Bio 1 Notes

Thursday, 25 August 2016
Bio 1
Lessons
A. The Scientific Method
B. Cell Theory
C. The Cell as the Basic Unit of Life
D. Prokaryotic vs Eukaryotic Cells
E. Parts of a Cell and Their Functions
BIOLOGY IS A BRANCH OF SCIENCE
- A way of understanding the natural world.

Scientists make predictions and test those predictions
THE NATURE OF SCIENCE
- Understand the natural world through observation and reasoning

Science begins with observations, therefore, much of science is purely descriptive.
Science uses both deductive and inductive reasoning.
- Deductive reasoning uses general premises to make specific predictions
If Then Logic of Hypothesis Based Science
- Inductive reasoning draws conclusions through the logical process of induction
Two approaches are used to understand natural causes for natural phenomena:
Discovery Science
- uses verifiable observations and measurements to describe science

- describes natural structures and process
Hypothesis-based Science
- Uses data from discovery science to explain science

- Observations can lead us to questions and propose hypothetical explanations called
hypotheses
A hypothesis must be testable and falsifiable

- Often makes use of two or more alternative hypotheses
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- Failure to falsify a hypothesis does not prove that hypothesis
Scientific Method
- An organised systematic way of solving problems

Theory and Certainty
Theory - set of hypotheses that have been thoroughly tested over time, and generally
accepted by the scientific community
- Acceptance is always provisional

Limitations of Science
- Scientific study is limited to area that can be observed and measured

Cannot be used to address all questions
Bound by practical limits
- Temporal and spatial considerations
The Cell Theory
- All organisms are composed of similar units of organization, called cells

- formally articulated in 1839 by Matthias Schneiden & Theodor Schwann, and has
remained the backbone of Biology
Modern Tenets of the Cell Theory
1. All known living things are made up of cells
2. The cell is structural and functional unit of all living things
3. All cells come from pre-existing cells by division (Spontaneous Generation doesnt
occur)
4. Cells contain hereditary info that is passed from cell to cell during cell division
5. All cells are basically the same in chemical composition
6. All energy flow (metabolism & biochemistry) of life occurs within cells
- Cells are the smallest living things
- Life evolved
Manifestations of Life
1. Highly organized
2. Requires constant input of energy and raw materials
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3. Strong internal control
4. Reacts to the environment
5. Reproduces
6. Grows
7. Varies and evolves
The Cell as the Basic Unit of Life
- an organisms basic units of structure and function

lowest level of organization that can perform all activities required for life
- ability to divide is the basis of all reproduction, growth, and repair of multicellular
organisms
What is DNA?
- DNA is a molecule, made up of units called nucleotides

- Nucleotide has a sugar molecule, a phosphate molecule, and a structure called a
nitrogenous base
- The bases: adenine (A), cytosine (C), guanine (G), and thymine (T) - the letters of the
genetic alphabet
- Two polynucleotide stands wrap around each other to form a DNA double helix
Two strands are associated because particular bases always hydrogen to one
another?
A pairs with T, and C pairs with G producing base pairs

Cell Theory
- Cells are the smallest living things

Two distinct groups of cells
- Prokaryotic Cells
Simple and small
Bacteria are prokaryotic cells
DNA in nucleoid
No membrane-bound organelles
1-10 microns in diameter
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- Eukaryotic Cells
possess organelles separated by membranes
plants, animals, and fungi are eukaryotic
DNA in nucleus
With membrane-bound organelles
The Cell as The Basic Unit of Life
Structures and organelles of eukaryotic cells can be grouped into four (4) functional
groups:
1. Manufacturing: nucleus, ribosomes, endoplasmic reticulum and golgi apparatus
2. Breakdown or hydrolysis of molecules: lysosomes, vacuoles (plants only), and

peroxisomes
3. Energy processing: mitochondria, and chloroplasts
4. Structural support, movement, and communication among cells: components of the

cytoskeleton, plasma membrane, and cell wall
Common Characteristics of Different Cells
1. All cells are surrounded by a plasma membrane
2. All cells have a semi-fluid substance within the membrane called the cytosol
3. All cells contain chromosomes which have genes in the form of DNA
4. All cells have ribosomes, tiny organelles that make proteins using the instructions
contained in the genes
Parts of the Cell
1. Plasma Membrane
Functions as a selective barrier that allows passage of oxygen, nutrients, and waste
The phospholipids and proteins on membranes create a unique physical
environment called the fluid mosaic model
2. Nucleus
- Contains most of the genes in the eukaryotic cells

- Includes DNA and associated proteins organised into chromatin which coil up during
cell division to become chromosomes
- Site where ribosomal RNA (rRNA) is synthesized
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3. Endoplasmic Reticulum (ER)
- Manufactures membranes, proteins, and lipids

- Accounts for nearly half the membranes in a cell
- Two Types of ER:
Smooth ER
- No ribosomes
- Contain catalytic enzymes
- Produces oils phospholipids and steroids
Rough ER
- With ribosomes
- Manufactures proteins
- Make more membrane
4. Golgi Apparatus
- Many transport vesicles from the ER travel to the Golgi Apparatus for modification of
their contents
- Center of manufacturing, warehousing, sorting and shipping

5. Lysosome
- A membrane-bound sac of hydrolytic enzymes that digests macromolecules.

- Lysosomal enzymes can hydrolyse proteins, fats, polysaccharides, and nucleic acids.
6. Vacuoles
- A membrane-bound sac with varied functions

- Types of Vacuoles
Food Vacuole
Contractile Vacuole
- Found in freshwater protozoans, pump excess water out of cell
Central Vacuole
- Found in many mature plant cells
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- For stockpiling proteins or inorganic ions depositing metabolic byproducts storing
pigments and storing defensive
7. Peroxisome
- Contains enzymes with varied functions

- Converts hydrogen peroxide to water
- Breaks fatty acids into smaller molecules
- Detoxifies alcohol and other harmful compounds
8. Mitochondria
- The site of cellular respiration generating ATP from the catabolism of sugar fats and
other fuels present in oxygen
- Has a smooth outer membrane and a highly folded inner membrane, the crista
9. Chloroplast
- Found in plants and eukaryotic algae

