This document provides an overview of key concepts from the Biology 212 course on Biochemistry, The Cell, and Genetics. It discusses the five unifying themes of biology, which are that all living things share heritable genetic information, organization and emergent properties, interactions with the environment, use of energy and matter, and evolution. Examples are given to illustrate these themes at different levels of biological organization from molecules to ecosystems. Key topics covered include cells, DNA, heredity, organization, biochemistry, and natural selection.

1. Biology 212
Biochemistry, The Cell, &
Genetics
1. The Big Picture
2. Five Unifying Themes of
Biology

2. Deep Reading
• Read as an overview
• Read and highlight
• Read and take notes
• Read, take notes, answer questions
• Read, take notes, answer questions, use the
text to fill in lecture notes
• Read, take notes, answer questions, synthesize
with lecture notes, write sample questions
• Teach someone/something what you learned

3. LE 1-3
Ecosystems
The biosphere
Organisms
Populations
Communities
Cells
Organelles
Molecules
Tissues
Organs and organ systems
Cell
1 µm
Atoms
10 µm
50 µm

4. 1. What is the correct order (from small to large)?
a) cells, organelles, organ system, community,
ecosystems
b) molecules, organism, population, communities,
biosphere
c) molecules, cells, tissues, ecosystems, communities
d) organelles, cells, population, biosphere, ecosystems
e) cells, organs, population, ecosystems, communities

5. 1. What is the correct order (from small to large)?
a) cells, organelles, organ system, community,
ecosystems
b) molecules, organism, population, communities,
biosphere
c) molecules, cells, tissues, ecosystems, communities
d) organelles, cells, population, biosphere, ecosystems
e) cells, organs, population, ecosystems, communities

6. Five Unifying Themes of Biology
1.Heritable Information for continuity of life: all
organisms begin with one cell
2.Organization: emergent properties of biological
systems from order–newest emerging properties from
bioinformatics; Structure and function are correlated at
all levels of organization
3.Interactions with other organisms & environment
4.Energy and Matter: Regulation through feedback
mechanisms
5.CORE THEME: Evolution Explains Unity &
Diversity

7. LE 1-2
Order.
Evolutionary adaptation.
Response to the
environment.
Regulation.
Energy processing.
Reproduction.Growth and
development.
Properties of life—this semester at a molecular level!
Emergent properties
from Organization
Energy and
matter:
Biochemistry &
feedback
Interactions
Hereditary Information for continuity
Core theme
All begins with one cell that
divides many, many times
Structure & function
correlated at all levels

8. Theme 1. The
cell houses
information
Membrane
Cytoplasm
EUKARYOTIC CELL PROKARYOTIC CELL
DNA
(no nucleus)
Membrane
1 µm
Organelles
Nucleus (contains DNA)

9. Dividing Cell—continuity of life
25 µm

10. DNA double helix Single strand of DNA
Nucleotide
Cell
Nucleus DNA
Theme 1. Heritable Information

11. Entire genome in every cell—differential gene expression to differentiate. DNA
directs the development of an organism.
Sperm cell
Nuclei
containing
DNA
Egg cell
Fertilized egg
with DNA from
both parents
Embryo’s cells
With copies of
inherited DNA
Offspring with traits
inherited from both parents

12. A Clone of Xenopus laevis Frogs
Nuclei from a
single female in
tail-bud tadpole
stage with 3
albino mutations
All clones are
female and
albino

13. Cloned Mammals, Whose Nuclei Came From
Adult Somatic Cells

14. Cloned Mammals, Whose Nuclei Came From Adult Somatic Cells

15. Understanding
information gave us
powerful tools

16. Theme 2. Organization leads to
Emergent Properties of Biological
Systems— e.g. ordering a myriad of
biochemical reactions results in
a- CELL
Nucleus
Cytoplasm
Outer membrane
and cell surface
Arabidopsis 2010: Projects to Determine the Function of Every Gene For a Systems
Map for the Small Mustard Plant, Arabidopsis
http://www.nsf.gov/bio/pubs/awards/2010awards.htm

17. Systems Biology
• High-throughput technology
output = mass quantities of data
• Bioinformatics
organizing the data to learn about relationships
and uncover hidden truths
• Interdisciplinary teams
requires knowledge & expertise from computer
science, mathematics, biology, chemistry, physics,
engineering, etc.

