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Unit One Notes

5/26/15 11:29 AM

Lecture One (Chapter One) 9/6
• Properties of life: What is living?
• Scope of Life: the hierarchy
• Unity and diversity of life
• Process of science
Properties of living organisms
• Reproduction and to grow and develop
• Cells (part of hierarchy)
• Adaptation
o Within lifetime
o Across generations
•
•
•
•
•

§ Evolution by Natural Selection
Metabolism
Catabolism
Energy released
Anabolism
Molecules built

DNA
• Code for maintenance , growth, reproduce
• Self regulation
• Order/organization
• Interpretation
What name is given to organisms that convert the carbon in organic
compounds into carbon dioxide?
A: Heterotrophs or Plants (actually all of the options)
Major differences between the two cells types
• Know difference between prokaryotic and eukaryotic cells
• Prokaryotes (bacteria)
o Domain bacteria
o Domain archea (bacteria)
• Eukaryotes (everything else)
• See chart p
...
The hypothesis may then
be tested via the steps of the scientific method
...
2 of notebook’
Nutrition, Digestion and Body Size
• Organisms need in their diet
o Energy
o Building blocks
•

o Minerals
o Vitamins
• How organisms acquire ingredients
o Plants: roots
o Animals: digestion
• The implications of body size on metabolism
Skeletons
• Most primitive life forms (water based) hydrostatic
• Exoskeleton
o Arthropods
• Exoskeleton
o Why insects are small
o Endoskeleton grows with humans
§ Protective functions
§ Red blood cells are born in the Skelton
§ Made within mammal skeleton
§ Skeleton is living
ú Contains calcium
ú Bone is a storage system for calcium
ú Phosphate is stored in bone
• Phosphate can be liberated
Vascular systems and skeletons
• Water: land
• Small: big

Give me three adaptations for moving onto land (either of plants or of
animals) that are really important
• Ridged skeleton
• Lungs
• Shelled eggs (for protection from water loss)
Three adaptations from small to big animals
• Circulatory system
• Endoskeleton (grows with organism)
• Respiratory system
Nutrients
• Plants do not need organic nutrients
•

•

•

Organic (things synthesized by our body)
o Hormones
o CO2
o Lactic acid
o ATP
o Proteins
o Vitamins
o Enzymes
o Some are taken in by our diet
Organic things in plant
o Every organic molecule is made by a plant
o Only thing that plants acquire that would be considered
nutrients are considered minerals
§ Obtained from its environments and needed to
complete its life cycle
§ Micro and Macro nutrients
§ Minerals in organic things have to be acquired by plants
§ Minerals have two general classes of functions (involved
in structure of the plant)
§ Minerals are also involved in regulation
Animals Nutrients
o Essential (organic)
§ Building blocks (make things of the body)
§ Fuel
o Minerals

§
§
•

•

All inorganic elements
Hemoglobin incorporates iron into 4 dimensional
structure

Vitamins
o Organic (fat insoluble or fat soluble)
o Obtained diet
o many associated with enzymes
How about minerals
o Inorganic
o Obtained in diet homeostasis, nervous system, bone, blood
(cofactors)

Stages of Digestion
• Ingestion
o Another word for eating
• Digestion
o The breakdown of food into molecules small enough for the
body to absorb
...
2 notebook
Know Water molecule and Hydrogen bonds
Polar is when the electrons tend to group to one side
...
(property of water)
• Hydrogen bond forms between the adjacent water molecules
...

Solids is less dense than liquid
Surface tension
o Due to the cohesion
Water is a solvent
It had a pH
o Acid can kill other plants

Organic Compounds
• What makes a compound organic?
• There are four classes of organic compounds and you should know
them by their general structures
...
Contain only carbon, hydrogen, and oxygen
...
If we eat too much sugar,
insulin is called into action
...