- Converts solar energy to chemical energy and synthesise new organic compounds
CO2 and H2O through the process of photosynthesis
- Inside is an inner membrane enclosing a fluid-filled space, the stroma, in which floats
membranous sacs, the thylakoids
10. Cytoskeleton
- A network of fibres extending throughout the cytoplasm

- Provides mechanical support and maintains shape of the cell
11. Cell Wall
- Found on plant cells; protects the cell, maintain its shape, and prevents excessive/
uptake of water
- Consists of cellulose embedded in a matrix of proteins and other polysaccharides

- With an outer cell wall inner cell wall and middle lamella
- Also found in Bacteria and Fungi:
Bacteria made out of peptidoglycan
Fungi made out of chitin
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Tuesday, 30 August 2016
BIO 1
Exploring Life
(Structure, Function and Control)
- Anatomy is the study of the biological form of an organism

- Physiology in the study of the biological functions an organism performs
- The comparative study of animals reveals that form and function are closely correlated
Integration of Animal Form and Function
- Integrated by the common problems that all animals must solve

- Evolutionary histories and varying complexities must solve these general challenges
of life
- Challenges of life:
1. How to extract oxygen from the environment
2. How to nourish themselves
3. How to excrete waste products
4. How to move
The adaptations observed in a comparative study of animals and plants evolved by

natural selection
Structural Adaptations
- Mimicry: Copying of the appearance of other organisms for protection or other

advantages; protective resemblance: normally resembles plant structures
- Camouflage: Body color blends in with surroundings (spots and stripes)
- Warning Coloration: Bright coloration to warn of danger
- Mechanical Defences: Physical covering that allows for defending from predators or to
aid in predation (Claws, sharp teeth, quills, shells)
Physical Constraints on Animal Size and Shape

- The ability to perform certain actions depends on an animals shape, size, and
environment
- Evolutionary convergence reflects different species adaptations to similar

environmental challenge
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- Physical laws impose constraints on animal size and shape
The laws of hydrodynamics constrain the shapes that are possible for aquatic
organisms that swim very fast
Fusiform Shape - fast swimmers and all have the same basic shape (sharks, tuna,
dolphins, penguins, etc.)
Hierarchical Organization of Body Plans
- Most animals are composed of specialised cells organised into tissues

- Tissues make up organs which together make up organ systems
Tissue Structure and Function
- Different tissues have different structures that are suited ti their function
- Tissues are classified into four main cate: epithelial, connective muscle nervous
- Epithelial Tissue
Covers the outside of the body and lines the organs and cavities within the body
It contains cells that are closely joined
The shape of the epithelial cells may be cuboidal (like dice), columnar (like bricks on
end) or squamous (like floor tiles) -> Depends on the tissues locations
Connective Tissue
- Connective tissue mainly binds and supports other tissues

- Sparsely packed cells scattered throughout an extracellular matrix
- The matrix consists of fibres in a liquid jellylike or solid foundation
Muscle Tissue
- Is divided in the vertebrate body into three (3) types:

Skeletal Muscle or started muscle, is responsible for voluntary body movement
Smooth Muscle is responsible for involuntary body activities
Cardiac Muscle is responsible for contraction of the heart
Nervous Tissue
- Nervous Tissues sense stimuli and transmits signals throughout the animal
- Contains:
Neurons or nerve cells that transmit nerve impulses
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Glial Cells, or Glia, that helps nourish, insulate and replenish neutrons
Coordination and Control
- Depends on the endocrine system and the nervous system

- The endocrine system transmits chemical signals called hormones to receptive cells
throughout the body via blood
A hormone may affect one or more regions throughout the body

Hormones are relatively slow acting, but can have long-lasting effects
- The nervous system transmits information between specific locations
The information conveyed depends on a signals pathway, not the type of signal
Nerve signal transmission is very fast
Nerve impulses can be received by neutrons, muscle cells, and endocrine cells
Adaptations of Organisms in the Desert
- Plant Adaptations
Structural Adaptation
- Shallow roots
- No leaves
Functional Adaptation
- Photosynthesis in stems
- Flowers open at night when cooler
- Animal Adaptations
Structural Adaptation
Both genes and environment affect plant structure
- This is a morphological adaptation that reduces water loss

- Some desert plants have reduced their leaves that the stem is actually the primary
photosynthetic material
Plastic Plants?
- Leaves extend above the surface form oval pads that aid in flotation
- Developmental plasticity, the ability to alter itself in response to its environment
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Physiological (Functional) Adjustments
- Most plants are rarely exposed to severe drought and rely mainly on physiological
adaptations to cope with drought stress
- Plant produces a hormone that cause the stomata the pores in the leaves through
which most of the water is list to close
The 3 Basic Plant Organs: Roots Stems and Leaves
- Basic morphology of vascular plants reflects their evolution as organisms that draw
nutrients from below ground and above ground
Shoot System and Root System
Roots
- Roots rely on sugar produced by photosynthesis in the shoot system

- Shoots rely on water and minerals on the roots system
- Roots are multicellular organs with important functions:
A taproot
Adventitious roots arise from stems and leaves
Near root hairs: absorption of water and minerals
Modified Roots
- Prop Roots
- Storage Roots
- Strangling Aerial Roots
- Buttress Roots
- Pneumatophores
Stem
- Axillary bud
- Apical bud
- Apical dominance
Modified Stems
- Rhizomes
- Bulbs
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- Stolons
- Tubers
Leaves
- Main photosynthesis organ of most vascular plants

