METACOGNITION- what does it mean?
Awareness and understanding of one's own thought processes
Simply put, the greater the student's involvement or engagement
in academic work or in the academic experience of college, the
greater his or her level of knowledge acquisition and general
cognitive development". Pascarella and Terenzini How College Affects Students

8/23/2024
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What do all these have in common?
Introduction to Instructor, course and resources
Student centered learning and metacognition
What Does It Mean to Say That Something Is Alive?
 Know the principles of experimental design
 Describe the three theories/unifying themes in biology
 Life is cellular, life evolves, life processes information
Overview of the tree of life
- Know the classification of the 3 kingdoms and domains of life
TODAY’S LEARNING OBJECTIVES

8/23/2024
4
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Chapter 1 Opening Roadmap
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
1.1 What Does It Mean to Say That Something is Alive?
• All living organisms share five fundamental characteristics:
1. Cells:
▪ All organisms are made up of membrane-bound cells
2. Replication:
▪ All organisms are capable of reproduction
3. Information processing:
▪ All organisms process hereditary information encoded in
genes as well as information from environment

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
1.1 What Does It Mean to Say That Something is Alive?
4. Energy:
▪ All organisms acquire and use energy to stay alive
5. Evolution:
▪ Populations of organisms are continually evolving -
genetic change over time!
Cell?
Cells are the smallest units of an organism that carry out all the basic functions of life;
nothing simpler than a cell is considered alive.
1. Cells - All organisms are made up of membrane-bound cells

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WHAT DOES IT MEAN TO SAY THAT SOMETHING IS ALIVE?
2. Replication
All organisms are capable of reproduction- cells give rise to
other cells
https://www.aplustopper.com/cell-division-icse-solutions-class-10-biology/
Replication
Is this a living cell? VIRAL PARTICLE NOT a CELL: Virus particles consist of genetic
material enclosed in a coat or capsid.
They do not function or reproduce unless they are inside a living cell of a true
biological organism. Here they take over the cell's processes and use them to make
more of themselves. https://www.biotopics.co.uk/A15/Virus_particles.html
A living cell has the ability to reproduce itself!

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WHAT DOES IT MEAN TO SAY THAT SOMETHING IS ALIVE?
All organisms process hereditary information encoded in genes
as well as information from the environment
White blood cell chases bacteria!
How does it know?
3. Information:
WHAT DOES IT MEAN TO SAY THAT SOMETHING IS ALIVE?
4. Energy
All organisms acquire and use energy
https://www.thinglink.com/scene/967057355827052546

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8
WHAT DOES IT MEAN TO SAY THAT SOMETHING IS ALIVE?
5. Evolution
Evolution is based on genetic variation that can result in a
change in the characteristics of a population over time.
Genetic Variation Natural selection
http://gardinerlab.blogspot.com/2010/10/power-of-natural-selection.html
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Introduction to Instructor, course and resources
Student centered learning and metacognition
What Does It Mean to Say That Something Is Alive?
 Know the principles of experimental design
 Describe the three theories/unifying themes in
biology
–Life is cellular, life evolves, life processes information
Overview of the tree of life
- Know the classification of the 3 kingdoms and domains of life
Today’s Learning Objectives

8/23/2024
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DOING BIOLOGY: THE NATURE OF SCIENCE
All scientists ask questions that can be answered by measuring
things—by collecting data
Science is about formulating hypotheses and finding evidence
that supports or conflicts with those hypotheses
For example, using carefully designed experiments, biologists test ideas
about the way the natural world works by testing the predictions made by
alternative hypotheses
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Terminology of scientific inquiry by Scientific method
• Hypothesis:
– Testable statement that explains something
observed
• Prediction—measurable or observable result
– Must be correct if hypothesis is valid
• Experiment—allows researchers to test effect of
factor on particular phenomenon
• Conclusions— generates data or observable
outcomes that should be quantified
– May be corrected or new hypothesis formed
Scientific Theory refers to explanations for broad patterns not a guess!

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THE PRINCIPLES OF EXPERIMENTAL DESIGN
Biologists practice evidence-based decision making
Ask questions about how organisms work
Pose hypotheses to answer those questions
Use experimental or observational evidence to decide which
hypotheses are correct
A scientific theory can come about after repeated testing with
same conclusions accepted broadly by scientists
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Terminology of scientific inquiry
• Hypothesis:
– Testable statement that explains something observed
• Experiment—allows researchers to test effect of factor on
particular phenomenon
• Prediction—measurable or observable result
– Must be correct if hypothesis is valid
Theory refers to explanations for broad patterns

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Theories
• Theory:
– Explanation for a very general class of
phenomena or observations supported by wide
body of evidence:
▪ Differs from everyday usage of word “theory,”
meaning “speculation” or “guess”
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Theories
• Three theories form framework for modern biological science:
– Cell theory:
▪ What are organisms made of?
– Theory of evolution by natural selection:
▪ Where do organisms come from?
– Chromosome theory of inheritance:
▪ How is hereditary information transmitted from one
generation to the next?

