Welcome to Biology 101

Foundations of Biology I
Fardad Firooznia, PhD
517 Marshak
Ext 6580
ffirooznia@ccny.cuny.edu
1
Scientific Literacy
National Science Education Standards (NRC 1996)

§Scientific literacy is the knowledge and

understanding of scientific concepts and processes
required for personal decision making, participation
in civic and cultural affairs, and economic
productivity.
§Scientific literacy entails being able to read with
understanding articles about science in the popular
press and to engage in social conversation about
the validity of the conclusions.

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Foundations of Modern
BIOLOGY

3
Cells are the structural and functional units of
life
§ The Cell Theory
– 1665 Robert Hooke: cellulae
– Late 1600s Antoni van Leeuwenhoek:
cells move

4
Cells are the structural and functional units of
life

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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

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Cells are the structural and functional units of
life
§ The Cell Theory
– 1858 Rudolf Virchow

– 1862 Louis Pasteur’s experiment

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Pasteur’s
Experiment

Image source:
Sadava,Hillis, Heller, and Berenbaum
(2011). Life: The science of Biology, 9th
ed. Sinauer Associates, Inc.,
Sunderland, MA
8
Pasteur’s Experiment

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

9
Scientific Literacy
National Science Education Standards (NRC 1996)

§Scientific literacy implies that a person can identify

scientific issues underlying national and local
decisions and express positions that are scientifically
and technologically informed.
§A literate citizen should be able to evaluate the
quality of scientific information on the basis of its
source and the methods used to generate it.
Scientific literacy also implies the capacity to pose
and evaluate arguments based on evidence and to
apply conclusions from such arguments
appropriately.
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The Good, The Bad, And The Ugly

The scientist fertilizes one lake with phosphorus

and takes 12 water samples 1 month later to
determine the amount of chlorophyll in the
lake. The scientist also takes 12 samples from a
control lake of the same size. The average
chlorophyll level is much higher in the fertilized
samples than in the control samples, so the
scientist concludes that phosphorus has a
significant effect on production of chlorophyll by
photosynthetic organisms.

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The Good, The Bad, And The Ugly

The scientist takes 12 different lakes and measures

their chlorophyll levels in May. The scientist then
fertilizes all the lakes with phosphorus and re-
measures chlorophyll levels in July. Because the
average chlorophyll concentration is much greater
in July, the scientist concludes that phosphorus has
a significant effect on production of chlorophyll by
photosynthetic organisms.

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The Good, The Bad, And The Ugly

Because the scientist has a limited budget to buy

fertilizer, s/he fertilizes the 6 smallest lakes in the
area with phosphorus and measures the change in
chlorophyll concentration over time. Because the
change in these lakes is significantly greater than
the change in 6 larger control lakes, the scientist
concludes that phosphorus has a significant effect
on production of chlorophyll by photosynthetic
organisms.

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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?

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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 feature—i.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.”
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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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Pasteur’s
Experiment
§Dependent variable?
§Indepdendent
variable?
§Standardized
variables?
§Control(s)?
§Hypothesis?
§Experimental
Prediction?
Image source:
Sadava,Hillis, Heller, and Berenbaum
(2011). Life: The science of Biology, 9th
ed. Sinauer Associates, Inc.,
Sunderland, MA
17
Cells are the structural and functional units of
life
§ The Cell Theory
– 1858 Rudolf Virchow
– 1862 Louis Pasteur’s experiment
– Early earth and origin of life?

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Cells are the structural and functional units of
life
§ Two distinct groups of cells exist A. Escherichia coli, a prokaryote
DN

Dr. Terry Beveridge/Visuals

Unlimited, Inc.
A
– Prokaryotic cells
– Eukaryotic cells
0.5

– What are the major differences? µm

B. Paramecium aurelia, a eukaryote

Nucleus with
DNA

Associates/Science
Biophoto
20
µm
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Hierarchical classification

• In traditional classification, species are grouped

into successively more inclusive categories:

Species > Genus > Family > Order >

Class > Phylum > Kingdom> Domain

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 Traditional Hierarchical Classification

Domain: Eukarya

Kingdom: Animalia

Phylum: Chordata

Class: Mammalia

Order: Carnivora

Family: Ursidae

Genus: Ursus

Species: Ursus americanus

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Figure 1-10 p9
Evolution: the unifying theme

§ Nothing in biology makes sense except in the light

of evolution - Theodosious Dobzhansky
§ Darwin’s contribution
– Evolution is not his idea
– How it occurs: natural selection
– Descent with modification:
– Unity and diversity

– Heredity?

