Welcome to Biology 101 Foundations of Biology I

Fardad Firooznia, PhD 535 Marshak Ext 6580 ffirooznia@ccny.cuny.edu

Syllabus and Course Policies Lectures, Labs, and Readings

Foundations of Modern BIOLOGY

Cells are the structural and functional units of life

The Cell Theory
1665 Robert Hooke: cellulae Late 1600s Antoni van Leeuwenhoek: cells move 1830s botanist Matthias Jakob Schleiden and the zoologist Theodor Schwann put forth the cell theory

Cells are the structural and functional units of life

The Cell Theory
1858 Rudolf Virchow

1862 Louis Pasteurs experiment

Pasteurs Experiment
Question being asked? Hypothesis? Experimental prediction?

Image source: Sadava,Hillis, Heller, and Berenbaum (2011). Life: The science of Biology, 9th ed. Sinauer Associates, Inc., Sunderland, MA

Pasteurs Experiment

Image source: Sadava,Hillis, Heller, and Berenbaum (2011). Life: The science of Biology, 9th ed. Sinauer Associates, Inc., Sunderland, MA

Cells are the structural and functional units of life

The Cell Theory
1858 Rudolf Virchow
All living cells arise from preexisting cells No spontaneous creation

1862 Louis Pasteurs experiment

Early earth and origin of life?

Cells are the structural and functional units of life

Two distinct groups of cells exist
Prokaryotic cells
Simple and small Bacteria are prokaryotic

Eukaryotic cells
Possess organelles separated by membranes Plants, animals, protists, and fungi are eukaryotic

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Prokaryotic cell DNA (no nucleus)

Eukaryotic cell

Membrane

Nucleus (contains DNA) Organelles

Evolution: the unifying theme

Nothing in biology makes sense except in the light

of evolution - Theodosious Dobzhansky

Darwins contribution
Evolution is not his idea How it occurs: natural selection

Descent with modification:

Unity and diversity

Heredity?

Modern genetics
Mendels contribution
1866, but ignored till 1900s Discrete heritable factors Retain individuality generation after generation

Modern biochemistry and molecular biology

Modern biochemistry
1953, Watson, Crick, and Wilkins Rosalind Franklin Structure of DNA Redefined genes and chromosomes and reproduction and inheritance!

Nucleus

DNA
Nucleotide

Cell

(a) DNA double helix

(b) Single strand of DNA

Darwins Insight
What did he know and what did he infer?
By mid 1800s, new knowledge due to
Global exploration: diversity and similarity of life Comparative anatomy Fossils and geology

Darwins Insight
Global exploration: diversity and similarity of life

Emu

Ostrich

Rhea

Image sources: http://gallery.hd.org/_exhibits/natural-science/_more2003/_more09/ostrich-in-Addo-Park-Eastern-Cape-South-Africa-WL.jpg http://agcj.tamu.edu/307/2003c/Parker/images/emu4.jpg http://agcj.tamu.edu/307/2003c/Parker/images/emu4.jpg

Darwins Insight
Global exploration: diversity and similarity of life

Image source: http://www.galapagoscruises.be/darwins-finches.jp

Darwins Insight
Comparative anatomy (Ernst Haeckels drawings from 1874)

Note: segmentation, tail, gill pouch, notochord

Image Source: http://home.honolulu.hawaii.edu/~pine/book1qts/embryo-compare.jpg

Forelimbs of vertebrates: start developmentally the same way http://www.talkorigins.org/faqs/anatomy.html

Darwins Insight
Fossils and geology Giant Irish Elk and Cuviers anatomical works Neither moose, nor reindeer, it was extinct

Image source: Freeman and Herron, 2007, Evolutionary Analysis, 4 th edition, Pearson Education, Inc.

Darwins Insight
Fossils and geology General pattern of correspondence between Fossils and living forms from the same locale Giant ground sloth in Argentina

Image source: http://library.thinkquest.org/5393/cindy_sloth.JPG

Darwins Insight
Fossils and geology General pattern of correspondence between Fossils and living forms from the same locale Glyptodonts and armadillos in Argentina

Darwins Insight
What did he know and what did he infer?
By mid 1800s, new knowledge due to
Global exploration: diversity and similarity of life Comparative anatomy Fossils and geology Georges-Louis Leclerc de Buffon and origin of species Charles Lyell: theory of uniformity

Darwins Insight
What did he know and what did he infer?
1. Malthus writings: human individuals produce more offspring than the environment can support
Inferred?