Why are lipids insoluble in water?
Cholesterol, fats, hormones

Proteins
• Nitrogenous organic compounds consisting of large molecules
composed of long chains of amino acids
• They have a nitrogen on them
• Amino acids join together
o Primary structure
o Secondary structure
o Tertiary structure
o Quaternary structure
• 100,000 to over a million different proteins in the human body
o their structure is determined by
o their functions are determined by
4 classes of organic compounds
• carbohydrate
o monosaccharide, disaccharide, 8polysaccharide
o CHO 1:2:1
o Function: energy
o Structure: cellulose
• Fats/lipids
o Nonpolar (not soluble in water)
o Structure: lipids are involved in energy
o steroids (hormones)
• Proteins
o Nitrogen is present
o C-O-O-H
o enzymes
o transporting molecules
o Carrying oxygen, etc
...
5 billion years ago
• Eukaryotic cells
o Larger
o more complex
o have organelles
o found in protists, fungi, animals
o 2
...

§ energy is produced for the cell
o Rough and smooth ER
§ Endoplasmic Reticulum
ú Smooth
ú Rough
§ Make lipids and proteins
...
plants cells
• plants
o have organelle that can make/produce energy
o large vacuole
§ have many functions
§ cannot be found in animal cells
§

Lecture Five

5/26/15 11:29 AM

1
...

2
...
We don’t live
without them
...
Allows chemical reactions to
occur easier
...
Proteins also occur in the cell membrane
...
They have specific functions and differ from person to person
...
Diffusion, osmosis, facilitated transport and active transport
...

• With enzyme: An enzyme speeds the chemical reaction by lowering
the activation energy barrier
...
They enter into the cytosol of the cell
...

Transport across cell membranes (membrane transport)
• Things are transported inside and outside of the cells
• Diffusion, facilitated diffusion, osmosis, active transport
• Diffusion
o higher solution concentration
• Facilitated Diffusion
o Presence of a protein transports molecules
• Osmosis
o Higher water concentration (lower water concentration)
•

•

o diffusion of water
Active Transport
o Higher solute concentration
o lower solute concentration
o only one that requires energy
o needs ATP energy to happen
o solutes are going against the gradient

Lecture Six (Biochemistry

5/26/15 11:29 AM

What you should know
• We eat food, and breath oxygen
...
What?
• cellular respiration is the process that converts energy from ffod to
ATP energy
• CR based on Redox reaction
...

Respiration
• O2 and CO2
Cellular respiration
• Occurs in muscle cells
• add heat to slide with equation
OIL: Oxidation is loss of electrons from a molecule, releases energy
RIG: Reduction is gain of electrons from a molecule, absorbs energy
Glycolysis
• Occurs in cytoplasm of cell
• Input: 6 carbon glucose and ATP
• Output: 3 carbon molecules of pyruvic acid, ATP and electron
carrier
• does not require oxygen
• most of energy in glucose contained in bonds of pyruvic acid
Intermediate step

2 pyruvic acid 3: C molecules converted to Acetyl CoA (2-C
molecule)
• Acetyl CoA: Acetic acid attached to an enzyme
Citric Acid Cycle
• Input: Acetic acid bonds to acceptor molecule to form citric acid
• Output: CO2, ATP and electrons carriers (FADH2 and NADH)
• Cycle of reactions that breaks bond of Acetic acid, releasing enery,
electrons, and H+
Electron Transport Chain
• Electron Carriers
• Water and ATP
•

•
•
•
•
•

Chain: chain of molecules that accept e- in cascade
...


Chapter Seven Lecture

5/26/15 11:29 AM

What to know
• Photosynthesis is superficially the reverse of cellular respiration
...
In other ways, very similar
...
Why?
• Photosynthesis involves two main steps: The light reactions and
The Calvin Cycle
• You need to where these processes occur, and their inputs and
outputs
Leaf Cross Section
• Opening on underside of leaf stoma
o Openings for the exchanges of gases and water
o Carbon dioxide, oxygen, water
o Fluid that is around the thylakoids
• Thylakoid
o Granum
§ A bunch of stacks
§ contains phosphobilayer membrane
§ thylakoid space is inside of thylakoid space
...