18. Figure 1-09—One of the early Human Genome Labs in Cambridge

19. Microarray Technique: view thousands of
genes that 2 cells express same/different

20. The entire library of genes is on a slide—see
which ones each cell light up

21. Microarray Analysis of Those Genes Whose Expression in the Early Xenopus
Embryo Is Caused by a specific transcription factor, Xnr1

23. 2. Which of the following scientific studies would
represent an example of a “systems biology”
approach?
a) measuring the effect of an invading insect that eats
oak leaves on the numbers of oak trees and on any
subsequent changes in the number and types of
decomposer fungi in the soil
b) discovering the structure of an enzyme that is important
in digestion of protein
c) comparing the microscopic structure of leaves of two
different species of magnolias
d) measuring the reproductive rate of emperor penguins
during exceptionally warm and exceptionally cold years
e) comparing the DNA sequence of two closely related
plants and inferring their evolutionary histories

24. Which of the following scientific studies would represent
an example of a “systems biology” approach?
a) measuring the effect of an invading insect that eats
oak leaves on the numbers of oak trees and on any
subsequent changes in the number and types of
decomposer fungi in the soil
b) discovering the structure of an enzyme that is important
in digestion of protein
c) comparing the microscopic structure of leaves of two
different species of magnolias
d) measuring the reproductive rate of emperor penguins
during exceptionally warm and exceptionally cold years
e) comparing the DNA sequence of two closely related
plants and inferring their evolutionary histories

25. Theme 2: Organization
Structure and Function
• At each level of the biological hierarchy we
find a correlation between structure and
function

26. Figure 1-22
Theme 2: Organization Structure
& function
Interdigit apoptosis does not happen as humans in
order to make webbing for flight

27. 3. The idea that form and function are related would
not be exemplified by which of the following
examples?
a) Cells in the intestinal lining of vertebrates have
many small projections that increase the surface
area for absorption of nutrients.
b) Plants that live in dry areas have large roots for
absorbing water.
c) Seeds that are dispersed by wind are very light.
d) Fish that swim rapidly have bodies that are
streamlined.
e) none of the above

28. 3. The idea that form and function are related would not
be exemplified by which of the following examples?
a) Cells in the intestinal lining of vertebrates have
many small projections that increase the surface
area for absorption of nutrients.
b) Plants that live in dry areas have large roots for
absorbing water.
c) Seeds that are dispersed by wind are very light.
d) Fish that swim rapidly have bodies that are
streamlined.
e) none of the above

29. Five Unifying Themes of Biology
1.Heritable Information for continuity of life: all
organisms begin with one cell
2.Organization: emergent properties of biological
systems from order–newest emerging properties from
bioinformatics; Structure and function are correlated at
all levels of organization
3.Interactions with other organisms & environment
4.Energy and Matter: Regulation through feedback
mechanisms
5.CORE THEME: Evolution Explains Unity &
Diversity

30. Theme 3: From Ecosystems to Molecules,
Interactions Are Important in Biological
Systems
• Interactions between the components of the
system ensure smooth integration of all the parts
• This holds true equally well for components of
an ecosystem and the molecules in a cell

31. Ecosystems: An Organism’s Interactions
with Other Organisms and the Physical
Environment
• At the ecosystem level, each organism
interacts continuously with other organisms
• These interactions may be beneficial or
harmful to one or both of the organisms
• Organisms also interact continuously with the
physical factors in their environment, and the
environment is affected by the organisms
living there

32. Figure 1.10
Sunlight
Leaves take in
carbon dioxide
from the air and
release oxygen.
Animals eat leaves
and fruit from the tree,
returning nutrients
and minerals to the
soil in their waste
products.
Water and
minerals in
the soil are
taken up
by the tree
through its
roots.
Leaves absorb light
energy from the sun.
Leaves fall to the
ground and are
decomposed by
organisms that
return minerals
to the soil.
CO2
O2

33. Molecules: Interactions Within
Organisms
• Interactions between components—organs,
tissues, cells, and molecules—that make up
living organisms are crucial to their smooth
operation
• Cells are able to coordinate various chemical
pathways through a mechanism called
feedback

34. Figure 1.11
Insulin
Circulation
throughout
body via
blood
Insulin-producing
cell in pancreas
STIMULUS: High
blood glucose level
Negativefeedback
Liver and
muscle cells
RESPONSE: Glucose
uptake by liver and
muscle cells

35. Theme 3. Interactions within organisms
Enzyme 1
A A
BB
C C
DD
D
D
D
D
D
D
D
DD
Enzyme 2
Enzyme 3
Negative
feedback
Enzyme 1

36. LE 1-12
W
Enzyme 4
W
XX
Y Y
ZZ
Z
Z
Z ZZ
ZZ Z
Enzyme 5
Enzyme 6
Positive
feedback
Enzyme 4
Enzyme 6
Enzyme 5
Z
Z Z Z
Z
Z
Z
Z
Z

37. Theme 4: Life Requires the Transfer and
Transformation of Energy and Matter
• The input of energy from the sun and the
transformation of energy from one form to
another make life possible
• When organisms use energy to perform work,
some energy is lost to the surroundings as heat
• As a result, energy flows through an
ecosystem, usually entering as light and
exiting as heat

