved
from inorganic matter
- Between 4 billion years ago when the
crust started to solidify, and 3.5 billion
years when stromatolites appeared, the
first organisms came into being
- Physical and Chemical Processes in the
Earth’s primordial environment
eventually led to the formation of life
- Four stages:
1.) Abiotic synthesis of small inorganic
molecules
2.) Small molecules join together into polymers
3.) Origin of self-replicating molecules
4.) Packaging of these molecules into
“protobionts”
- Rotobionts
 Self assembling biomolecules
 Living cells may have arisen
from them
Limitations of origin of life hypothesis:
- No definitive proof
- Only describes what could have happened
Cellular function:
- DNA
- Stores information
- No catalytic action
- Very stable
- RNA
- Replicates
- Contains (less) information
- Has catalytic action
- Protein
- Carries out chemical reactions
- No means for replication
The Cell
Common ancestors of all life:
- Bacteria
- Archaea
- Eukarya
The cell
- Basic unit of life
- Exhibits all life properties
- Comes only from pre-existing cells
- Possesses an evolutionary identity
Cell theory
- Matthias Schleiden and Theodor Schwann
- All organisms are composed of smaller units of
organisms called cells
The importance of cells:
- All organisms are made up of cells
- It is the simplest collection of matter that can be
alive
- Cell structure is correlated to cellular function
- All cells are related by their descent from earlier
cells
Basic Features of ALL cells
- Plasma membrane
- Cytosol – a semifluid substance
- DNA (chromosomes – carry genes)
- Ribosomes (make protein)
2 Basic cell types
- Prokaryotic cells
- NO NUCLEUS
- DNA is found in an unbound region
called the nucleoid
- No membrane-bound organelles
 - Cytoplasm is bound by plasma - Continuous with the nuclear membrane
membrane - SMOOTH ER
- Energy sources  Produces membranes, proteins,
- Organotrophic and lipids
 Feeds on organic matter  Metabolizes carbohydrates
- Phototrophic  Detoxifies drugs and poisons
 Utilizes light energy to  Stores calcium ions
synthesize organic matter - ROUGH ER
- Lithotrophic  Produces protein with
 Uses inorganic substrate to ribosomes
obtain reducing equivalents for  Has bound ribosomes
use in biosynthesis  Distributes transport vesicles
- Eukaryotic cells  Membrane factory of the cell
- DNA in a nucleus, bounded by a - Golgi Apparatus
membranous nuclear envelope - Shipping and receiving
- Membrane bound organelles - Modifies and sorts proteins from ER for
- Cytoplasm is between plasma transport
membrane and nucleus - Vacuoles
- Larger cells (require more energy) - A plant cell or fungal cell may have one
- May have originated as predators or several vacuoles
- Nucleus - Derived from the endoplasmic
- Contains DNA reticulum and golgi apparatus
- Site for DNA replication and RNA - My function in digestion, storage, waste
synthesis disposal, water balance, cell growth,
- Nuclear membrane and protection
- Nucleolus – ribosome production - Different kinds:
- Nuclear lamina – composed of protein,  Food vacuoles- formed by
maintains shape of nucleus phagocytosis
- Pores – regulates the entry and exit of  Central Vacuole- in plants
molecules from the nucleus  Contractile vacuole – pumps
- Ribosomes water out of cells; in protozoans
- Particles made of ribosomal RNA and - Plasma membrane
protein - Selective barrier that allows for the
- Involved in protein synthesis (in two passage of oxygen, nutrients, and waste
locations)  Phospholipids
 Cytosol (free ribosomes)  Proteins
 Outside of the endoplasmic  Carbohydrate side chain
reticulum or the nuclear - Passive transport
envelope (bound ribosomes)  Flows from higher to lower
- Endomembrane system concentration
- Regulates protein traffic  Diffusion
- Perform metabolic functions in the cell o Hydrophobic
- Components: molecules
 Nuclear envelope  Facilitated diffusion
 Endoplasmic reticulum o Polar molecules
 Golgi apparatus - Active transport
 Lysosomes  Energy is needed to transfer
 Vacuoles against the concentration
 Plasma membrane gradient
- These components are either continuous or - Lysosomes
connected by vesicles - Digestive compartments containing
- Endoplasmic reticulum hydrolytic enzymes
- Biosynthetic factory
 - Can hydrolyze proteins, fats, - Grows and produces independently within the
polysaccharides, and nucleic acid cell
- Phagocytosis – cells engulfing other Other parts:
cells forming food vacuoles - Peroxisomes
- Autophagy – using enzymes to recycle - Converts hydrogen peroxide (by
the cell’s own organelles and product of aerobic respiration) into
macromolecules water
- Breakdown of fatty acids to smaller
Similarities of Mitochondria and Chloroplast with molecules
Bacteria: - Cytoskeleton
- Enveloped by a double membrane - A network of fibers extending
- Contains free ribosomes and circular DNA throughout the cytoplasm
molecules - Organizes the cell’s structure and
- Grow and reproduce somewhat independently activities
in cells - Anchoring organelles
- Maintains cell shape
Endosymbiotic Theory - Separates chromosomes in mitosis
- Involved in cell mobility
Cell wall of plants
- Extracellular structure that distinguishes it from
animal cells
- Protects, maintains the shape, and regulates the
intake of water
- Made of cellulose fibres
- Prokaryotes, fungi, and some protists also have
cell walls
- Parts:
- 1st wall – primarily cellulose
- 2nd wall – cellulose + lignin suberin cutin
- Middle lamella – outside cell wall
Extracellular matrix (ECM)