Darwins Insight
What did he know and what did he infer?
1. Malthus writings: human individuals produce more offspring than the environment can support 2. Variation in populations
Inferred?

Darwins Insight
What did he know and what did he infer?
1. Malthus writings: human individuals produce more offspring than the environment can support 2. Variation in populations 3. Some variation is heritable
Inferred?

Darwins Insight
What did he know and what did he infer?
1. Malthus writings: human individuals produce more offspring than the environment can support 2. Variation in populations 3. Some variation is heritable 4. Artificial selection by animal breeders
Inferred?

Evolution explains the unity and diversity of life

In 1859, Charles Darwin published On the Origin of

Species by Means of Natural Selection

The book accomplished two things

Presented evidence to support the idea of evolution Proposed a mechanism for evolution called natural selection

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1 Population with varied inherited traits

2 Elimination of individuals with certain traits

3 Reproduction of survivors

Evolution explains the unity and diversity of life

Darwins four tenets
Organisms produce more offspring than the environment can support; this leads to competition There is variation in a population Some variation is heritable

There will be differential survival AND reproduction: natural selection of adaptive traits

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The Scientific Method

Steps
1. Observation 2. State the problem

3. Form a Hypothesis
4. Test/ Experiment 5. Collect and analyze the data 6. Draw conclusions 7. Repeat

Observations
What do you see?
Why is it interesting? Can it be tested?

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Hypothesis
The statement of the problem. Is the statement testable? Is the statement falsifiable? State the hypothesis as a null hypothesis. Cant prove something true but can prove something false.

Methods and Procedures

Variables
Independent = what is altered

Dependent = what is studied

Standardized (controlled) Intra and inter subject variability

Methods and Procedures

Control treatments
Repetition Reproducibility

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Result and Analysis

Data collection Data organization and analysis Using tables Using graphs

Conclusion
Reexamine the hypothesis in light of the evidence collected Did the data disprove the null hypothesis? Restate the hypothesis in light of the evidence

Future Directions
What new questions are raised?
What should be the next step?

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The Good, The Bad, And The Ugly

I grow two tomato plants from seed in separate pots next to each other on my porch. I use the same potting soil in each pot and water both at the same time each day. To one pot I add a small amount of Miracle-Gro, while I add no extra fertilizer to the other. At the end of 6 weeks, the Miracle-Gro plant has increased in weight by 210%, while the other plant has increased by only 65%. Does Miracle-Gro aid in plant growth?

The Good, The Bad, And The Ugly

150 patients with Crohns disease are given an experimental treatment in which they all drink cocktails containing thousands of pinworm eggs. Within one week, 72% of the patients report a reduction in their abdominal pain. Is ingesting pinworm eggs an effective treatment for the symptoms of Crohns disease?

The Good, The Bad, And The Ugly

A study at a Southern university reported that the average final exam grade of students who chose to enroll in an online version of a class was equal to that of students who took the class on-campus from the same professor. Is on-line learning as effective as traditional in-class learning?

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The Good, The Bad, And The Ugly

In 1972, half of a group of 111 low-income children from Chapel Hill, NC were randomly chosen for enrollment in an intensive pre-school program, while the other half were not enrolled in any preschool program. 30 years later the preschool group had a higher % attending college, higher average GPA for those who did attend college, and higher average wages than the non-preschool group. Does preschool have some lasting effects on career outcomes?

The Good, The Bad, And The Ugly

The following is from a study published in 1946 by a Scottish physician who claimed there was a relationship between morning sickness and excessive mother attachment: A study of the emotional state of these patients revealed a common featurei.e., sexual relationship with the husband gave rise to disgust I have confirmed the findings in many hundreds of women. In doing so I noted that a high proportion of them at marriage were unduly attached to their mothers.

The Good, The Bad, And The Ugly

An article in the nursing literature reported on successful coping strategies in women with severe pregnancy sickness: Most women reduced their social commitments during the early months of pregnancy, becoming much more dependent on their mothers and close friends for help in meal preparation and child care.