- Generally flat
- Some plant species have evolved and modified their leaves that serve various
functions (spines, storage leaves, etc)
Modified Leaves
- Tendrils
- Bracts
- Spines
- Reproductive Leaves
- Storage Leaves
Common Types of Plant Cells
- Parenchyma
Thin and flexible primary wall
Lack secondary wall
Least specialised
Perform the most metabolic function
Retain the ability to divide and differentiate
- Collenchyma
Thicker and uneven cell walls
Lack secondary walls
Provide flexible support without restraining growth
Grouped in strand and help support younger parts of plant shoot
- Sclerenchyma
Rigid because of thick secondary wall strengthened with lignin
Dead at functional maturity
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- Water-conducting Cells of the Xylem
Vessel elements are common to most angiosperms and a few gymnosperms
- Sugar-Conducting Cells of the Phloem
Sieve-tube elements are alive at functional maturity, though they lack organelles
Sieve plates are the porous end walls that allow fluid to flow between cells along
the sieve tube
Each sieve-tube element has a companion cell whose nucleus and ribosomes
serve both cells
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Thursday, 1 September 2016
BIO 1
Reproduction1
- Reproduction is the property of life by which new individual organisms are produced
- Important to the survival of species
- 2 Types
Asexual: one parent
- No gametes involved
- No fertilisation
- Only mitotic cell division
- Genetically identical to parent (Clone)
- Relative speed by which offspring are produced: Faster
- All members can produce viable offspring
- Can proceed via:
Budding: Parent cell produces bud, it gets detached and develops into new
individual
- Hydra and Yeast
Fission: A single parent cell divides into two daughter cells (Binary Fission)
- Amoeba, paramecium, bacteria (prokaryotes)
Fragmentation/Regeneration: Organism with filamentous body, break into two
or more fragments. Each fragment grows into a new individual
- Spirogya
Sexual: joining of eggs and sperm
- 2 (or 1 if parent is a hermaphrodite)
Have sex organs which produce sex cells
Sex cells are called gametes and are produced in gonads
- Gametes involved
1 Videos from BioFlix (Pearson) about Mitosis and Meiosis
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- Genetically different to either parent (Variation)
- Relative speed by which offspring are produced: Slower
- Only one sex (female) can produce viable offspring
Sexual Reproduction is the creation of an offspring by fusion of a male gamete (sperm)
and female gamete (egg) to form a zygote
What is Sex?
- Genotypic Sex: X and Y chromosomes

- Phenotypic Sex: determined by external and internal genitalia
- Gender: subjective perception; sexual orientation
Sexual Reproduction: An Evolutionary Enigma
- Sexual females have half as many daughters

- Despite this, almost all eukaryotic species reproduce sexually
Sexual reproduction results in genetic recombination, which provides potential
advantages:
- An increase in variation in offspring, providing an increase in the reproductive
success of parents in changing environments
- An increase in the rate of adaptation

- A shuffling of genes and the elimination of harmful genes from a population
Some hermaphrodites can self-fertilize
One solution is hermaphroditism in which
Individuals of some species undergo sex reversals (Clown Fish)
Fertilisation can be:
- External (Takes place outside the female body)

- Internal (Takes place inside the female body)
Both need water or a watery environment as the sperm needs to swim to the egg
Sexual Reproduction in Animals
Male
- Gamete - sperm
- Gonad - testes
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- Many sperm cells
- Spermatogenesis
- Sperm cells are (n) haploid/monoploid
Female
- Gametes - egg
- Gonad - ovary
- few to many eggs
- Oogenesis
- Egg cells are (n) haploid/monoploid
Fertilisation depends on mechanisms that bring together sperm and eggs of the same
species
Internal Fertilisation
- has been crucial to the colonisation of lands by animals

- is needed by land animals to provide
- requires behavioural interaction
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Tuesday, 6 September 2016
BIO 1
Plant Reproduction
Sexual Reproduction in Plants
Alternation of generations in plants
- Sporophyte produces haploid spores by meiosis

- A spore develops by mitosis into a Multicellular haploid gametophyte (n)
As the plant becomes more complex, there is a reduction on the size of the gametophyte
Fruits
- A fruit typically consists of a mature ovary but can also include other flower parts
- Fruits protect seeds and aid in their dispersal
- Mature fruits can be either fleshy or dry
- Various fruit adaptations help disperse seeds
- Seeds can be carried by wind, water, or animals
- Seeds:
Wings
Within berries
Barbs
Pollination
- Bringing in of male gametophyte (pollen grain) to the female gametophyte

- Can be either animal-aided or wind-pollinated
Fertilisation
- Haploid spores in Anthers develop into pollen grains

- Haploid spore in each ovule develops into female gametophyte which produces egg
DEVELOPMENT OF PLANT EMBRYO
- Angiosperms undergo double fertilization

- The embryo is contained in the seed
- NOTE:
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OVARY BECOMES THE FRUIT
OVULE BECOMES THE SEED
Seed Germination
-
- Radicle
embryonic root
the first to emerge
- Coleoptile
embryonic shoot
Development from Totipotent Cells
- Totipotent Cells: undifferentiated cells

- All cells in an organism are genetically equivalent (having the same genes)
- Cells become structurally, functionally, & biochemically different by expressing
different genes at different times during development
- Callus induction in plants
Endosperm
- Liquid endosperm (buko juice)

- Solid endosperm (meat)
- It is triploid
Asexual Reproduction in Plants
Cloning
Plants can be cloned from single cells