Possible origins of mitochondrion - Animal cells don’t have cell walls but have this
- Rickettsia Prowazekii instead
- Aerobic bacteria - Made up of collagen, proteoglycans, and
- Something here intayin mo slides ni sir fibronectin
- Functions
Mitochondria - Support
- Chemical energy conversion - Adhesion
- Site for cellular respiration - Movement
- In nearly ALL eukaryotic cells - Regulation
- Has outer and inner membrane folded into the
cristae
- Inner membrane: Cell Division
- Intermembrane space In unicellular organisms
- Mitochondrial matrix - Means of reproduction
- Cristae presents a large surface area for
enzymes that synthesize ATP In multicellular organisms
Chloroplasts - Growth and repair cells
- Capture of light energy - Responsible for the continuity of life
- Contains chloroplast and other molecules that
function in photosynthesis The cell cycle
- Maintains an autonomy compared to to other - Consists of
cellular compartments
 - Interphase – cell growth and copying of Meiosis
chromosomes in preparation for cell - Formation of gametes
division - Second round of division
 About 90% of the cell cycle - Takes place in two sets of cell divisions
 Parts
 G1 phase (first gap)
 S phase (synthesis of
DNA – replication)
 G2 phase (second gap)
- Mitosis (M) phase – mitosis and
cytokinesis
 Mitosis- Mitotic Nuclear
division
1.) Prophase – condensation of chromosomes
2.) Prometaphase – nuclear membrane
disintegrates
- Microtubules attach to sister
chromatids
3.) Metaphase – alignment of sister chromatids
4.) Anaphase – migration to opposite poles
5.) Telophase

- Cytokinesis
 Division of the rest of the cell Mitosis Meiosis
 Animal cells
 Forming of a cleavage Same number of Half the number of
furrow chromosomes chromosomes
 Plant cells 2 daughter cells 4 daughter cells
 Cell plate
Cells are identical Cells are NOT identical
Separation of sister chromatids controls
genetically genetically
- Cyclin – a family of proteins that control the
progression of cells through the cell cycle by
Energy flow and Chemical recycling
activating cyclin-dependent kinase (Cdk)
- 2 major routes of energy flow and nutrient
enzymes
recycling:
- Cellular respiration
 For mitochondrion
 Adenosine triphosphate (ATP) –
source of energy in cells
 Involves the conversion of
biochemical energy from
nutrients into ATP , and then
release waste products
 Phosphoryation- transfer of a
phosphate group to ADP
(adenosine diphosphate)
 Aerobic respiration
 Glycolysis- breakdown
of glucose
o Produce ATP
 Oxidative
posphorylation
 o Produces most
ATP
 Anaerobic respiration
 Fermentation – enables
more cells to produce
ATP
o Alcohol
fermentation
o Lactic acid
fermentation-
straneous
activities:
fatigue
- Photosynthesis
 Process by which plants use
light to make food molecules
(glucose)from carbon and
oxygen
 Stages of photosynthesis
 Light reaction- grana
 Calvin cycle – stroma
o Produces sugar
- Apoptosis- programmed cell death
- Mediated by an intracellular proteolytic
cascade
- In density dependent inhibition,
crowded cells will stop dividing
- Cancer cells manage to escape the usual
controls on the cell cycle
Organization in Multicellular Forms
- Absorbs minerals and water
- Some store carbohydrates and reserves
- Specialized roots
 Sweet potato
 Storage roots (buttress)
- Stem
- Has leaves and buds
- Elongates and orients the shoot to
maximize photosynthesis
- Elevates flowers
- Auxiliary bud
 Gives rise to stems
- Apical bud
 To elongate
- Each stem consists of an alternating
system of nodes, the points at which
are attached to the internodes
- Specialized stems
 Potato
 Ginger
- Leaves
- Main photosynthetic organ
- Exchanges gases with the atmosphere
- Dissipates heat
- Defends against herbivores and
pathogens
- Density < surface area = more light
absorption
- Specialized leaves
 Leaves of cacti (needles)
 Onion (overlapping leaves)

Plant tissues
Levels of organismal complexity - Dermal
1.) Protoplasmic grade - Outermost protective layer
- Organization is limited within the protoplasm - Epidermis (non woody plants)
- i.e. unicellular organisms - Vascular
2.) Cellular grade - Facilitate the transport of materials
- Organisms are made up if multiple cells but are - Provides mechanical support
not organized into tissues - Passive transport
- Contentious point = all cells are functionally  Xylem – water, dissolved
equivalent minerals
- i.e. volvox, sponge  Phloem – Food, product of
3.) Cell Tissue photosynthesis, sugar
- Cells form distinct tissues - Ground
- i.e. non-vascular plants, cnidarians - Everything between the dermal and
4.) Tissue-organ vascular tissue
- Tissues form distinct organs  Cortex- outside the vascular
5.) Organ systems tissue
 Pithe- Inside the vascular tissue
Plant structure and Function - Storage
- Root - Photosynthesis
- Anchors a vascular plant in the soil - Support
 - Short-distance transport - Non-conspicuous flower
- Biotic or something
Plant cells - Wind- Lowkey
- Parenchyma - Animal pollinated – vibrant to attract
- Thin primary cell wall Fertilization
- No second wall - Double fertilization
- Collenchyma - Ovary- fruit
- Thick primary cell wall - Ovule – seed
- No secondary wall - The embryo is contained in the seed
- Sclerenchyma Other plant functions
- Thick secondary wall - Plant responses
- Phototropism
Indeterminate growth in Plants  Action of the hormone auxin
- Plants are capable of growth throughout their - Gravitropism
lifetime  Plastids in the root cap cell tens
- Due to meristematic tissues to settle at the bottom of the
- Meristems cap (?)