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Modern genetics

§ Mendel’s contribution
– 1866, but ignored till 1900’s
– Discrete heritable factors
– Retain individuality generation
after generation

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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!

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Darwin’s 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

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Darwin’s 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

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Darwin’s Insight

– Global exploration: diversity and similarity of life

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

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Darwin’s Insight

– Comparative anatomy
Image source:
Solomon et al. (2011) Biology, 9th edition

– Forelimbs of vertebrates: start developmentally the same

way http://www.talkorigins.org/faqs/anatomy.html

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Darwin’s Insight

– Fossils and geology

• Giant Irish Elk and Cuvier’s anatomical works

• Neither moose, nor reindeer, … it was extinct

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Darwin’s 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
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Darwin’s Insight

– Fossils and geology

• General pattern of correspondence between Fossils and living
forms from the same locale

• Glyptodonts and armadillos in Argentina

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Darwin’s 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

– Enough time for evolution
– But what was the mechanism?

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Darwin’s Insight

§ What did he know and what did he infer?

1. Malthus’ writings: human individuals produce more
offspring than the environment can support
§ Inferred?

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Darwin’s Insight

§ What did he know and what did he infer?

1. Malthus’ writings: human individuals produce more
offspring than the environment can support.
2. There is variation in populations.
§ Inferred?

Image source:
https://copr.nrs.ucsb.edu/natural-resources/invertebrates/acorn-barnacle 34
Darwin’s Insight

§ What did he know and what did he infer?

1. Malthus’ writings: human individuals produce more
offspring than the environment can support.
2. There is variation in populations.
3. Some variation is heritable.
§ Inferred?

35
 Artificial Selection

(A) Granger, NYC — All rights reserved

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Darwin’s Insight

§ What did he know and what did he infer?

1. Malthus’ writings: human individuals produce more
offspring than the environment can support.
2. There is variation in populations.
3. Some variation is heritable.
4. Artificial selection by animal breeders
§ Inferred?

37
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 39
 Camouflage in Rock Pocket Mice

Hopi Hoekstra, Harvard University

40
Distributions of Rock
Pocket Mice

Arizona New Mexico

Mouse
color N = 18 N = 11 N = 15 N=5 N = 12 N=8
Rock
color
Pinacate Armendaris
Most mice sampled on pale
rocks had sandy-colored fur.
Most mice sampled on dark 41
rocks had black fur.
Evolution explains the unity and diversity of life

§ Darwin’s 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: this
leads to natural selection of adaptive traits.

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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

43
Atomic Nuclei of Isotopes

§ What are isotopes?

§ What is the difference among the following?
§ C12
§ C13
§ C14

44
Origin of Life

§ When and How did life begin?

§ When:
§ Chemical indicator of organic synthesis:
§ C12 : C13 Ratio
§ Living organisms “prefer” C12: Why?
§ Inorganic reactions?
§ About 3.7 BYA deposits have high C12 : C13 Ratio!
Suggestion?
§ Controversial evidence (2017) from northeastern Canada
suggests 3.95 BYA
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Origin of Life

§ When and How did life begin?

§ When:
§ oldest bacteria impressions ~ 3.5 BYA
§ controversial evidence of fossilized microbes from
Quebec ~ 3.77 BYA (2017)
§ South Africa and Australia microfossils: 3.1-3.4 BYA
§ eukaryotic cells about 2 BYA

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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 earth’s
atmosphere?

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Origin of Life

§ atmosphere:
§ CO, CO2, H2, N2, NH3, CH4, H2S, H2O vapor

§ no ozone, lots of reactive H2

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

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Origin of Life

§ What does it mean to be living?