• Electron transport chain produces hydrogen ion gradient and H+ to
drive ATP systnesis
Light Reactions
• Occurs in thylakoid
Lught, water, AFO
• foes not requite CO2
• use photons of ligt nary to intiate electon carries for…
• first described in bacteria

•

second photo system 2 is first, phorosyntheses 1 comes later
...

Water is spilt into H+
H+ accumulates in Thylakoid space, creating diffusion gradient
H+ gradient used to drive ATP production in ATP Synthase
...

Fermentation
• There is no oxygen present
• No citric acid cycle
• Pyruvic Acid is converted either to lactic acid or ethanol
Calvin Cycle
• Occurs in stoma
• Input: ATP, NADPH (from light reaction) and CO2
• Output: G3P (sugar), ADP, NADP+
• A cycle whereby a 5-C sugar (RuBP) binds with carbon dioxide
• This ^-C molecule splits into two #-C molecules
• ATP and NADPH used to make G3P, which is building block of
glucose
•
•
•

Review for test one
Functions and structures
• carbohydrates
o fuel
o support
• proteins
o support
o transport
o movement
o regulation
o insulation
o etc
...

What to know
• chromosomes
• cell types
Cell reproduction (mitosis and Meiosis)
• know the processes
• what kind of cells
• where they occur
• how they differ
Two major phases
• Interphase: growth and chromosomes duplication
• Mitotic phase
Chromosome Terminology
• Chromosomes: humans have 23 pairs (in the middle for
comparison)
o 22 of these pairs of autosomes (nothing to do with sex
related traits)
• Homologous chromosomes
o one of a pair of chromosome
• Chromatid
o ½ of two identical copies of replicated chromosomes
Cell terminology
• Diploid cells
o Have the full complement of chromosomes (2N)
o They are somatic cells: non-sex cells (most of the body)
• Haploid cells
o they contain ½ the number of chromosomes (N)

o They are gametes, germ or sex cells (Located in the ovaries
or testes) Sperm and eggs
§ Refer to slide on lecture eight for cell division
Celle Reproduction
• Mitosis
o two exact replicate daughter cells are produced from parent
cell
• Meiosis
o Four daughter cells are produced from parent cell; they
contain only ½ of chromosomes of the parent cell
• where
o In testes in males and in ovaries the female (occurs when you
are a fetus)
Steps in cell division
• gap 1 phase
• s phase
• gap 2 phase (DNA repair, corrects the mistakes)
• mitosis phase
The stimulus
• death or damage of neighboring cell
• cell signaling
why cancer occurs
• out of control growth of cells
Controls over Cell cycle
• G! checkpoint
o Checks if cell is large enough to enter S phase
o Checks for errors in DNA, fixes them and determines if cell is
large enough to enter M phase
o if the DNA are properly separated between the daughter cells
• Consequences
o Run-away growth
Meiosis and sexual reproduction
• Zygote: fertilized egg that might become and organism
• Chromosomes duplicate
• homologous chromosomes separate
• sister chromosomes separate

•

meiosis does not cross over and mutate like mitosis
o It produces chromosomes in the daughter cells that are not
the same as the cells from the parent cells
...
15)

Chapter Nine notes

5/26/15 11:29 AM

Patterns of Inheritance
• Mostly it’s about Mendel
• Mendel’s science: His work was largely an example of discovery
science
• From his work we have the following terminology: genes’ alleles,
dominant traits, recessive traits, phenotype, genotype, loci
• Mendel gave us two laws
Principle of segregation
Principle of Independent assortment
What happens during Meiosis?
• Crossing over (Variability created in the offspring)
• Haploid gametes
• The cells divide twice
Chromosome theory of inheritance
• Chromosome contain DNA; genes are in the chromosomes
• Chromosomes replicated and passed on to offspring, but also from
cell to cell
• Nucleus of a diploid cell contains two sets of chromosomes, which
are found in homologous pairs
...
Fertilization leads
to diploid zygotes
What is the function of genes
• Proteins
• Nucleotides will eventually lead to the protein
Alleles: different categories of genes
How are traits Inherited?
Mendel’s Peas
• http://www
...
org/Mendel
...
g
...
Lead
to production of over 100,000 types of proteins
• Genetic changes in the genes will lead to phenotype changes in the
proteins, which may affect function
• M in front of something stand for messenger
Transcription
• Transcribing the code of DNA
o Unwinding and RNA synthesis
o Re-winding and release of pre-mRNA
• Premessenger RNA
Transcription in the nucleus
• Product messenger RNA
• Translate one language another lange to the grsss sjk
Trnalation
•
•
•
•
•
•
•
•
Proteins
•
•