- Any plant tissue composed of actively - Roles of hormones in plant growth
dividing stems - Synthetic hormones
- Apical Meristems - Used by horticulturists in home gardens
 Growth in height/length - Encourage root growth in cuttings
 Shoot AM and Root AM - Discourage… potatoes??
- Lateral Meristems - Plant defence
 Growth in girth and width - Produce compounds such as
 Vascular and cork cambium terpenoids, alkaloids, and fatty acids as
- Wood – secondary xylem secondary metabolites
- Flowers - Defends against parasites and utilized in
- Sexual reproductive organs of plants medical research
- Produce male (pollen) and female
(ovule) gametes
- Gives rise to fruit after pollination
- 4 Whorls
 Sepal Animals: Form and Function
 Petal
 Stamen
 Carpel Four main categories of animal tissues
- Receptacle- point of attachment of the 1.) Epithelial tissue
4 whorls to the stem 2.) Connective Tissue
Type of Flowers 3.) Muscular tissue
- Based on presence of the whorls 4.) Nervous tissue
- Complete- all of the whorls are present
 BISEXUAL Epithelial Tissue
- Incomplete- one or more of the whorls - Forms outer coverings and inner linings
are absent - E.g. skin, intestine, digestive track
Plant life cycle and Reproduction - Compact; tightly packed cells
Alternation of generations - Little intercellular substance
- Characteristics of all plant groups - Polarized
Angiosperm life cycle - With apical (exposed to air or fluid) and
- The sporophyte is the dominant characteristic basal surface (attachment to underlying
- Microspore tissue)
- Megaspore - May contain microvilli, cilia, and flagells
Pollination
- Bring the pollen grain to the ovule
 - Types according to layering
1.) Simple epithelium
 Single layer of cells
2.) Stratifies epithelium
 Made up of many layers of cells
3.) Pseudostratified epithelium
 Made up of a single layer of
cells but appears stratified
- Types according to shape
1.) Cuboidal
 Somewhat equal dimensions
2.) Squamous
 Compacted
3.) Columnar
 Tall
- Simple squamous epithelium
- Flattened cells
- Lining of blood capillaries, lungs, and
other surfaces
- Stratified Squamous Epithelium
- Adapted to withstand mild mechanical
abrasion
- Basal layers of cells undergo continuous
mitotic division
- Lines the oral cavity, esophagus, anal
canal, vagina of mammals, skin
- Simple cuboidal
- Short, boxlike cells
- Usually lines small ducts and tubules
- Active secretory and absorptive
functions
- E.g. produce urine
- Simple Columnar
- Like cuboidal epithelium but cells are
taller
- Found on highly absorptive surfaces
such as the intestinal tract and female
reproductive tract
- In some organs, cells may be ciliates
- Stratifies columnar
- Consists of at least 2 layers of columnar
cells
- Salivary duct
Connective Tissue
- “connects”, binds, and supports different
organs
- Allows space for exchange of metabolites
between blood and tissues
- Few cells, large intercellular substance
- Aka Extracellular matrix (EXM)
- Permits the diffusion of nutrients,
substances, water, and gases
- Major types in Vertebrates
A.) Fibrous connective tissue
- Dense parallel bundles of collagenous
fibres
- Forms tendons (muscle to bone) and
ligaments (bone to bone)
B.) Loose connective tissue
- Binds epithelial to underlying tissue
- Functions to hold organs in place
C.) Adipose tissue
- Specialized loose connective tissue for
fat storage
- Pads and insulates the body
- Stores fuel as fat molecule
D.) Cartilage
- Has abundant collagenous fibres
imbedded in a matrix called chondroitin
sulphate
- Chondrocytes secretes collagen and
chondroitin sulphate
- Main skeletal support among sharks
and embryos of most vertebrates
E.) Bone
- The skeleton supporting most
vertebrates
- Osteoblasts are cells that deposit a
matrix of collagen
F.) Blood
- Made of
 Plasma (55%)
 Matrix consisting of
water, salts, and a
variety of dissolved
proteins
 Formed elements (45%)
Muscle Tissue
- Composed of long cells
- Muscle fibres that are capable of contracting
when stimulated by nerve impulses
- Most abundant tissue
1.) Skeletal Muscle
- Has cylindrical and striated cells with
multiple nuclei
- Occurs in muscles attached to skeleton
- Functions in voluntary movement of
body
- Supportive structure
- Structure of skeletal muscle here
2.) Smooth Muscle
 - Spindle shaped cells, each with a single - Regulatory function
nucleus  Temperature regulation
- Cells have no striations - Sensory, excretory, respiratory, function
- Involuntary movement - Behavioural interactions between
- Blood vessel walls and digestive tract individuals
- Functions in movement of substance of - Composed of the Epidermis and Dermis
lumens (?) in the body - Epidermis
3.) Cardiac Muscle  Stratified squamous epithelium
- Has cylindrical but branching striated  Keratinization takes place
cells, each with a single nucleus  Cornified cells (dead)
- Involuntary contraction  Highly resistant to abrasion and
- In the walls of the heart water diffusion
- Functions in the pumping of blood  No blood vessels
- Dermis