50
Origin of Life

§ Need:
1 basic blocks of life

2 cellular organization
3 reproduction/heredity and self-replication

51
Review chemical bonds

§ Ionic bond
§ Covalent bond
§ Polar
§ Nonpolar

52
Stabilizing Effect of Hydrogen Bonds

§ How is a hydrogen
bond formed?

Hydrogen
bond

53
 pH
The pH Scale Hydrochloric acid (HCl) 0 § What is pH?
Gastric fluid (1.0–3.0) 1
Lemon juice, cola drinks, some acid rain 2

Vinegar, wine, beer, oranges 3

Tomatoes 4
Bananas
Black coffee 5
Bread
Typical rainwater
Urine (5.0–7.0) 6
Milk (6.6)
Pure water [H+] = [OH–] 7
Blood (7.3–7.5)
Egg white (8.0) 8
Seawater (7.8–8.3)
Baking soda
Phosphate detergents, bleach, antacids 9
Soapy solutions, milk of magnesia 10
Household ammonia (10.5–11.9) 11

12
Hair remover
Oven cleaner 13 54
Sodium hydroxide (NaOH) 14 Figure 2-16 p37
INTRODUCTION TO ORGANIC
COMPOUNDS

55
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 molecule’s

function in a characteristic way

56
Identify the functional groups

A. Estradiol, an estrogen B. Testosterone

57
Identify the functional groups

58
Identify the functional groups

59
What is the formula? What is the difference?
What type of molecule?
A. Glucose B. Fructose

60
Glucose ring formation

C. Simplified ring structure

A. Glucose B. Formation of
(linear form) glucose rings

D. Space-filling model

61
Formation of Maltose: What kind of reaction?

62
What kind of reaction?

Molecule with
joined subunits

Separate subunits

63
Glycogen
What kind of molecule?

α(1 4)
linkage

Glycogen particles
(magenta) in liver cell

64
Cellulose
What kind of molecule?

β(1 4)
linkage

Cellulose
molecule Cellulose microfibrils
Glucose
in plant cell wall
subunit

Cellulose microfibril

65
What kind of reaction?
What kind of molecule?
A. Formation of a triglyceride
Triglyceride B. Triglyceride model

Glycerol

Ester
linkage

Fatty
acids

66
What kind of molecule?

A. Stearic acid, B. Oleic acid,

67
Phospholipid Structure
A. Structural plan of B. Phosphatidyl C. Phospholipid model D. Phospholipid symbol
a phospholipid ethanolamine

Polar
unit

Phosphate
group

Polar
Glycerol

Nonpolar

Fatty Fatty
acid acid
chain chain

68
Formation of a Membrane

Polar water solution

outside cell Water
molecule
Polar end of
membrane
molecule

Nonpolar end
Nonpolar region Membrane
of membrane
inside membrane covering cell
molecule
surface

Polar water solution

inside cell
69
What functional groups?
What kind of molecule?

70
Polar or non-polar R groups?

71
What kind of reaction?

Side Amino N-terminal C-terminal

group group end end

Carboxyl
group Peptide bond
Amino acid 1 Amino acid 2 Peptide

72
 a-helix,
b-pleated sheet,
or random coils

Source: Campbell et al. 2008

73
Lysozyme: 1 polypeptide
What level of structure?
Lysozyme Space-filling model of lysozyme

Disulfide
linkage Cleft

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Hemoglobin: 4 polypeptides
What level of structure?
Failure of cells to produce
adequate amounts of β
chain
→ excess of α chains
→ harmful deposits in
cells
→ Thalassemia major
(Weatherall et al. 1965
paper in Nature)

Symptoms: wide or brittle

bones, fatigue, slow
growth, enlarged spleen,
heart problems, etc.
75
What kind of molecule?