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
All Organisms Are Made up of Cells
• 1660s—Robert Hooke and Anton van
Leeuwenhoek were first to observe cells
• Cells:
– Highly organized compartments
– Separated from their environment by
membrane barrier
• Formed first part of cell theory:
– All organisms are made up of cells
– All cells come from preexisting cells
1.2 Life is Cellular and Replicates through Cell Division
Figure 1.1 What Hooke and Van Leeuwenhoek
Saw through Their Microscopes
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Together, the cell theory and the theory of evolution
provided the young science of biology with two central,
unifying ideas:
•The cell is the fundamental structural unit in all
organisms.
•All species are related by common ancestry and have
changed over time in response to natural selection.
Cell theory and the theory of evolution

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Cell Theory and Spontaneous Generation
• Cell theory challenged spontaneous generation:
– All-cells-from-cells explanation was a hypothesis:
▪ Cells are produced when pre-existing cells grow and divide
– Spontaneous generation was an alternative hypothesis:
▪ The belief that organisms could arise spontaneously under
certain conditions
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Louis Pasteur’s Experiment
• Louis Pasteur’s hypothesis led to experimental design:
• Hypothesis: Microbes (bacteria) come from cells of
organisms on dust particles in the air; not the air itself.
• Experiment:
– Two glass flasks:
▪ Both flasks had nutrient broth
▪ One flask had swan neck open to the air

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Louis Pasteur’s Classical Experiment
Figure 1.2 The Spontaneous Generation and All-Cells-From-Cells
Hypotheses Were Tested Experimentally
Concluded that all-cells-from-
cells hypothesis was correct
Cells arise from cells
Cells do not arise by spontaneous
generation from liquid broth
Cells
Cells do not arise by spontaneous
generation from liquid brothCan you describe in your own words?
Louis Pasteur (1822–1895)
PASTEURIZATION
https://www.sciencehistory.org/historical-profile/louis-pasteur
WHY SHOULD I CARE ?
He originally invented and patented (in 1865) to fight the “diseases” of wine. He realized that
these were caused by unwanted microorganisms that could be destroyed by heating wine to a
temperature between 60° and 100°C. The process was later extended to all sorts of other
spoilable substances, such as milk.
Pasteur embraced the emerging ideal of applying
science to practical problem-solving in industry
https://www.explainthatstuff.com/pasteurization.html

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
1.3 Life Processes Information and Requires Energy
• Chromosomal theory of inheritance proposed by Sutton and Boveri:
– Hereditary or genetic information is encoded in genes
– Genes are units located on chromosomes
• 1950s—Chromosomes are molecules of deoxyribonucleic acid (DNA):
– DNA is the hereditary material
– Genes are segments of DNA that code for cell products
• Double helix:
– Each stand is made up of four building blocks:
▪ A, T, C, and G
• Sequence of this code is like letters in a word
• DNA carries, or encodes, information needed for an organism’s growth and
reproduction
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Figure 1.4 The Central Dogma Describes the Flow of
Genetic Information RNA and proteins:
RNA:
Molecules that carry out
specialized functions in cells
Messenger RNA (mRNA) is read
to make proteins
Proteins:
Crucial to tasks required by cells
Form structural components to
promote chemical reactions

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Introduction to Instructor, course and resources
Student centered learning and metacognition
What Does It Mean to Say That Something Is Alive?
 Know the principles of experimental design
 Describe the three theories/unifying themes in biology
–Life is cellular, life evolves, life processes information
Overview of the tree of life
- Know the classification of the 3 kingdoms and domains of life
Today’s Learning Objectives
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
1.5 the Tree of Life Depicts Evolutionary History
• Tree of life depicts evolutionary history:
– Family tree of organisms
– Describes genealogical relationships among species with single
ancestral species at its base
• Phylogeny:
– Actual genealogical relationships among all organisms

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Classification of living things
Three domains of life
 How is genetic variation
analyzed?
 Biologists study R N A and D N A
from different organisms:
 Compare sequences of
building blocks (A,T,C,G)
 Fewer sequence variations
between two species may
indicate closer relationship
INTERPRETING THE TREE OF LIFE
The tree of life indicates three major groups
of organisms:
The eukaryotes
Eukarya
Two groups of prokaryotes
Bacteria and Archaea
(a) Eukaryotic cells have
a membrane-bound
nucleus.
(b) Prokaryotic cells do not
have a membrane-bound
nucleus.