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Pasteurs Experiment
Dependent variable? Indepdendent variable? Standardized variables? Control(s)?
Image source: Sadava,Hillis, Heller, and Berenbaum (2011). Life: The science of Biology, 9th ed. Sinauer Associates, Inc., Sunderland, MA

Cells are the structural and functional units of life

The Cell Theory
1858 Rudolf Virchow
All living cells arise from preexisting cells No spontaneous creation

1862 Louis Pasteurs experiment Early earth and origin of life?

Origin of Life
When and How did life begin? When:
earth formed about 4.5 BYA radiometric dating of the oldest known rocks: 3.9 BYA Chemical indicator of organic synthesis:
C12 : C13 Ratio

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Electron cloud
Nucleus 2e

2 2

Protons Neutrons

Mass number = 4

Electrons

Atoms consist of protons, neutrons, and electrons

Although all atoms of an element have the same atomic number, some differ in mass number
The variations are isotopes, which have the same numbers of protons and electrons but different numbers of neutrons
One isotope of carbon has 8 neutrons instead of 6 (written 14C)
Unlike 12C, off energy
13C 14C

is an unstable (radioactive) isotope that gives

has 7 neutrons in stead of 6 and is stable and nonradioactive

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Origin of Life
When and How did life begin? When:
earth formed about 4.5 BYA radiometric dating of the oldest known rocks: 3.9 BYA Chemical indicator of organic synthesis:
C12 : C13 Ratio

Origin of Life
When and How did life begin? When:
oldest bacteria impressions ~ 3.5 BYA South Africa and Australia microfossils: 3.1-3.4 BYA eukaryotic cells about 2 BYA

Origin of Life
When and How did life begin? How?

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Origin of Life
When and How did life begin?
How do we know the conditions of the early earths atmosphere?

Origin of Life
atmosphere:
CO, CO2, H2, N2, NH3, CH4, H2S, H2O vapor no ozone, lots of reactive H 2

energy: cooling earth: inorganic metals in rocks and clay:

Origin of Life
What does it mean to be living?

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Origin of Life
Need:
1 basic blocks of life 2 cellular organization

3 reproduction/heredity and self-replication

Origin of Life
Need:
1 basic blocks of life

organic compounds: monomers and polymers Time to review some basic chemistry

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Ionic bonds are attractions between ions of opposite charge

An ion is an atom or molecule with an electrical charge resulting from gain or loss of electrons
Loss: Gain:

Two ions with opposite charges attract each other

When the attraction holds the ions together, it is called an ionic bond

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Transfer of electron

Na Sodium atom

Cl Chlorine atom

Na+ Sodium ion

Cl Chloride ion

Sodium chloride (NaCl)

Na+ Cl

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Covalent bonds join atoms into molecules through electron sharing

A covalent bond results when atoms share outershell electrons
A molecule is formed when atoms are held together by covalent bonds

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Unequal electron sharing creates polar molecules

In water:
Oxygen attracts electrons more strongly than hydrogen Electrons spend more time near oxygen Polar covalent bond

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()

()

O H (+) H (+)

Hydrogen bonds are weak bonds important in the chemistry of life

Water molecules are electrically attracted to oppositely charged regions on neighboring molecules
Because the positively charged region is always a hydrogen atom, the bond is called a hydrogen bond

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Hydrogen bond

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Ion in solution

Salt crystal

2.15 The chemistry of life is sensitive to acidic and basic conditions

A few water molecules can break apart into ions
Some are hydrogen ions (H+) Some are hydroxide ions (OH)
Both are extremely reactive

A balance between the two is critical for chemical processes to occur in a living organism

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2.15 The chemistry of life is sensitive to acidic and basic conditions

Chemicals other than water can contribute H + to a solution
They are called acids
An example is hydrochloric acid (HCl)

An acidic solution has a higher concentration of H + than OH

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The chemistry of life is sensitive to acidic and basic conditions

Some chemicals accept hydrogen ions and remove them from solution
These chemicals are called bases For example, sodium hydroxide (NaOH) provides OH that combines with H+ to produce H2O (water) This reduces the H+ concentration