``mrn sequence contains coe eera,omp acid ming rorder in which amino
adids aae aade
amino acids combine to the conveyor belt that delivers DNA to the ribosome
...

Gene Regulation in Eukaryotes
• Euakaryotes have many complex gene regulating mechanism with
many points where the process can be turned on or off
...
Limits access for
transcription
• In locked state, DNA transcription cannot occur
• Remodeling of chromatin allows access to DNA
• Most important stage regulation of gene expression
• Transcription controlled by activator proteins, which act like keys
• Activator proteins call transcription factors (thousands of different
types)
• Default for most genes is off position
...
Gene expression is off by presence of repressor
• 2
...
Repressor removed from operator; transcription can occur
Master Control Genes
• Most cell signaling and regulation of gene expression occurs early in
development
• Homeotic genes control gene expression in different parts of the
body
• Homeotic gene organization is similar in plants and animals
Gene Expression
• There are trillions of cells, and most contains same DNA
o All somatic cells contain same DNA, but not all cells express
the same genes
o Gene expression is regulated

Chapter 11 notes
Focus
• Cloning and cancer
Cloning
• Reproductive cloning
o Nuclear transplantation
• Therapeutic cloning
o Embryo
o Umbilical cord
o Adults
Indirect (ex vivo)
o DNA
o Targeted cell
o Non-viral
• Direct (In vivo)
o Viral
o DNA
o Non-viral
Germline Gene therapy
• Fixing the egg cells
• Fixing the genes that give rise to human disorders
• We could have the genes passed on to offspring
• Everyone would be perfect
...
DNA unpacking
• B
...
RNA processing
• D
...
Protein Activation
•
Terms
•
•
•

•

•

Review
•

F
...

Often species are not closely related
for test
Methylation
o Leads to gene expression

Chapter 13, Lecture 12

5/26/15 11:29 AM

Evolution
• What is evolution
• Theory of Evolution
o Focusing on the fundamentals
• Science and non-science
Evolution: the genetic change in a population or species over generations
Darwin’s theory of Evolution
• First person who brought evolution to the scientific community
• Five components
o The mechanism is natural selection
o Common descent
o Gradual change
o Periodic change
o Speciation
§ Evolution of new species
Theory of Evolution
• Reproductive Success
o Tendency for geometric increase in number
o + environmental Restrictions
• Struggle for Existence
o Competition
o + heritable variations
• Natural Selection
o Persistence of adaptive traits
o +Environmental changes
• Evolution
o Change in a trait
Modern Synthesis (1900’s)
• Several mechanisms of evolution in addition to natural selection
• Characteristics are inherited as discrete entities called genes
o Mendel
• Variation within a population is due to the presence of multiple
alleles of a gene
• Speciation is (usually) due to the gradual accumulation of small
genetic change
Mechanisms

Natural selection
Genetic drift
Gene flow
Mutation
Non Random mating (inbreeding)
o (Point of all mechanisms is to see genetic change in
populations)
Microevolution
• Genetic change in population (changes in gene frequencies)
Macroevolution
• New species evolve from old species
•
•
•
•
•