Charles Steward
Single cells grew and divided to form a ball of undifferentiated cells
- Clones
- Organisms created by asexual reproduction
- No fusion of egg and sperm
- Genetically identical
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- Simply identical genetic copies
- Cloning is wide spread in nature
- Paramecium
- Clones are organisms that are exact genetic copies. Every single bit of their DNA is
identical
- Clones can happen naturally - identical twins are just one of many examples
- The creation of an exact genetic replica of DNA
- DNA cloning yields multiple copies of a gene or other DNA segment
Artificial Cloning (Cloning Technology Timeline)
1952: Rovert Briggs and Thomas King of the Institute for Cancer Research, developed
the first major technique, Somatic Cell Nuclear Transfer (SCNT)
1966: John Gurdon of Oxford University created an adult frog clone using a tadpole
somatic cell
1980: Embryo splittin, developed for livestock breeding
1980-1996: Various research groups cloned frogs, mice, and cattle
1996: Ian Wilmut and colleagues of Roslin Institute in Scotland created the first clone of
an adult mammal using adult somatic cells and SCNT.
1997: Ian Wilmut and colleagues cloned two other sheep, Molly and Polly
1998: University of Hawaii announced the creation of 50 mice clones using adult somatic
cells
2000: PPL Therapeutics, Inc. cloned pigs from adult female pig body cells.
2001: PPL Therapeutics, Inc. applied genetic engineering
2004: South Korean scientists achieved the first successful human somatic cell nuclear
transfer
DOLLY, the inspiration
- born on 1996
- lived until the age of 6
- first cloned mammal
- several hundred other Dollies were created
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Animals can be cloned by several methods
- Embryo Splitting
bisecting the multicellular embryo at an early stage of development to generate
twins
The (two) embryos from the splitting are in the same stage of development, exactly
the same age as the undivided embryo would have been and genetically completely
identical
- Nuclear Transfer
Transfer of the whole nucleus (which contains all the genes) from a donor cell into
an unfertilised egg cell whose nucleus has previously been removed
This technique basically offers the possibility of replicating an adult individual and
their complete genetic make-up
Errors In Nuclear Transfer
- Most clones die early in gestation, and only a few survive to birth or beyond
- Cloned animals have common abnormalities regardless of the type of donor cell or the
species used
- These abnormalities correlate with aberrant gene expression, which most likely results
from faulty genomic reprogramming
- The efficiency of cloning depends on the state of differentiation of the donor cell
Benefits of Human Cloning
- Cure for Heart Problems

possible to treat heart attack victims by cloning their healthy heart cells and injecting
them into areas of the heart that have been damaged
- Organ and Tissue Repair

- Cure for Incurable Diseases
- Infertility
- Plastic Reconstructive and Cosmetic Surgery
- Downs Syndrome
- Liver Failure
- Kidney Failure
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- Leukemia
- Cancer
- Cystic Fibrosis
- Spinal Cord Injury
- Testing for Genetic Disease
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BIO 1
Human Reproduction
Male Reproductive System
Epididymis
- storage of sperm
Vas Deferens
- pathway the sperm takes from epididymis to the urethra

Bulbourethral Gland
- alkaline like fluid from this washes away the acid

Testes
- The male gonads
- Sperm form in these seminiferous tubules
- Leydig cells produce hormones and are scattered around tubules
- Production of normal sperm cannot occur at the body temperature of most mammals
Ducts
- From the seminiferous tubules of a testis sperm pass into the coiled tubules of the
epididymis
- During ejaculation, sperm are propelled through the muscular vas deferens and the
ejaculatory duct, and then exit the penis through the urethra
Accessory Glands
Semen
- The two seminal vesicles

- The prostate gland
- The bulbourethral glands secrete a clear mucus before ejaculation that neutralises
acidic urine remaining in the urethra
The formation of sperm and egg requires meiosis
Spermatogenesis
- Occurs in seminiferous tubules
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- Primary spermatocytes
- Secondary spermatocytes
- Rounds spermatids
Oogenesis
- Begins before birth - diploid cells start meiosis and stop
- Each month about one primary oocyte resumes meiosis
- A secondary oocyte arrested at metaphase if meiosis II is ovulated
- Meiosis of the ovum is completed after fertilisation
Difference between Spermatogenesis and Oogenesis
Spermatogenesis
- four sperms each cycle

- continues throughout the adult life of males
- produces sperm from precursor cells in a continuous sequence
Oogenesis
- one egg each cycle
- ceases later in life
- has long interruptions
Ovarian and menstrual cycles2
- Occur about 28 days

- Hypothalamus signals the anterior pituitary to secrete follicle-stimulating hormone
(FSH) and leuteinizing hormone (LH), which trigger
Growth of a follicle
Ovulation
After ovulation, ovarian follicle becomes corpus luteum
Corpus luteum secretes estrogen and progesterone, which
Inhibit hypothalamus, reducing FSH and LH
If egg is fertilised,
2 Table 27.6
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- Menstruation does not occur
- Embryo releases hormones that maintain the uterine lining
If egg is not fertilised,
- drop in LH shuts down corpus luteum and its hormones

- menstruation is triggered
- hypothalamus and pituitary stimulate development of a new follicle
Sperm are adapted to reach and fertilise an egg
- Streamlined shape moves more easily through fluids

- Many mitochondria provide ATP for tail movements
- Head contains
A haploid nucleus
Tipped with an acrosome containing penetrating enzymes
Fertilisation
- brings about the haploid nuclei of sperm and egg together, forming a diploid
The Acrosomal Reaction
- triggered when sperm meets egg

- sperm releases hydrolytic enzymes that digest material surrounding the egg
In mammals the first cell division occurs 12-36 hours after sperm binding
Implantation
- Stage after fetilization in humans where a blastocyst develops from a fertilised zygote
- Egg moves along oviduct to uterus
- 6th day after fertilisation blastocyst attaches to uterine wall or endometrium
Embryo releases human gonadotropin (hCG), which prevents menstruation
Pregnancy or gestation is the carrying of one or more embryo
Gastrulation
Cells migrate
Ectoderm
Endoderm: forms the digestive tract
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Mesoderm: forms muscle and bones
A rudimentary digestive cavity forms
4 Extra Embryonic Membranes developed:
Amnion
Yolk sac
- no yolk in humans
- source of important cells
first germ cells
first blood cells
Allantois
- contributes to the umbilical cord

- forms part of urinary bladder
Chorion
- contributes to the placenta

- secretes HCG
Placenta
- Close association of
Embryonic ____________?
Mothers blood vessels
- Gas, nutrient and waste exchange
Apoptosis?
Mammary glands
- not part of reproductive system

- for feeding
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BIO 1
Sexual Reproduction (Film Showing)

Evolve
Secret to survival: Sex
Corals
- Mass spawning
Sharks
- Sharks invented sex

- First vertebrates who reproduce through penetration
- First internal fertilisation
Reptiles
- Amniotic Egg to adapt for land reproduction