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The chemistry of life is sensitive to acidic and basic conditions

A pH scale (pH = potential of hydrogen) is used to describe whether a solution is acidic or basic
pH ranges from 0 (most acidic) to 14 (most basic) A solution that is neither acidic or basic is neutral (pH = 7)

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pH scale 0

1 Battery acid Increasingly ACIDIC (Higher concentration of H+) 2 Lemon juice, gastric juice

Acidic solution

3 Grapefruit juice, soft drink, vinegar, beer 4 Tomato juice

5 Rain water 6 Human urine Saliva

NEUTRAL [H+]=OH]

7 Pure water Human blood, tears 8 Seawater

Neutral solution

Increasingly BASIC (Lower concentration of H+)

10 Milk of magnesia 11 Household ammonia 12 Household bleach 13 Oven cleaner

Basic solution

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EVOLUTION CONNECTION: The search for extraterrestrial life centers on the search for water
An important question is, has life evolved elsewhere?
Water is necessary for life as we know it

The National Aeronautics and Space Administration (NASA) has evidence that water was once abundant on Mars
Scientists have proposed that reservoirs of water beneath the surface of Mars could harbor microbial life

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INTRODUCTION TO ORGANIC COMPOUNDS

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3.2 Characteristic chemical groups help determine the properties of organic compounds
An organic compound has unique properties that depend upon
The size and shape of the molecule and The groups of atoms (functional groups) attached to it

A functional group affects a biological molecules function in a characteristic way

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Estradiol

Female lion

Testosterone

Male lion

CARBOHYDRATES
Sugars: (CH2O)n

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Glucose (an aldose)

Fructose (a ketose)

Disaccharide (condensation / dehydration reaction)

Polysaccharide
Starch granules in potato tuber cells STARCH Glucose monomer

Glycogen granules in muscle tissue

GLYCOGEN

CELLULOSE Cellulose fibrils in a plant cell wall Hydrogen bonds

Cellulose molecules

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LIPIDS Glycerol + Fatty Acids

May have other modifications, such as phosphate groups

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Lipids in Typical Biological Membranes

Hydrophilic heads (phosphate groups) Hydrophobic tails Water

Water

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PROTEINS
Polymers of Amino Acids = Polypeptides May have several polypeptides together as one protein

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Amino group

Carboxyl group

Different Amino Acids have Different Properties

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Peptide Bonds

Groove

Polypeptide chain

Collagen

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NUCLEIC ACIDS Polymers of nucleotides

Nucleotide: sugar, phosphate, and nitrogenous base

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Nitrogenous base (adenine) Phosphate group Sugar

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Figure 5.27 Components of nucleic acids

Base pair

Origin of Life
Theory of Abiogenesis: Alexander Oparin Needed:
synthesis of macromolecules, esp. proteins separation from their environment heredity and replication machinery

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Origin of Life
Miller-Urey experiments 1950s
atmosphere: CH4, NH3, H2O, H2 gases no O2

liquid water
temperature less than 100 C bombarded with electrical energy

Origin of Life
Miller-Urey experiments 1950s

Results:
formaldehyde (CH2O) hydrogen cyanide (important for amino and nucleic acids) formic acid (HCOOH) some amino acids urea (N H2CON H2)

Origin of Life
Later experiments:
other amino acids adenine (need for nucleic acids) from
HCN and NH3

fatty acids sugars from formaldehyde

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Origin of Life
Polymerization:
Sidney Fox's work near hydrothermal vents The importance of clay particles

Origin of Life
Cellular Organization
membrane-bound bag derived primarily through production of fatty acids and some polypeptides beginning of plasma membrane

Lipids in Typical Biological Membranes

Hydrophilic heads (phosphate groups) Hydrophobic tails Water

Water

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Origin of Life
Replication
need RNA for protein synthesis in cells need enzymes to replicate RNA the chicken or egg question! Thom Cech (and Sidney Altman) discovered ribozymes in 1986
1989 Nobel Prize!

Origin of Life

The First Prokaryotes!

Origin of Life

The First Eukaryotes?