Theory of Evolution
• Genetically based change, generally (Microevolution)
• Variability is inherited (Mendialian inheritance)
• Genotype: phenotypes (gene expressions)
• Populations evolve, not individuals
...
systematics
o Phylogenetic systematics
• How do we know these things?
The Cambrian explosion
• After 15 million years all animals appear in fossil record
• Increase in diversity (number of marine families)
Mass extinctions
• Permian extinction
• There may have been an asteroid
• Half of the families of marine animals died
• Dinosaurs extinction
o Cretaceous extinction
Precambrian Era
• Prokaryotes
o Gave rise to eukaryotes
• Eukaryotes
• 4600-500 mya
Paleozoic Era
• 500-250 mya
• Most animals appear
• Plants
• Vertebrates: fish, reptiles, amphibians
• Beginning of Cambrian explosion
• Most animals appear on earth
• Plants exist

Mesozoic Era
• 250-65 mya
• age of reptiles
• flowering plants
• insects
• most modern vertebrates
• mammals and birds first appear
• Pangaea (major sea in NA)
Cenozoic Era
• 65-0 mya
• mammals and birds first appear
humans evolve
continents move into modern configurations
a species
Biological species concept defines a species as “A group of
populations whose members have the potential to interbreed with
another in nature to produce fertile offspring
How do new species evolve
• Geographic (allopatric speciation)
o Physical separation between population
o Most common
• Sympatric speciation
o No geographic separation
o Behavioral
Know slide from homework
How are species Classified
• Species (panthera)
o Genus (Panthera)
§ Family (feldae)
ú Order (carnivora)
• Class (mammalia)
o Phylum (chordate)
§ Kingdom (animila)
ú Domain (eukarya)
Howa are species classified
• Homologies, clades, derived traits, primitive traits, convergent traits
•
•
What is
•

•
•

Phylogeny is analogous to genealogy
All organisms that are alive today have a common history

Tree
Cladogram
o Built using traits that enable you to move from most inclusive
to least inclusive groups
o Sister groups are close relatives within the tree
...
Systematics
• 2
...
Protista
The rates of decay that can be measured today are the same as the rates
many years ago/
Derived traits vertebra is associated with the same group
Domain Archea
• Live in the most extreme, harshest environments in the world
Viruses
• All parasites

Lecture 16, Chapter 15

5/26/15 11:29 AM

What You need to know
• Protista
o Diversity
o Major Characteristics
• Fungi
o Diversity
o Major characteristics
• Plants
o Diversity
o Major characteristics
• Subtheme: life cycle comparisons
Sporic
Gametic
Zygotic
•
Kingdoms
Domain Bacteria
Domain Archea
Domain Eukarya
§ Kingdom Protista
ú No derived trait (polyphyletic)
§ Kingdom Plantae
ú Derived trait (monophyletic)
§ Kingdom Fungi
ú Derived trait
§ Kingdom Animalila
ú Derived traits
Genetic basis is the key to shared DNA
• There is no trait for protiists that contains all other kingdoms
Protista
• Single cell or not
• Cell membrane or wall
• Form colonies or chains
• Absorbs, ingests or photosynthesize food
• >100,000 spp
Classifying protists
• Animal like
o
o
o
Four
o
o
o

Plant like
Fungi like
o Cell wall made up of protein called kyotin
o Lack features of cell wall
o Are not multicellular
o Contain cell wall that contains
o Chqacr3w oor 5h3 ihrim3 tuny
§ Reprrpisodesom a
Characteristics of the Kingdom Fungi
• 1
...

o Animals: nutrients water and sunlight
• Helping in Predation
o Plants: Growth, physical and chemical defenses
• Gravity
o Plants: Roots, lignin
Vascular , Seed bearing Plants
• Pollen is not sperm
Plants with Seeds
• Gymnosperms
o Naked seeds
• Angiosperms
o Seeds with vessels
Pollen contains to cells that produce sperm
• Gametophyte
monocots: palm trees, grasses
dicots: all other plants
Animals
`trends in animal changes
Diversity of animals
Types of Tissue
• Epithelial
• Connective
• Muscle
• Nervous
• Bilateral symmetry