Dinosaur Reproduction
- still a question
- theories to reproduce like cats
Crocodiles
- no penis but has a cloaca around 3 in? long

Insects
- most diverse reproductive parts

- copulatory plug
Bees
- males detach their penis and dies

- females (queen) however can remove the penis and choose to mate with better males
Cockroach
- female has sex only once

- can store fetilized eggs for its whole life
Sexual Selection
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- males display, females choose
Monkey (macacks)
- the louder the female makes noise, the more likely the male ejaculates
- mostly have sex hourly
Sexual Currency?
Humans
- Brain evolved
-
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BIO 1
Detecting Disorders During Pregnancy

- Amniocentesis and chorionic villus
- Noninvasive procedures usually use ultrasound
- Genetic testing of the fetus poses ethical questions and can prevent parents with
difficult decisions
New born screening tests
- Genetic predisposition
Treating Infertility
- Modern technology can provide infertile couples with assisted reproductive

technologies
Artificial Reproductive Technology (ART)
- Used primarily by couples with infertility issues or with genetic conditions

- Kinds of ART
In vitro fertilisation (IVF)
- fertilisation outside of the body
- used when the females Fallopian tubes are blocked or when a man produces too
few sperm
- The women is treated with a drug that causes the production of many eggs
- Mature eggs are removed and put in a dish with the mans sperm for fertilisation
- After 3 to 5 days, healthy embryos are implanted in the womans uterus (embryo
transfer, 8 cell stage)
Artificial Insemination
- A procedure used to treat infertility that involves directly inserting semen to fetilize
a womans egg
Sperm/egg/embryo cryopreservation
- A procedure to preserve sperm cells, egg cells or embryos
- Cooling to sub-zero temperatures, typically in liquid nitrogen (-196oC)
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- women or men who will undergo treatments that may destroy their future fertility
(such as cancer)
Contraception
- The deliberate prevention of pregnancy

- Three Categories
Preventing release of eggs and sperm
Keeping sperm and egg apart
Preventing implantation of an embryo
Types of Contraceptives
- Ovulation-suppressing methods
pregnancy rate of 1%
Oral contraceptives
- usually contain a combination of hormones that prevent release of oocytes
Time-release capsules (e.g. Norplant)
- can be implanted under the skin of the upper arm and offer long-term suppression
of ovulation
- Barrier methods (physical and chemical)

block fertilization with a pregnancy rate of less than 10%
Condoms (female and male condoms)
Cervical Cap
- also covers the cervix
Spermicidal jelly or foam
- kill sperm on contact and must be placed in the vagina prior to intercourse
- Surgical methods
Vasectomy (for men)
- vas deferens connecting the testes with the urethra is cut and sealed to prevent
the transport of sperm
Tubal ligation (for women)

- the oviduct is cut and ends tied off to prevent eggs from reaching the uterus
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- Implantation-suppressing methods
Morning-after pill
- interferes with the implantation of the fertilised egg into the uterine wall
- blocks the action of progesterone, which leads to the non-synthesis of the
proteins necessary to begin and maintain pregnancy
- other types contains progestin that blocks ovulation, fertilisation and

- Intra uterine device (IUD)
- pregnancy rate is less t
- physically blocks the fertilised egg
- Others
Rhythm Method or Natural Family Planning
- refrain from intercourse when conception is most likely
- pregnancy rate of 10-20%
Coitus Interruptis
- the withdrawal of the penis before ejaculation, unreliable
Abortion
- termination of pregnancy
- spontaneous abortion or miscarriage
- a drug that _____________ in the first 7 weeks of pregnancy
Abstinence XD
Some diseases passed on through sexual intercourse
- Chlamydial infections
- Gonorrhea
- Syphilis
- Genital herpes
- Genital Warts
- AIDS & HIV infection
- Trichomoniasis
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- Candidiasis
How to avoid STDs
Safer sex such as using condoms is the most reliable way to reduce risk of acquiring
STDs
Viruses
- Exists in a gray area between the living and the nonliving
- Must replicate within a host cell
- not cells
- very small infectious particles consisting
- Viral Genome
double or single stranded DNA, or
double or single stranded RNA
Depending on its type of nucleic acid, a virus is called a DNA virus or RNA virus
Capsid
- protein shell that encloses the viral genome
- built from protein sub
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BIO 1
Genetics
Many inherited disorders in humans are controlled by a single gene
Inherited Human Disorders Show
- Recessive Inheritance
Two recessive alleles are needed to show disease
Heterozygous parents are carriers of the disease-causing allele
Probability of inheritance increases with inbreeding, mating between close relatives
- Dominant Inheritance
One dominant allele is needed to show disease
Dominant lethal alleles are usually eliminated from the population
Variations on Mendels Laws
Incomplete dominance results in intermediate phenotypes
Incomplete Dominance
- Expression of both alleles is observed as an intermediate phenotype

Multiple Alleles
- More than two alleles are found in the population

- A diploid individual can carry any two of these alleles
- The ABO blood group has three alleles, leading to four phenotypes: type A, type B,
type AB, and type O blood
Codominance
- Neither allele is dominant over the other

- Observed for type AB blood
Type O
- Universal donor since the cells do not have either carbohydrate A or carbohydrate B
so that antibodies in the other blood types will not cause a reaction with these cells
Bombay Phenotype
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- H substance is the precursor molecule for the A and B antiens to which one or two
terminal sugars are added
- 1952 - woman in Bombay

- Incompletely formed H substance
Inadequate substrate for the enzyme that adds the terminal sugar
- Results in Blood type O and is known as the Bombay Phenotype
- Rare recessive mutation, h, at a locus separate from that controlling the A and B
antigens
- hh genotype
- Behaves as type O, but genetically type B
A single gene may affect many phenotypic characters
Pleiotropy
- One gene influencing many characteristics

- The gene for sickle cell disease
Affects the type of hemoglobin produced
Affects the shape of red blood cells
Causes anemia
Cause organ damage
Is related to susceptibility to malaria
A single character may be influenced by many genes
Polygenic Inheritance
- Many genes influence one trait