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Prokaryotic cell DNA (no nucleus)

Eukaryotic cell

Membrane

Nucleus (contains DNA) Organelles

10 m
Human height

1m

100 mm (10 cm) 10 mm (1 cm)

Chicken egg

Frog egg

1 mm 100 m
Most plant and animal cells Nucleus Most bacteria Mitochondrion Mycoplasmas (smallest bacteria) Viruses

Unaided eye Light microscope

Length of some nerve and muscle cells

10 m

1 m

100 nm

10 nm 1 nm

Ribosome Proteins Lipids Small molecules

0.1 nm

Atoms

Electron microscope

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Figure 6.7 The plasma membrane and the membranes of organelles

Pili Nucleoid Ribosomes Plasma membrane Bacterial chromosome Cell wall Capsule A typical rod-shaped bacterium Flagella A thin section through the bacterium Bacillus coagulans (TEM)

Eukaryotic cells are partitioned into functional compartments

Manufacturing involves the nucleus, ribosomes, endoplasmic reticulum, and Golgi apparatus
Manufacture of a protein, perhaps an enzyme, involves all of these

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Eukaryotic cells are partitioned into functional compartments

Breakdown of molecules involves lysosomes, vacuoles, and peroxisomes
Breakdown of an internalized bacterium by a phagocytic cell would involve all of these

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Eukaryotic cells are partitioned into functional compartments

Energy processing involves mitochondria in animal cells and both mitochondria and chloroplasts in plant cells
Generation of energy-containing molecules, such as adenosine triphosphate, occurs in mitochondria and chloroplasts

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Eukaryotic cells are partitioned into functional compartments

Structural support, movement, and communication involve the cytoskeleton, plasma membrane, and cell wall
An example of the importance of these is the response and movement of phagocytic cells to an infected area

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Eukaryotic cells are partitioned into functional compartments

Membranes within a eukaryotic cell partition the cell into compartments, areas where cellular metabolism occurs
Each compartment is fluid-filled and maintains conditions that favor particular metabolic processes and activities

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NUCLEUS: Nuclear envelope Smooth endoplasmic reticulum Rough endoplasmic reticulum Chromosomes Nucleolus

Lysosome Centriole Peroxisome CYTOSKELETON: Microtubule Intermediate filament Microfilament Ribosomes Golgi apparatus Plasma membrane Mitochondrion

NUCLEUS: Nuclear envelope Chromosome Nucleolus Golgi apparatus

Rough endoplasmic reticulum Ribosomes Smooth endoplasmic reticulum CYTOSKELETON:

Central vacuole Chloroplast Cell wall Plasmodesmata Mitochondrion Peroxisome Plasma membrane Cell wall of adjacent cell

Microtubule Intermediate filament Microfilament

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Mitochondrion

Outer membrane Intermembrane space

Inner membrane

Cristae
Matrix

Chloroplast Stroma Inner and outer membranes

Granum Intermembrane space

Flagellum

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Cross sections:

Outer microtubule doublet

Central microtubules Radial spoke Flagellum Dynein arms Plasma membrane Triplet Basal body Basal body

Bacterial flagellum

Salmonella
Image sources: http://media-2.web.britannica.com/eb-media/02/58702-004-429BF178.jpg http://morayeel.louisiana.edu/SeaweedsLab/Gavio/bacterial%20cell%20copy

Figure 16.4 D

Origin of Life

The First Eukaryotes?

Lynn Margulis and the Serial Endosymbiotic Theory (SET)

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Origin of Life
1. 2. Trace the history of prokaryotic and eukaryotic life on earth as outlined in the article. What was Wallins theory of mitochondrial evolution and why was it rejected at the time?

3.
4. 5. 6.

Why does Lynn Margulis believe that endosymbiosis was the result of adaptation to an aerobic environment?
What are the basic tenets of the theory of Autogeny? What are some problems associated with this theory? What evidence is presented in support of the SET? If the assumption that endosymbiosis was the result of adaptation to an aerobic environment turns out to be incorrect, how might it affect the scientific acceptance of the theory of serial endosymbiosis?

Origin of Life

The First Eukaryotes?

Evolution of nucleus: role of viruses?!
Virus injecting its gene into a proto-nucleus in a bacterium? The mimivirus evidence? See article

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