Lecture 18, Chapter 17
Classification of Animals
• Tissue
o No: Parazoa
o Yes: eumetazoa
Porifera
• Aquatic
• Mostly Marine
• Filter feeders
• Intracellular digestion
• Collar cell is defining feature of a cells
Cnidaria
• Mouth/anus in the same opening
• Gastro vascular cavity
Echinodermata
• Deuterostomes
• Unique vascular system
• All marine
• <10,000 brain species
• No brain
Tetrapod’s
•

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Lecture 19, Chapter 18

5/26/15 11:29 AM

The Rest of the semester
• 1
...
Self-regulation: what, how, and why?
• 3
...


5/26/15 11:29 AM

Chapter 20, Lecture 19

5/26/15 11:29 AM

Self Regulation
• Circulatory: Transports system
Transpirations
• Regulated by guard cells surrounding the stomata
• Cohesion and adhesion in xylem (cohesion of H2O molecules to
each other and adhesion of H2O molecules to xylem cell walls)
• Water uptake via root hairs
Circulatory Systems
• None: gases, nutrients, diffuse through epidermis
• Open systems: insects, spiders, crab, snails
o Blood vessels, heart is in a chamber, blood vessels will fill the
chamber and then the heart
• Closed system: chordates, squid
Mammals
• Pulmonary Circuit
o Puts oxygen and removes CO2
o Involves lungs and two chambers of the heart
o Two chambers are called ventricles
• Systemic circuit
o Delivers oxygen from tissues and gets rid of CO2 within the
blood
o Left ventricle, aorta, system, right atrium (right atrium is like
reservoir)
o If vessel is traveling to the heart it’s called a vein
o If it travels away from the heart, it’s called an artery
Respiratory System
• Blood in the pulmonary circuit releases CO2 and picks of oxygen
• Oxygen is carried on to protein (hemoglobin)
• At low ph, hemoglobin will relapse oxygen
• At high PH it will bind with oxygen

Self Regulation

5/26/15 11:29 AM

How does it work
• Anatomical, behavioral and physiological adaptations
• Negative feedback
Why does it occur
• Law of tolerance
What is being regulated
• Temperature
• Heart rate
• PH level
o PH: 1
...
2
o Water
o Salts
o Gases
o Blood pressure
o Metabolism
o Sugar
o Fat
o Thirst
o Pain
o Light
o Survival
o Hormones
• Every organism interacts with an environments
• We interact with internal and external
o Digestive
o Respiratory
o Excretory
o Circulatory
o Nervous
o Endocrine
o Integumentary
Self Regulations
• Temperature: thermoregulation
o Endotherm
§ Mammals and Birds

o Ectothermic
§ An organisms who’s’ temperature fluctuates with its
environment
Water and Salts: Osmoregulation
• Osmregulator
• Osmoconformer
Stimulus: Heat
• Regulator
• Conformer
• Response/cool
Thermoregulation
• Heat exchange
• At night, we lose heat
• First exchange of energy is radiation
• Wind pushes or pulls heat away from body
• Sweating or evaporation
• You get exchange between surface and body (conduction)
• Heat either comes in or goes out
Thermoregulation
• Adaptations
• Anatomical adaptations
• Adaptations to cope with cold or hot weather
o Hair
o Large appendages
o Bulky body (SA/V)
o Fat
o Pores for sweating
o Feathers
o Air blanket
o Big or small
• Behavioral adaptations
o Night or day (nocturnal) (diurnal)
o Hibernation
o Herding
o Eating habits
o Migration

Physiological Adaptations
• Stimulus
o Heat
o Sugar
o Salt
o Water
o PH
o Hormones
o ATP
• Sensor
• Control
• Effectors
Negative Vs
...
Electrical signal
2
...
Neurotransmitter leaves cell and binds to surface receptor of target
4
...
Stimulus
6
...
Sensory neuron
8
...
Motor neuron
Target (response)
Features of the Nervous System
• Electrical signaling
• Chemical signaling



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