38. Figure 1.9
ENERGY FLOW
Light
energy Heat
Chemical
energy
Plants take
up chemicals
from the soil
and air.
Chemicals
Decomposers
return
chemicals
to the soil.
Chemicals
pass to
organisms
that eat the
plants.
Producers, consumers, decomposers

39. Theme 5. Evolution explains both Unity &
Diversity
• 1.8 million species diversity
• Unity at every level
– Highest level of unity
1. composed of cells; membrane bound
cytoplasm
2. DNA is the hereditary material
3. use solar or chemical energy to do work
4. water-based chemistry
5. universal genetic code

40. Figure 1-19. Diversity among 3 orchid species, yet share organs & organ systems,
shape of flower, etc.

41. Figure 1-13. Great Diversity, yet unified features
Organisms are classified by their unifying characteristics.

42. LE 1-16a—Diversity Across Kingdoms
Cilia of windpipe cellsCilia of Paramecium
15 µm 5 µm

43. LE 1-16b--Unity
Cilia of windpipe cellsCilia of Paramecium
Cross section of cilium,
as viewed with an
electron microscope
0.1 µm

44. The Three Domains of Life
• At the highest level, life is classified into three
domains:
– Bacteria (prokaryotes)
– Archaea (prokaryotes)
– Eukarya (eukaryotes)
Eukaryotes include protists and the kingdoms
Plantae, Fungi, and Animalia

45. LE 1-15
Bacteria 4 µm 100 µm
0.5 µm
Kingdom PlantaeProtists
Kingdom AnimaliaKingdom FungiArchaea

46. LE 1-14. Classifying Life
Ursidae
Ursus
Carnivora
Mammalia
Chordata
Animalia
Eukarya
Species Genus Family Order Class Phylum Kingdom Domain
Ursus
americanus
(American
black bear)

47. Theme 5. The CORE of Biology--
Evolution
1859 published The Origin of The Species

48. Figure 1-17
The earth is old and its inhabitants have changed.

49. Mechanism:
Natural
Selection
Evolution of adaptations
in the population
Differences in
reproductive success
Overproduction
and competition
Population
of organisms
Hereditary
variations

50. LE 1-21
Population with varied inherited traits
Elimination of individuals with certain traits
Reproduction of survivors
Increasing frequency of traits that enhance
survival and reproductive success

51. Descent with modification in the Galapagos finches
Large
ground finch
Large cactus
ground finch
Sharp-beaked
ground finch
Geospiza
magnirostris
Geospiza
conirostris
Medium
ground
finch
Geospiza
fuliginosa
Small
ground
finch
Woodpecker
finch
Camarhynchus
psittacula
Large
tree finch
Medium
tree finch
Cactus
ground finch
Geospiza
difficilis
Cactus flower
eaters
Geospiza
scandens
Seed eater
Ground finches
Seed eaters
Tree finches
Common ancestor from
South American mainland
Insect eaters Bud eater
Warbler finches
Mangrove
finchGeospiza
fortis
Cactospiza
pallida Small
tree finch
Camarhynchus
pauper
Camarhynchus
parvulus
Green
warbler
finch
Gray
warbler
finch
Certhidea
olivacea
Certhidea
fusca
Vegetarian
finch
Platyspiza
crassirostris
Cactospiza
heliobates
Anatomical classification has now been confirmed with molecular evidence

52. 4. Examine the figure on the next slide and predict
which species pair has the most similar DNA
sequence.
a) vegetarian tree finch (Platyspiza crassirostris) and
mangrove finch (Cactospiza heliobates)
b) medium tree finch (Camarhynchus pauper) and
large tree finch (Camarhynchus psittacula)
c) large tree finch (Camarhynchus psittacula) and
small tree finch (Camarhynchus parvulus)
d) sharp-beaked ground finch (Geospiza difficilis) and
large ground finch (Geospiza magnirostris)
e) No such predictions are possible.

54. 4. Examine the figure on the previous slide and predict
which species pair has the most similar DNA sequence.
a) vegetarian tree finch (Platyspiza crassirostris) and
mangrove finch (Cactospiza heliobates)
b) medium tree finch (Camarhynchus pauper) and
large tree finch (Camarhynchus psittacula)
c) large tree finch (Camarhynchus psittacula) and
small tree finch (Camarhynchus parvulus)
d) sharp-beaked ground finch (Geospiza difficilis) and
large ground finch (Geospiza magnirostris)
e) No such predictions are possible.