Nervous Tissue  Connective tissue
- Irritability and conductivity  Blood vessels and nerves
- Senses stimuli and transmits signals from one present
part of the animal to another  Support cushion and nourish
- Neurons compose of a cell body, dendrites, and the epidermis
axons  Macrophages and lymphosites
- Dendrite - Epidermal Derivatives
 Transmits nerve impulses from - Epidermis
their tips towards the rest of  Feathers
the neuron  Hair
- Axon  Nails
 Transmits impulses toward  Scales of reptiles
another neuron or towards and  Hooves
affector (responding), such as a  Horns
muscle cell  Claws
- Types of Neurons  Turtle scale
- Sensory (afferent) - Dermis
 Detects signals  Scales of fish
- Motor (efferent)  Antlers
 Causes response  Scales of armadillo
 Transmits  Turtle shell
- Interneuron - Hairs
 Processing signals - Epidermal growth that function in
- Nerve structure here protection
- Shaft, root, and follicle
- Sebaceous glands
 Pili muscle (goose bumps) and
Animal Organ System hair root plexus (nerve endings)
Structural Organ Systems: - Nails
- Plates of highly packed, keratinized cells
1.) Integumentary System - Protection, scratching, and
manipulation
- Functions - Formed by cells in nail bed called the
- Protective wrapping matrix
 Protects against physical - Grows 1mm per week
injury/bacteria - Skin glands
 Moisture proofing - Sebaceous (oil) glands
 Protect underlying cells against - Usually connected to hair follicles
UV - Moistens hair/waterproofs skin
 - Animal Coloration  Red marrow (where new blood
- Vivid and dramatic when serving as cells are being produced) vs.
important recognition marks or warning yellow marrow (lipids, fat)
coloration - Types of bone ossification
- Subdued or cryptic when for  The natural process of bone
camouflage formation
A.) Intramembranous bone
2.) Skeletal System  Any bone that develops without
- A solid (rigid) or fluid (hydrostatic) system any associated cartilage
- Providing a medium for antagonistic muscle B.) Endochondral or replacement bone
interaction  Any bone that develops in and
- May or may not have protective and supportive replaces cartilage
functions  i.e. long bone
- Movement - Renewal of bones
 Osteoclasts
a.) Hydrostatic skeleton  Breaks down bone
- Involves cavities filled with fluids that are  Removes worn cells
incompressible  Works with osteoblasts
- Something here to heal broken bones
- Hydra – gastrovascular cavity - Vertebrae Skeleton
- Earthworm – fluid-filled coelom - 2 Main divisions
b.) Rigid  Axial
- Consists of rigid elements  Skull, vertebral column,
- Usually jointed sternum and ribs
- Two types of Muscle attachment  Appendicular
- External skeleton  Limbs, fins, wings,
 Molluscs – calcium carbonate pectoral and pelvic
 Anthropods – chitin gurdles
 Protection and locomotion - Classification of Joints
-points of connection for muscles - Fibrous Joint
 Immovable
- Endoskeleton – internal  Between cranial bones, tibia
 Echinoderms and vertebrates and fibula & radius and ulna
 Mineralized bone and cartilage - Cartilaginous Joints
 Support, protection, and  Slightly moveable
reservoir of calcium and  Between vertebrae
phosphorous - Synorial Joints
c.) Grows as the animals grow  Freely moveable
- Does not limit space for internal organs  Bones separated by a cavity
- Does not limit weight  Ball and socket, hinge joings

Bone 3.) Muscular System

- Living tissue having significant deposits
- Types:
- Compact bone
 Bone substance that is dense
 Thin intersecting lamellae
- Cancellous or spongy bone
 Thin intersecting lamellae
usually found internal to
compact bone
- Skeletal Muscles
- Attached to the skeleton by cable-like
fibrous connective tissues called
tendons
- Contracting and relaxing
- Not pushing
- 1 contracts and it “stretches” its
antagonistic partner
- “Sacromere”
- The sliding filament model
 - Muscle performance - Human Mouth and Esophagus
- Slow oxidation fibers  Food is called bolus if it passes
 Red muscles through the esophagus
 For slow and sustained - Human Stomach
contraction without fatigue  Food is called chime after it
 Contains extensive blood supply passes through the stomach
 Has a high density of - Human SMALL intestine
mitochondria  3 regions
 Abundant stored myoglobin  Duodenum
(energy)  Nearest stomach
 Important in maintaining  Pancreatic enzymes are
posture in terrestrial released
vertebrates  Jejenum
- Fast Fibers  Next to duodenum
- Fast glycolytic fibers  2.5 m
 White  Ileum
 Lacks efficient blood supply  Last segment of small
 Pale in color intestine
 Functions anaerobically  Peyer’s patches
 Fatigue rapidly o Organized
- Fast oxidative fibers lymphoid
 Extensive blood supply tissues
 High density of mitochondria - Human Large Intestine and colon
and myoglobin  Recovers water that got into
 Functions aerobically the alimentary canal
 For rapid, sustained activities  Rich in harmless bacteria
Oxidative % Glycolytic %  Rectum – terminal portion of
Marathon 82 18 colon; feces are stored
runners - LENGTH OF VERTEBRATE DGESTIVE SYSTEMS