Uracil Thymine Cytosine

(U) (T) (C)

Adenine Guanine
(A) (G) 76
Nucleotide Structure

Phosphate groups
Nitrogenous base
(adenine shown)

Sugar (ribose in ribonucleotides;

deoxyribose in deoxyribonucleotides)
in ribose)
in deoxyribose
Nucleoside (sugar +
nitrogenous base)
Nucleoside monophosphate (adenosine
or deoxyadenosine monophosphate)
Nucleoside diphosphate (adenosine
or deoxyadenosine diphosphate) Nucleotides
Nucleoside triphosphate (adenosine
or deoxyadenosine triphosphate)
77
What kind of molecule?

A. DNA B. RNA

Phosphate groups
Phosphodiester bond

78
Pathway of Information Flow

Genetic information is stored in

DNA double-Stranded DNA.

Transcription

The information in DNA is

mRNA transcribed into single-stranded
mRNA.
Translation

Amino Amino Amino Amino The information in mRNA is translated

Amino acid acid acid acid acid
into an amino acid chain.
chain
Protein folding

The chain of amino acids folds into a

Folded specific shape to form a functional
protein protein.
molecule
79
What can you make with…

a) b)

80
What can you make with…

a) b)

81
Origin of Life

§ Theory of Abiogenesis: Oparin (and Haldane)

§ Needed:
§ synthesis of macromolecules, esp. proteins
§ separation from their environment

§ heredity and replication machinery

82
Origin of Life

§ Miller-Urey experiments 1950’s

§ atmosphere: CH4, NH3, H2O, H2 gases

§ no O2
§ liquid water
§ bombarded with electrical energy

83
Miller-Urey Experiments

84
Origin of Life

§ Miller-Urey experiments 1950’s

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

85
Origin of Life

§ Later experiments:
§ other amino acids
§ adenine (need for nucleic acids) from HCN and NH3 (Joan Oro 1961)
§ fatty acids
§ sugars from formaldehyde

86
Origin of Life

§ Polymerization:
§ Sidney Fox's work with proteinoids
§ Polymerization of clay-associated organic molecules
(Bernal 1951)

87
Origin of Life

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

88
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!

89
Origin of Life

The First Prokaryotes!

90
Prokaryotic Cell Structure
What is each component?
Plasma membrane
Cytoplasm
Nucleoid Cell wall
Dr. G. Cohen-Bazire

0.5 µm

Cell Nucleoid Ribosomes

Pili
Bacterial Plasma Wall Capsule Cytoplasm
flagellum membrane

91
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
Source: Campbell
et al., 2008 92
Animal Mitochondrion Microbody Nuclear pore
cell complex

Nuclear Nucleus
Tether envelope
proteins Chromatin
involved
Nucleolus
in
organelle Ribosome
contact Endo-
Lysosome Rough ER plasmic
reticulum
Ribosome
(ER)
Smooth ER
Microtubules

Microfilaments

Centrioles Plasma membrane

Vesicle Golgi complex Cytosol

93
A plant
cell
Mitochondrion Cytosol Nuclear pore
complex
Tether Golgi
proteins complex
involved Nuclear Nucleus
in Vesicle envelope
organelle Chromatin
contact Tonoplast
Nucleolus

Central
vacuole

Chloroplast
Plasmodesmata
Microtubules Rough ER Endo-
Ribosome plasmic
Cell wall reticulum
Smooth ER
Plasma membrane Ribosome 94
Mitochondrion

Mitochondrion

Intermembrane compartment
(between outer and inner
membranes)

Cristae (folds of
inner membrane)

Inner Matrix Outer

mitochondrial (inside bothmitochondrial
membrane membranes) membrane 95
Chloroplast

Chloroplast

Inner boundary
Outer boundary membrane
membrane

96
Thylakoids Granum Stroma (fluid interior)
Chloroplast
Granum Stroma (fluid interior)

97
Eukaryotic flagellum

Flagellum

Source: Campbell et al., 2008 98

Eukaryotic flagellum

Base of flagellum or
cilium

Plasma
membrane (cell
Basal body surface)
or centriole

99
Eukaryotic flagellum

Plasma membrane
Dynein arm
Two central
microtubules

Central sheath
Spoke
Links of the
connective system

100
Origin of Life

The First Eukaryotes?

§ Lynn Margulis and the Serial Endosymbiotic
Theory (SET)
§ On the Origin of Eukaryotes

101