- Skin color is affected by at least three genes
The environment affects many characters
Phenotypic variations are influenced by the environment
- Skin color is affected by exposure to sunlight

- susceptibility to diseases, such as cancer, has hereditary and environmental
components
32
BIO 1
Sex Chromosomes and Sex-Linked Genes

Sex-linked genes exhibit a unique pattern of inheritance
Sex-linked genes are located on either of the sex chromosomes
- X-linked genes are passed from mother to son and mother to daughter
- X-linked genes are passed from father to daughter
- Y-linked genes are passed from father to son
Males express X-linked disorders such as the following when recessive alleles are
present in one copy
- Hemophilia
Inherited condition where blood is slow to clot or does not clot at all
Only expressed when individual has no copies of the normal allele
Royal Hemophilia - Sex-linked
- Colorblindness
Due to X-linked recessive allele b, while the X-linked dominant allele B leads
Several X-linked genes
Person with normal vision can see more than 150 colors
One with red-green color blindness can see fewer than 25
Red/Green color blindness is by far the most common form
Mutations in Human Heredity

Mutations are accidental changes in genes
- Rare, random, and usually result in recessive alleles.
Pedigrees used to study heredity
The Y Chromosome provides clues about human male evolution
Similarities in Y chromosome sequence
- Show a significant percentage of men related to the same male parent
33
Like the Y chromosome, mitochondrial DNA (mtDNA) can be used to trace maternal
ancestry (because mitochondria are characteristically inherited from the egg)
Chromosomal Aberrations
Alterations of chromosome structure
- Deletion
- Duplication
- Inversion
Sex Chromosomes Syndrome Origin of Frequency in

Nondisjunction Population
XXY Klinefelter Syndrome Meiosis in egg or sperm

(Male) formation
XYY None (normal male) Meiosis in sperm

formation
XXX None (normal female) in egg or sperm

formation
XO Turner syndrome in egg formation

(female)
Turner Syndrome
- Barrel Chest
- Webbed Neck
Down Syndrome
- Trisomy 21
Patau Syndrome
- Trisomy 13
Edwards Syndrome
- 3 copies of Chromosome 18 (Trisomy 18)
Cri Du Chat Syndrome
- Deletion in chromosome 5
Williams Syndrome
- Deletion of chromosome 8
34
Wolf Syndrome
- Deletion in chromosome 4
Digeorge Syndrome
- Deletion in chromosome
Sex-related Traits
- Sex-controlled genes
- Genome Imprinting
Prader-Willi Syndrome (extreme obesity)
- More severe if it comes from the mother
Angelman-syndrome (neurologic defect)
- Happy Puppet Syndrome
Diabetes more severe if it comes from the father
Fragile X
- Most common form of mental retardation

- The X chromosome of some people are unusually fragile at one tip - seen hanging
35
BIO 1
Human Genome Project

- began in 1990
- Mission of HGP: The quest to understand the human genome and the role it plays in
both health and diseases.
- Human Genome: more than 3M letters A, C, T, & G
- First mapped and sequenced from 1990 to 2003
- international initiative
- Sequencing the human genome
identify important genes and regulatory regions
better understand their role in disease
investigate our origins using variations in the DNA sequence
Goals
- Identify all of the genes in human DNA

- Determine the sequences of the 3 billion chemical nucleotide bases that make up
human DNA
- Store this info in databases

- Develop faster, more efficient sequencing technologies
- Develop tool for data analysis
The genome is our Genetic Blueprint
- Nearly every human cell contains 23 pairs of chromosomes
1-22 and XY or XX
- XY = male
- XX = female
- Length of chr 1-22, X, Y together is 3.2 billion bases (about 2 meters diploid)
The Genome is who we are on the inside
Chromosomes consist of DNA
- molecular strings of A,C,T&G
36
- base pairs, A-T, C-G
Genes
- DNA sequences that encode proteins

- less than 3% of human genome
What is the Human Genome?
- The entire genetic makeup of the human cell nucleus

- Genes carry the information for making all of the proteins required by the body for
growth and maintenance
- The genome also encodes rRNA and tRNA which are involved in protein synthesis
Annotation
The sequence is like a topographical map, the annotation would include cities, towns,
schools, libraries
So where are the genes?
How do genes work?
And, how do scientists use this info for scientific study to benefit us?
Humans and Mice have about the same number of genes.
However, one human gene can make many different proteins while a mouse gene can
only make a few
DNA Replication
- The two DNA strands separate
- Each strand is used as a pattern to produce a complementary strand, using specific
base pairing
- Each new DNA helix has one old strand with one new strand
DNA replication proceeds in two directions at many sites simultaneously
- DNA replication occurs in the 5 3 direction
Replication is continuous in 5 3 direction
Replication is discontinuous in 3 5 direction, forming shorter segments
- Proteins involved in DNA replication
DNA polymerase adds nucleotides to a growing chain
37
DNA ligase joins small fragments into a continuous chain
The Flow of Genetic Information From DNA to RNA to Proteins
DNA is transcribed into RNA
RNA is translated into protein
The DNA genotype is expressed as proteins, which provide the molecular basis for
phenotypic traits
- Demonstrating the connections between genes and proteins

Transcription is the production of RNA using DNA as a template
Translation is the production of protein, using the sequence of nucleotides in RNA
Translation occurs in the cytoplasm for both prokaryotic and eukaryotic cells
Genetic info written in codons is translated into amino acid sequence
- The sequence of nucleotides in DNA provides a code of constructing a protein

Translation involves switching from the nucleotide language to amino acid
language
- Protein construction requires a conversion of a nucleotide sequence to an amino acid
sequence
Transcription rewrites the DNA code into RNA language, using the same nucleotide
language
- Each amino acid is specified