Weight lifters 45 55 DEPENDS ON DIET
Sprinters 37 63 - Ruminants (deer, cattle, and sheep) –
Average humans 45 55 elaborate adaptations for a herbivorous
diet
4.) Digestive System - Nutritional Requirements
- Types of Digestive Systems: - Nutritionally adequate diets satisfy:
- Incomplete – there is only one opening  Fuel (chemical energy)
 NO ANUS  Organic raw materials
 Ex. Hydra, Paramecium, Faciola  Provide essential nutrients
- Complete- with Mouth and Anus - Undernourishment – chronically
 Earthworms, annelids, deficient in calories
vertebrates  Marasmus – diet low in calories
- Four Stages of Digestion and protein
- INIGESTION - Malnourishment- a diet missing one or
 Mechanical digestion (chewing) more essential nutrients
- DIGESTION  Kwashiorkor – protein
 Chemical Digestion malnourishment; adequate
 Enzymatic Hydrolysis calories but low deficient
- ABSORPTION protein
 Nutrient molecules enter body - Overnourishment – Obesity or excessive
cells food intake
- ELIMINATION - Leptin (in mammals) – produced by adipose
 Undigested material cells
- Human Digestive System
 - Complex feedback mechanism  Ventricle – pumps blood to
regulating fat and storage blood vessels
- 20 Amino Acids = Proteins - The Cardiac Cycle
- Essential amino acids - Systole- contraction
- 8 essential in adult life: Phenylalanina, - Diastole – relaxation
lysine, isoleucine, leucine, valine, 1.) Atrial and ventricular diastole
methionine, tryptophan, and threonine) 2.) Atrial systole, ventricular diastole
- Vitamins- organic molecules required in small 3.) Ventricular systole, trial diastole
doses in the diet - Heart sounds heard through a stethoscope are
- Minerals – simple inorganic nutrients; small due to the valves closing
amounts - Measurement of Blood Pressure
- Make use of a sphygmomanometer and
5.) Respiratory System the brachial artery
- Systolic Pressure- peak pressure in
- Cellular respiration arteries
- Oxidative processes within cells  Occurs near end of cardiac cycle
- External respiration  Ventricles are contracting
- Exchange of oxygen and carbon dioxide - Dyastolic Pressure- minimum pressure
- Gas Exchange Surfaces in arteries
- Effective Diffusion requires areas to be:  Near beginning of cardiac cycle
 Moist  Ventricles are filed with blood
 Thin - The blood
 Relatively large - 55% Plasma
*enhanced by vascularization  Water
- Respiratory Organs  Ions
- Cutaneous Respiration – direct diffusion  Plasma Proteins
- Tracheal Systems  Substances transported by
 Branching system of tubes blood
- Gills or Branchia- outfoldings - 45% Cellular Elements
 Operculum on a fish opens and  Erythrocytes
closes  Leukocytes
- Lungs – invaginations  Platelets
- Macrophage – develop from monocytes
6.) Circulatory System  Attacks foreign microes by
phagocytosis
- Functions  Involved in non-specific
- Transport immunity
- Defence - Lymphocytes
- Regulation  Key cells of the immune system
- Animals without circulatory systems:  Utilizes antigen-antibody
- Protozoans, sponges, flatworms, interactions
cnidarians - Antigen
- Two types of Circulatory Systems:  A foreign molecule that elicits a
- Open specific response by
 Insects, other anthropods, most lymphocytes
mollusks  Reacts to specific antibodies
- Closed - Lymph node – masses of macrophages
 Earthworms, squids, octopuses, and lymphocytes
vertebrates
- The Vertebrate Circulatory System 7.) Excretory system
- Closed
- Heart: - Excretion
 Atrium – receives blood
 - Removal of metabolic wastes from the - The endocrine system:
bloodstream - Pineal Gland
- Animal Nitrogenous Wastes - Hypothalamus
- Fishes – Ammonia - Pituitary gland
- Mammals and Amphibians – Urea - Parathyroid glands and Thyroid
- Birds and Reptiles – Uric Acid  Regulation of calcium levels in
- Excretory organs blood
- Kidneys – produce urine  Pituitary Gigantism
- Ureters – transport urine  GH in excess even
- Urinary bladder – stores urine before puberty
- Urethra- passes urine to the outside  Hypopituitary Dwarfism
 Decrease bodily growth
8.) Nervous System  Height and growth of all
- Functions: other structures of
- Detection of internal and external individual are
stimuli decreased
- Controls and coordinates responses of - Thymus
stimuli - Adrenal glands
- Includes the brain, spinal cord, sense organs - Pancreas
- Neuron – basic unit  Is both endocrine and exocrine
- Sensory  Exocrine: secretion of
- Motor bicarbonate ions and digestive
- Nerve nets (Hydra) enzymes
- Cephalization  Endocrine: insulin and glucagon
- Development of the head secreted by islets of langerhans
- Leads to more developed types of - Ovaries and Testes
nervous systems  Produce sex hormones
 Testes: Androgens
 E.g. testosterone
- Vertebrate Nervous Sys tem  Sperm formation
- Central Nervous System  Development and
 Brain maintenance of male
 Spinal cord sex characteristics
- Peripheral nervous system  Ovaries: Estrogens/Progestins
 Cranial Nerves  Uterine lining growth
 Ganglia outside CNS  Development and
 Spinal Nerves maintenance of female
sex char.