55. Themes Uncovered by many using Scientific Inquiry Type I: observation-
based discovery
e.g. Jane Goodall describing (qualitative) and measuring (quantitative) aspects
of chimp behavior

56. Scarlet king snake
Eastern coral
snake
Scarlet king snake
Key
Range of scarlet
king snake
North
Carolina
Range of eastern
coral snake
South
Carolina
Scientific Inquiry Type II: hypothesis-based inquiry
not poison
poisonous

57. LE 1-28
(a) Artificial king snake
(b) Artificial brown snake that has been attacked
Dr. Stephenson’s lab
does similar work if
looking for research

58. In areas where coral
snakes were present,
most attacks were on
brown artificial snakes.
In areas where coral snakes
were absent, most attacks
were on artificial king snakes.
LE 1-29
% of attacks on
artificial king snakes
% of attacks on
brown artificial snakes
Field site with
artificial snakes
83%
North
Carolina
South
Carolina
17%
16%
84%
Key
The hypothesis is supported
by the field experiment.

59. Terminology in Science
• Hypothesis: a testable, falsifiable educated
guess; a tentative answer to a well-framed
question
• Theory: much broader in scope than a
hypothesis; general enough to spin off many
new hypotheses; supported by a massive body
of evidence; explain a great diversity of
observations EVOLUTION

60. Science, Technology, & Society —understanding the connections between
science & society is important for our culture today e.g. Forensic science

61. TECHNOLOGIES
• DNA fingerprinting
– Not well-received at first
– Now a common tool of forensic science
• Mammalian cloning
– In 1997, Ian Wilmut and colleagues cloned the first
mammal
– Fears that the technology may be applied to humans
led to legislative bans on human cloning
1-8

62. • Genetic technologies allow the modification of animals in various ways
• For example, mice can be made to glow green (Figure 1.3)
– A jellyfish gene encoding a green fluorescent protein is introduced into lab
mice
– Upon exposure to ultraviolet light, the mice emit a bright green color

64. 8n 2n

65. Practice Deep Reading p 19-20 and
box on page 21 of text
Group Work!
• How does mouse coat color affect survival?
• Would you expect different colors in different
habitats if the species were strictly nocturnal?
Explain.

66. 5. Now you will look at data from two different enclosures:
one with light-colored soil (left), and one with dark-colored
soil (right). How many dark brown mice were caught in the
light-colored soil enclosure on a moonlit night?
a) 12
b) 17
c) 19
d) 37

67. 5. Now you will look at data from two different enclosures:
one with light-colored soil (left), and one with dark-colored
soil (right). How many dark brown mice were caught in the
light-colored soil enclosure on a moonlit night?
a. 12
b. 17
c. 19
d. 37

68. 6. On a moonlit night, would a dark brown mouse be
more likely to escape predation by owls on dark- or light-
colored soil? What data support your conclusion?
a. On light-colored soil; the lowest
level of predation was light brown
mice on light soil.
b. On dark-colored soil; fewer light
brown mice than dark brown mice
were caught on light soil under no
moon.
c. On dark-colored soil; fewer dark
brown mice were caught on dark
soil than on light soil under a full
moon.
d. On light-colored soil; fewer dark
brown mice were caught on dark
soil than on light soil under a full
moon.

69. 6. On a moonlit night, would a dark brown mouse be
more likely to escape predation by owls on dark- or light-
colored soil? What data support your conclusion?
a. On light-colored soil; the lowest
level of predation was light brown
mice on light soil.
b. On dark-colored soil; fewer light
brown mice than dark brown mice
were caught on light soil under no
moon.
c. On dark-colored soil; fewer
dark brown mice were caught
on dark soil than on light soil
under a full moon.
d. On light-colored soil; fewer dark
brown mice were caught on dark
soil than on light soil under a full
moon.

70. The Flexibility of the Scientific
Process
• The scientific method is an idealized process
of inquiry
• Hypothesis-based science is based on the
“textbook” scientific method but rarely
follows all the ordered steps
• Backtracking and “rethinking” may be
necessary part way through the process

71. Figure 1.23
EXPLORATION
AND
DISCOVERY
FORMING
AND
TESTING
HYPOTHESES
SOCIETAL
BENEFITS
AND
OUTCOMES
COMMUNITY
ANALYSIS
AND
FEEDBACK

72. Testing Ideas
• Forming hypotheses
• Predicting results
• Doing experiments and/or
making observations
• Measuring results
Interpreting Test Results
Data may…
• Support a hypothesis
• Contradict a hypothesis
• Inspire a revised or new
hypothesis
• Prompt revised
assumptions
• Observing nature
• Asking questions
• Sharing data and ideas
• Finding inspiration
• Exploring the scientific
literature

73. Figure 1.23c
• Feedback and
peer review
• Replication of
experiments and
observations
• Discussion with
colleagues
• Publication
• Devising new ideas
and questions
• Theory building
• Developing technology
• Addressing societal
issues
• Informing policy
• Solving everyday
problems
• Satisfying curiosity
• Building knowledge