The genetic code is the Rosetta stone of life
Characteristics of the genetic code
Triplet: 3 nucleotides specify one
Redundant: more than 1 codon
Overview of transcription
- 2 DNA strands separate
- One strand is used as a pattern to produce an RNA chain, specific base pairing
For A in DNA, U in RNA
- RNA polymerase catalyzes the reaction
Stages of transcription
38
Genes are Important
By selecting different pieces of a gene, your body can make many kinds of proteins.
(This process is called alternative splicing)
What we learned from the Human Genome Project

- Small number of genes around 30,000
- 85% are known
- only know about 20% of what genes do
Which branches of Biology will benefit from this knowledge?
- Medicine
- Pharmacogenomics
- Biotechnology
- Bioinformatics
- Proteomics
39
BIO 1
Genetically Modified Organisms

GMO is any living organism whose genetic material has been altered using genetic
engineering techniques
Result of technology that has altered the DNA
Other Terms
- Genetically engineered
- Transgenic
- Recombinant DNA (rDNA) technology
DNA from two different species are combined to create a new species
- Goat & Spider
Goats that produce spider silk protein in their milk could enable researchers to
collect large quantities of silk
- Soybean & BT (bacteria)

- Corn & bacteria
GM vs Selective Breeding
Selective Breeding
- slow
- precise
- modification of genes that naturally occur in the organism
GM
- very fast
- precise
- can introduce genes into an organism that would not occur naturally
Benefits
- Society
Increased food security for growing population and growth challenges
GM Plants
40
- Resistance to herbicides
- Resistance to pests
Bt corn produces an insect toxin, derived from the bacterium Bacillus thuringiensis
DNA technology has changed the pharmaceutical industry and medicine
- Products of DNA technology
- Therapeutic hormones
- Diagnosis and treatment of diseases
- Vaccines
Stimulate an immune response by injecting
GM Animals
- Improved qualities
- Production of proteins or therapeutics
Benefits of Genetic Engineering and Modifying
1. Higher yielding crops, more efficient use of land
2. Can save money and promote higher profits
3. Longer shelf life, less waste
4. Enhance taste and quality
5. Increased and improved nutrients and stress tolerance
6. Improved resistance to disease or illness
7. Improved crop resistance to disease, pests, weeds, and herbicides
8. New products and growing techniques
Genetically modified organisms raise concerns about human and environmental health
- Concerns related to GM organisms

Can introduce allergens into the food supply
May spread genes to closely related organisms
- Scientists use safety measures to guard against production
Risks associated with GM
1. Safety
41
Potential human health implications
Potential environmental impact
Creation of biological weapons
2. Access and Intellectual Property
3. Ethics
Playing God
Tampering with nature by mixing genes among species
4. Labeling
Not mandatory in some countries

Mixing GM crops with non-GM confounds labeling attempts
5. Society
New advances may be skewed to the interests of their countries

Bio-tech Companies
FDA Role: Expects the bio-tech companies to test their own products
GMO: Why
- Increased herbicides in ground & water

- Cross pollination with other plants
- Contaminates organic crops
- Increased super weeds
- Push heirloom crops into extinction
- Creates nutrient-deficient soil
GMO: Why do some people avoid them?
- No long term human feeding studies done

- It kills bugs
- Unpredictable side effects of genetic engineering
- Increased infertility and miscarriages amongst farm animals
42
Gene therapy may someday help treat a variety of diseases
Gene Therapy
- aims to treat a disease by supplying a functional allele but do not replace the defective
one
SCID (severe combined immune deficiency) was the first disease treated by gene
therapy
- First trial in 1990 was inconclusive

- is the alteration of an afflicted individuals genes
- holds great potential for treating disorders traceable to a single defective gene
Human Gene Therapy
- Vectors are used for delivery of genes into specific types of cells, for example bone
marrow
- Gene therapy raises ethical questions, such as whether human germ-line cells should
be treated to correct the defect in future generations
Pharmaceutical Products
Advance in DNA technology and genetic research
Synthesis of small molecules for use as drugs
Pharmaceutical products that are proteins can be synthesized on a large scale
Transgenic animals are made by introducing genes from one species into the genome of
another animal
Pharm plants are also being
Environmental Cleanup
Biofuels make use of crops such as corn, soybeans, and cassava to replace fossil fuel
Most public concern about possible hazards centers on GMO used as food
Some are concerned about the creation
43
Tuesday, 25 October 2016
BIO 1
Concept of Species
- Lake Victorias cichlids diversified 100,000 years ago.
- Groups isolated by diet or female mate choice may have lost the ability to interbreed
A species can be defined as a group of organisms whose members can breed and
produce fertile offspring, but who do not produce fertile offsprings with members of other
groups.
- Females of each species prefer brightly colored males with the right color
- The more brightly colored the male, the fewer parasites he has.
- 200 species of cichlids have disappeared from Lake Victoria over the last 30 years
Some were eaten by the Nile perch, an introduced predator
- In the polluted waters of Lake Victoria, it is more difficult for females to choose brightly
colored males of the right species.
- As a result, the gene pools of separate species are mixing, as two species fuse back
into one
Speciation
- The origin of new species, is at the focal point of evolutionary theory

- Evolutionary theory must explain how new
- Speciation is at the boundary between microevolution and macroevolution
- Microevolution consists of adaptations that evolve within a population, confined to
one gene pool
- is a change over the generations in a population

- Macroevolution refers to evolutionary change above the species level (new genera,
new families, new kingdoms)
- While the changes after any speciation event may be subtle, the cumulative change
over millions of speciation episodes must account for macroevolution, the scale
of changes seen in the fossil record.
Mechanisms of Macroevolution
Continental drift has played a major role in macroevolution
44
- Continental drift is the slow, continuous movement of Earths crustal plates on the hot
- The supercontinent Pangaea, which formed 250 years
- breakup of Pangaea led to the modern arrangement of continents
- India collision with Eurasia 55 million years ago formed Himalayas
The origin of species is the source of biological diversity
Speciation is the emergence of new species
Speciation occurs when a populations genetic divergence from its ancestral population
results in reproductive isolation
Several ways to define a species