9.) Endocrine System
- Endocrine Signaling Reproduction and Developmental Biology
- Secreted molecules diffuse into the
bloodstream - Asexual Reproduction
- Trigger responses in target cells in body - Involves the formation of individuals
- Hormones a.k.a Signaling Molecules whose genes all come from one parent
- Chemical messengers utilizing the - “genetically equivalent”
bloodstream - Fission: asexual reproduction on which
- Regulate growth and development a parent seperates into two or more
- Control the function of various tissues approx. equal sized individuals
- Support reproductive functions (eukaryotes and prokaryotes)
- Regulate metabolism - Budding: asexual rep in whch new
- Same hormones = different functions individuals split off from existing ones
- Due to different receptors (hydra)
- Or different target tissue types - Gemmules: of sponges
 - Fregmentation: the breaking of the
body into several pieces, some or all of
which develop into complete adults
 Regeneration of lost body parts
(sea stars etc.)
- Parthenogenesis is the process by which
a unfertilized egg develops into (often)
haploid adult
 Plays a role in the social
organization of bees, wasps,
and ants
 Male honeybees are
haploid; female
honeybees are diploid
- Hermaphroditism: one individual is
function as both a male and a female
 Some self- fertilize
 Most mate with another
member of the same species
 Sequential hermaphroditism: an
individual reverses its sex
during its lifetime
 Protogynous: female
first
Saddle wrasse HAREM
 Protandrous: Male first
o Sparus aurata
o More
commonly
occurring
- Asexual reproduction is easier in terms of
expenditure of energy
- Advantages of asexual reproduction:
- Can produce without having to find a
mate
- Numerous offspring in a short period of
time
- In stable environments, allows for the
perpetuation of successful genotypes
- Disadvantages of sexual reproduction
- Complicated
- Requires more time
- Uses much more energy than asexual
rep
- Sexual Reproduction
- Is the formation of offspring by the
fusion of haploid gametes
- With its breakup and recombination of
genetic material, keeps producing novel
genotypes that in times of
environmental change may survive and
reproduce, whereas most other die
- A variation far greater than that of
asexual reproduction
- External fertilization requires a moist
habitat that will protect a developing
egg from desiccation and heat stress
 Spawning can be induced
 Male and female need not have
contact
 Contact is optional
 Some do it (frogs)
others don’t
 Gametes must be released in an
aquatic environment (or else
they might dry out)
- Internal Fertilization requires
cooperative behaviour that leads to
copulation
Parental care of offspring may occur regardless of
whether fertilization is external or internal
- Sperm: it only really needs its tail and a few
mitochondria to function
- Ovium: source of cytoplasmic content
- Monozygotic or Identical twins are a result of
the fertilization of a single oocyte
- Dizygotic or fraternal twins are the result of two
different oocytes
Parasitic twins
- Asymmetrical or unequal conjoined
twins
- The pair does not fully separate
- One embryo maintains dominant
development
- Ex. Rudy Santos Octoman
- Usually occurs in monozygotic conditions but a
mitotic inhibitor doesn’t allow for the division of
the cell
Stages of Development
1.) Gamete formation
2.) Fertilization
3.) Cleavage
4.) Gastrulation- three embryotic germ layers
form
a. Ectoderm – epidermis of the skin and
derivatives; epithelial lining
 b. Endoderm- epithelial lignin of the can interbreed and produce
digestive track, respiratory system, fertile offspring
reproductive system  Not applicable to
c. Mesoderm- Notochord, Skeletal,
 Fossils
Muscular, circulatory, and lymphatic
system; dermis of the skin  Asexual organisms
6.) Organogenesis - Reproductive Barriers Between Species
5.) Growth - Prezygotic barriers – before fertilization
 Habitat Isolation
Reproductive health  Populations live in
- State of physical, metal, and social well-being in
different habitats and
all matters relating to the reproductive system,
do not meet
at all stages of life
- Ability to have a satisfying and safe sex life, the  Temporal Isolation
capability to reproduce, and the freedom to  Mating or flowering
decide if, when, and how often to do so occurs at different
- Should be informed about and have safe, seasons or times of day
effective, affordable, and acceptable methods  Behavioural isolation
of family planning of their choice, and the right
 Little or no sexual
to appropriate health care services that enable
women to safely go through pregnancy and attraction between
childbirth males and females
- Contraceptives: remedies for possibility of  Mechanical Isolation
unregulated incidents =/= state of well being  Structural differences In
genitalia or flower
Sexually Transmitted diseases
prevent copulation or
pollination
Species  Gametic isolation
- Groups of individuals similar to one another  Male and or female
- Species concepts gametes die before
- Morphological Species concept uniting or fail to unite
 Physical appearance to identify
species
 Used by Linnaeus when he - Postzygotic barriers
developed the binomial system  Hybrid sterility
of naming organisms  Hybrid breakdown
 Ex. Eastern meadowlark vs.  Offsprings of hybrids
western meadowlark are weak or fertile
 Taxonomists: Lumpers
(grouping organisms together - Ecological Species Concept
based on similarities) vs.
- defines species by its ecological role
___(separate organisms in
- Occupancy of an ecological niche
different species based on even
minimal differences
- Biological Species Concept - Evolutionary Speces Concept
 Defines a species as a
population or group of - “a species is a single lineage of
populations whose members ancestor-descedant populations thet
maintains its identity from other such
 lineages and that it has its own - Species : Homo Sapiens
evolutionary tendencies and historical - Genus: Homo
fate” - Family: Hominidae
- Order: Primata
- Phylogeny - Class: Mammalia
- sharing common ancestry - Phylum: Chordata
- Kingdom: Animalia
- Two patterns of Speciation - Domain: Eukarya
- Anagenesis – is the accumulation Systematics
- - A study of biological diversity and classification
changes associated with the - Employs taxonomy and evolutionary biology to
transformation of one species to arrange organisms in categories that reflect
another phylogeny
- Cladogenesis, branching evolution, is - Phylogeny
the budding of one or more new - Evolutionary history of a species or a
species from a parent species group of species
- Mode of Speciation - Clade
- Allopatric speciation - Goup of species that includes an
 Speciation among populations ancestral species and all its descendants
living in two different ranges or - Monophyletic group
territories; geographic isolation - Paraphyletic group
leads to reproductive isolation - Polyphyletic group
- Sympatric speciation
 Species living in the same or - The 5-Kingdom Scheme
overlapping ranges adapt to - Proposed by R.H. Whittaker in 1969
differnet - Carl Woese used signature sequences,
- Peripatric speciation regions of SSU-rRNA that are unique, to
 Special allopatric variation establish a phylogeny of prokaryotes
 Mode and happens when on of
he isolatied populations FUCK MAN YOU SKIPPED THIS MEETING ASK WHAT
- Parapatric speciation HAPPENED: Film showing HAHAHAHA
 Population is continuous but
the population does not mate 07/11/2017
randomly
 Individuals are more likely to HUMAN EVOLITION
mate with their geographic
neighbors than with individuals “taxonomy of humans”
in a different part of a
population’s range Order Primata
- Tempo of Speciation - Opposable thumbs
- Gradualist model - Frontally directed eyes with binocular vision
 New soecies evolve by the - Complex social behaviour
gradual accumulation of
changes brought about by - Suborder Prosimii
natural selection
- Punctuated equilibrium
 Speciation occurs in spurts - Prosimians
- Do you believe in Evolution - Tropical rainforests in Madagascar, Africa and
SEA
Taxonomy - -large orbits, reduced brain case, elongated
- Pioneered by Carolus Linneaus snout, and well developed olfactory
- Concerned with classifying
- Hierarchal classification - Suborder Anthropoidea
 - Bipedalism
- Obligately having to walk on two feet
- Monkeys, apes, humans - Encephalization
- Larger brain relative to body size
Hominoids
- Ancestral family of apes including humans
Old world monkeys - Terrestrial lifestyle
- Africa and Asia - 22-32 million years ago
Hominins
- Ancestral to humans only
- - tails are NOT prehensile - Characterized by bipedalism and
- Nostrils face downwards encephalization
- Arboreal and ground- dwelling - Fossils of around 20 extinct species are
discovered
New world monkeys
Homo Sapiens
- Central and sout amricall
Homo neanderthalensis
- Prehensile
Homo erectus
- Nostrils are facing sideways
Homo habilis
- Tree dwelling
Homo rudolfensis
Humans are APES not Monkeys
Ardipithecus ramidus (“Ardi”)
Austrolopithecus afarensis
- Apes are capable of BRACHIATION (arm
swingin)
Why did bipedalism become the primary adaptation of
- Collar bones in apes are longer
hominins
- Shoulders free to move
- Carrying behaviour
Apes/Hominids
- Reduction of overall heat stress
Other apre traits
- Most energy efficient way to travel long
- Lack tails
distances
- Most have forelimbs linger than their hindlimbs
- Allows for better vision in open environment
- Humans and apes – common ancestor
- Defensive action against predators (free hands)
The missing link fallacy
Homo
- Midway between modern apes and modern
-chracterized by use of tools
humans there existed a direct intermediary ape
- increased brain capacity
- No such intermediate is expected
- 6-7 million years ago – common ancestor
Homo habilis
- Earlier fossils placed in genus
Humans from other apes:
- 2.4 to 1.6 million
- Upriht posture
- Handy man
- Bipedal locomotion
Homo erectus
- Larger brains
- Originated in Africa
- Language capabilities
- First to leave Africa
- Symbolic thought
- Java
- Use of complex tools
- Prominent brow rides
- Shortened jaw
- Chin recessed
- Shorter digestive track
Homo neanderthalensis
- 28,00-225,000
Key events in human evolution
- Belgium, Croatia, Germany, Frnace, Iraq, Israel,
- Terrestriality
Italy
- Coming down from trees
- Increased brain size
Homo sapiens
- Modern Man - Organismal ecology
- Appeared in Africa by 195,000 - How and organism’s structure,
- All living humans are descended from these physiology and behaviour meet the
African ancestors challenges posed by tis environment
- Protruding chins - Population ecology
- Smaller brow - Factors that affect population size and
- Characterstics of modern humans distribution
- Each adaptive feature arose at different points - Community ecology
in our his - How interactions between species
Hypothesis on the origin of humans affect community structure and
- Multiregional hypothesis distribution
- AFRICA origin’ - Ecosystem ecology
- Modern man evolved independently in - Energy flow and chem. Cycling between
different regions organisms and env.