- Taxonomy is the study of
- Carolus Linnaeus developed the binomial system of naming organisms using physical
characteristics to distinguish
- The biological species concept defines a species as a population or group of

populations whose members have the potential ti interbreed in nature and produce
fertile offspring
- Reproductive isolation prevents gene flow and maintains separate species

- Can the biological species concept always distinguish species from each other?
No, for example, one cannot test the reproductive isolation of morphologically-
similar fossils
many species reproduce entirely asexually and are assigned to species based
mainly on structural and
The morphological species concept classifies organisms based on observable

phenotypic traits
It can be applied to asexual organisms, fossils, and in cases when we dont know about
possible interbreeding
There is some objectivity
The ecological species concept defines a species by its ecological role or niche
Focuses on unique adaptations
The phylogenetic species concept defines a species as a set of organisms representing

a specific evolutionary lineage
Morphological or DNA similarities or differences can be used to define a species
45
Reproductive Barriers serve to isolate a species gene pool and prevent interbreeding
Reproductive Barriers are categorized as prezygotic
46
Thursday, 3 November 2016
BIO 1
Evolution
- Change in the genetic pool of the population
- NOT about the origin of life
- Explains the origin of life
- NOT about turning monkey into men
- Man evolves along with the monkeys not from them
Alfred Russell Wallace
- Another naturalist from Darwins time
Charles Darwin
Most people of his day believed that each species had been created by a separate
divine act.
- The Origin of Species presented facts that disputed this belief.

- The Origin of Species developed 2 main ideas:
Descent with modification explains lifes unity and diversity
Natural Selection is a cause of adaptive evolution (mechanism behind descent with
modification)
- Darwin never used evolution in the first edition of the book

- All organisms are related through descent from an ancestor that lived in the remote
past
- Darwin noted that humans have modified other species

- Darwins Observations
Members of a population often vary greatly in their traits
Traits are inherited from parents to offspring
All species are capable of producing more offspring than the environment can
support
Owing to lack of food or other resources, many of these offspring do not survive
47
Thursday, 3 November 2016
Darwins Inferences
- Individuals whose inherited traits give them a higher probability of surviving and
reproducing in a given environment tend to leave more offspring than other individuals
- The unequal ability of individuals to survive and reproduce will lead to the
accumulation of favorable traits in the population over generations
If some heritable traits are advantageous, these will accumulate in the population, and
this will increase the frequency if individuals with adaptations
Natural Selection: A Summary
- Natural Selection increases the adaptation of organisms to their environment over

time
- If an environment changes over time, natural selection may result in adaptation to

these new conditions and may give rise to new species
Population
Localized group of individuals capable of interbreeding and producing fertile offspring

- A gene pool consists of all alleles for all loci in a population
- A locus is fixed if all individual in a population are homozygous for the same allele
Darwins Theory of Natural Selection
- Four key components of natural selection:

Variation
Competition
Fitness
Adaptation
Darwinism
1. Evolution explains lifes unity and diversity
2. Natural selection is the cause of adaptive evolution
Evolution is supported by an overwhelming amount of scientific evidence
48

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Thursday, 25 August 2016

C. The Cell as the Basic Unit of Life

D. Prokaryotic vs Eukaryotic Cells

E. Parts of a Cell and Their Functions

BIOLOGY IS A BRANCH OF SCIENCE

- A way of understanding the natural world.

- Understand the natural world through observation and reasoning

- uses verifiable observations and measurements to describe science

- Uses data from discovery science to explain science

A hypothesis must be testable and falsifiable

- An organised systematic way of solving problems

- Acceptance is always provisional

- Scientific study is limited to area that can be observed and measured

- All organisms are composed of similar units of organization, called cells

Modern Tenets of the Cell Theory

1. All known living things are made up of cells

2. The cell is structural and functional unit of all living things

5. All cells are basically the same in chemical composition

2. Requires constant input of energy and raw materials

4. Reacts to the environment

7. Varies and evolves

The Cell as the Basic Unit of Life

- an organisms basic units of structure and function

- DNA is a molecule, made up of units called nucleotides

A pairs with T, and C pairs with G producing base pairs

- Cells are the smallest living things

1. Manufacturing: nucleus, ribosomes, endoplasmic reticulum and golgi apparatus

2. Breakdown or hydrolysis of molecules: lysosomes, vacuoles (plants only), and

3. Energy processing: mitochondria, and chloroplasts

4. Structural support, movement, and communication among cells: components of the

Common Characteristics of Different Cells

1. All cells are surrounded by a plasma membrane

Parts of the Cell

- Contains most of the genes in the eukaryotic cells

- Manufactures membranes, proteins, and lipids

- Center of manufacturing, warehousing, sorting and shipping

- A membrane-bound sac of hydrolytic enzymes that digests macromolecules.

- A membrane-bound sac with varied functions

- Contains enzymes with varied functions

- Found in plants and eukaryotic algae

- A network of fibres extending throughout the cytoplasm

- Consists of cellulose embedded in a matrix of proteins and other polysaccharides

- Anatomy is the study of the biological form of an organism

- Integrated by the common problems that all animals must solve

2. How to nourish themselves

3. How to excrete waste products

The adaptations observed in a comparative study of animals and plants evolved by

- Mimicry: Copying of the appearance of other organisms for protection or other

Physical Constraints on Animal Size and Shape

- Evolutionary convergence reflects different species adaptations to similar

Hierarchical Organization of Body Plans

- Most animals are composed of specialised cells organised into tissues

- Connective tissue mainly binds and supports other tissues

- Is divided in the vertebrate body into three (3) types:

- Depends on the endocrine system and the nervous system

A hormone may affect one or more regions throughout the body

- This is a morphological adaptation that reduces water loss

The 3 Basic Plant Organs: Roots Stems and Leaves

Shoot System and Root System

- Roots rely on sugar produced by photosynthesis in the shoot system

- Main photosynthesis organ of most vascular plants

1 Videos from BioFlix (Pearson) about Mitosis and Meiosis

- Genotypic Sex: X and Y chromosomes

- Sexual females have half as many daughters