- Out of Africa Hypothesis - Abiotic factors
- Landscape ecology
Tracing human history through genetic mutations - Multiple ecosystens
- Global ecology
PROJECT TOPIC POSSIBILITIES: - Global interaction of ecologies
- Human Microbione
- DNA Forensics The study of populations in relation to the environment
- Climate Change
- Emerging and re-emerging infectious diseases Population
- Biodiversity Conservation Density
- Cancer Dispersion
- Any visual work
- Drawing Population Density – interplay between processes that
- Infographic add individuals to a population and those that remove
- Poetry individuals from it
- Songs
- Video Birth and immigration
- Film (maximum of 20 minutes0\ Death and emmigration
- Model
- One page paper explaining the concepts behind 3 patterns of dostributin in a population
the topic
Individual, or in groups Max. 3 - Clumped
- More members higher expectations - Aggregates in different ares
Due: December 7 - Protection in large numbers
Second Exam : [December 5] finalize by next meeting - School of fish
- Uniform
09/11/2017 - Resources available is evenly distributes
as well
ECOLOGY - Random
- No significant pattern
The study between interactions between organisms and
their environments [FLOW CHART]

Interactions determine Strategies used by organisms to cope with selection in

- Distribution diff environments
- Abundance
K- strategy
Scopes of ecological research
Stable, predictable env - Mullerian mimicry
Large size  Two unpalatable species mimic
High energy to reproduce each other
Few offsprings produced - Peckhamian mimicry
Late maturity - Aggressive mimicry
Long life expectancy - Mimic resembles something palatable
Reproduction takes place more than once to lure prey
*higher chances of survival
Trophic levels
r-strategy Primary Producers
untable, undredictable env Primary consumers
small size Secondary consumers
lower energy to make individuals Tertiary consumers
many offsprings Quaternary consumers
early maturity Decomposers
short life expectancy
[FOOD CHAINS]
Population growth rate - Rarely unbranched
- Feeding relationships in an ecosystem form
Most species are capable of exponential growth, elaborate food webs
assuming there are enough resources to sustain such
growth - Parasitism
- The parasite derives nourishment from
Mostly logistic growth rate [pataas then there will be a another organisms, the host, which is
max point where the env can sustain their needs] harmed in some way
= carrying capacity - A GOOD PARASITE WILL NEVER KILL ITS
HOST
- Max number of individuals that can be
sustained by a given environment - Commensalism
Importance - Interaction in which the symbiont
- Population as basic evolutionary unit benefits and the host is unaffected
- Population as basic conservation unit - Clown fish and sea anemone
- Hard to assess if no harm is being done
Community ecology - Mutualism/symbiosis
- Distribution, abundance, and interactions of - Two species of organisms that benefit
different species both species
Interspecific interactions in a community - Requires the evolution of adaptations in
“exploitation” both species
[herbivory, predation, parasitism] - Obligate mutualism – specialized
- Predation interaction that one individual could not
- PREDATOR eats the PREY survive without the other
- Animal- animal interactions [predation]  Lichen –fungus/algae
- Animal –plant interactions [herbivory] - Interspecific Competition
- Adaptation - Two or more species in a community
- Mimicry rely on similar limited sources
 Camoflauge- mimic bears a - Fundamental niche
superficial resemblance to  Resources an organism or
another species, the model, or population in theoretically
the environment capable of using under ideal
 Bright coloration [toxins] circumstances
- Batesian mimicry  Area that can be occupied
 Palatable species mimics an without environmental
unpalatable or harmful model constrains
 - Realized niche  cellular respiration
 Constricted by competition - Nitrogen cycle
- Resource partitioning  Amino acids in proteins and
Competitive exclusion principle nucleic acids
- No two species can occupy the same niche  Production of nitrogenous
- They will be forced to compete wastes
- Only one will survive - Phosphorus cycles
3 possible outcomes  ATP
- Fight – character displacement Biomes
- Belonging in the same area but utilizing - Major ecological associations occupying broad
different resources in the area geographc regions of land and water
- Flight- range restriction
- Fright- leads to extinction Aquatic
- Fresh
Succession - Ponds and lakes
- The transition in species composition of a - Rivers and streans
community over ecological time - Wetlands
- Classified as either primary or secondary - Salt water
- Primary succession - Coral reefs-shallow areas/ neritic zones
- Barren of life- soil composition os - Oceanic – deep sea
different - Benthic and abyssal biomes- ocean floor
- Follows certain geological events - Intertidal zone
- Secondary succession - Land and sea meat
- Land is cleared but soil is intact - Brackish
- Follows the destruction or partial - Estuaries
destruction of the vegetation but the Terrestrial
soil is intact - Characterized by precipitation and temperature
- Desert
Species diversity - Temperate grassland
- Number and relative abundance of species in a - Tropical forest
biological community - Temperate broadleaf forest
- Species richness and relative abundance - Northern coniferous forest
- Artic and alpine tundra
“evenness vs. dominance”

Species richness
- The number of species in a community
Relative abundance
- Measure of the proportion-

Ecosystem ecology

2 processes involved in a ecosystem

- Energy flow
- Nutrients cycled
- Global cycle
 Gaseous component and uses
the atmosphere as reservoir
- Local cycle
- Water cycle
 Maintaining homeostasis
- Carbon cycle
 biomolecules