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BACTERIA ARCHEA EUKAROYTES
Protists Fungi Plants Animals
4 Kingdoms
3 DOMAINS
Classification of living things
CLASSIFICATION SUMMARY
Taxonomy is the grouping of
species based on common
ancestry
3 domains
 Bacteria- unicellular prokaryote
 Archaea- unicellular prokaryote
 Eukarya- unicellular to multicellular
eukaryotes
 4 kingdoms
 Protista, fungi, plantae and

Chapter 2 Opening Roadmap

2/7/2024
2
© 2017 Pearson Education, Inc.
Learning objectives for today’s class
 Introduction- Why chemistry in biology? Life has chemical foundations
 Explain the levels of organization and chemical basis of life, list the big four
elements that make up the human body
 Review of atomic structure and the importance of valence electrons
 Explain valency and how molecules are formed
 Know the three types of chemical bonds and differentiate between them
 Explain how electronegativity properties of atoms influences the chemical
properties of molecules in polarity of chemical bonds.
 Describe the properties of water that make it a molecule that is vital for life
◼ Biology and chemistry increasingly
overlap
◼ Chemistry makes life possible!
◼ Living things have chemical foundations
Why Chemistry in bio?
https://www.cancerquest.org/sites/default/files/styles/large/public/molecules_all_lab.jpg?itok=BsZNSgsX

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CHEMISTRY IN BIOLOGY!!!
WHY DOES IT MATTER?
Breathe air
Food
Water
Raw material and fuel for our bodies
DNA
Cells are built from organic molecules
LIFE has chemical foundations!
Why should I care
Chemical basis of life!
COMPOSITION OF EARTH AND HUMAN BODY

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Levels of
organization of
human life
https://i1.wp.com/buffonescience9.wikispaces.com/file/view/hierarchy.jpg/231441410/hierarchy.jpg
8

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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Basic Atomic Structure (1 of 10)
• Nucleus made up of protons and neutrons:
– Protons—positive charge (+1)
– Neutrons—neutral charge
• Surrounded by orbiting electrons:
– Negative charge (−1)
• Atom with equal number of protons and
electrons:
– Charges balance
– Electrically neutral
The Big 4 atoms!
Make up 96% of all matter in living organisms

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6
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Basic Atomic Structure
• Outermost shells of elements:
– Atom’s valence shell is outermost shell
– Electrons in this shell called valence electrons
– Number of unpaired valence electrons is called
the valence of an atom
• Different atoms have different numbers of unpaired
electrons
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Figure 2.3 The Atomic Structure of the First 18 Elements

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7
Valency
measure of an
atom’s combining
power with other
atoms when it forms
chemical
compounds or
molecules
MOLECULE STABILITY
Molecules tend to be the most stable when they share enough electrons
to completely occupy the outermost energy level, or shell
OCTET RULE!
Covalent bonds form when unpaired valence electrons are shared by
two atoms
Electrons of an atom fill innermost shells first, then fill outer shells

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8
Learning objectives for today’s class
 Introduction- Why chemistry in biology? Life has chemical foundations
 Explain the levels of organization and chemical basis of life, list the big
four elements that make up the human body
 Review of atomic structure and the importance of valence electrons
 Explain valency and how molecules are formed
 Know the three types of chemical bonds and differentiate between
them
 Explain how electronegativity properties of atoms influences the
chemical properties of molecules in polarity of chemical bonds.
 Describe the properties of water that make it a molecule that is vital for
life
3 kinds of chemical “bonds”:
 1. Ionic
 2. Covalent
• Polar and non polar covalent
3. Hydrogen
Chemical Bonds

2/7/2024
9
© 2017 Pearson Education, Inc.
Ionic Bonding, Ions, and the Electron-Sharing Continuum
• Ionic bonds result when electrons are transferred from one atom to
another to give both atoms full valence shells
• An ion is an atom or molecule that carries a charge
• Cation—an atom that loses an electron and becomes positively charged
• Anion—an atom that gains an electron and becomes negatively charged
• Ionic bonds are the attraction between oppositely charged ions
Figure 2.6
(a) A sodium ion being formed (c) Table salt (NaCl) is a crystal composed of two ions.
Cl–
Loss of electron
Cation formation
Sodium ion
has positive
charge
Na+
(b) A chloride ion being formed
Gain of electron
Anion formation
Chloride ion
has negative
charge
© 2017 Pearson Education, Inc.
Attraction results from the strength of electronegativity
Ionic bonds are strong in crystal form but weak in water
Ionic compounds are called salts
Electron is not shared; it is completely
transferred from one atom to another:
Transfer gives each atom a full valence
shell

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10
Figure 2.4
Covalent bond
Hydrogen atoms each have
one unpaired electron
H2 molecule has
two shared electrons
© 2017 Pearson Education, Inc.
Covalent bonds form when unpaired valence electrons are shared
by two atoms
This effectively gives each atom a full outer shell
How Does Covalent Bonding Hold Molecules Together?
One end is slightly positive and the other slightly negative due to
unequal electron sharing
A polar bond is a covalent bond in which there is a
separation of charge between one end and the other
POLAR
NON POLAR
http://www.chemguide.co.uk/atoms/bonding/electroneg.html

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© 2017 Pearson Education, Inc.
Differences in electronegativity dictate how electrons are
distributed in covalent bonds
• Nonpolar covalent bond
• Electrons are evenly shared between two atoms
• The bond is symmetrical
• Example: C–H bond
• Polar covalent bond
• Electrons are shared unevenly
• Example: O–H bond
H = 2.1
C = 2.5
N = 3.0
O = 3.5
Relative EN values

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Oxygen and hydrogen bonds are________?
H = 2.1
O = 3.5
Figure 2.7
Equal sharing
of electrons
Nonpolar covalent bonds
(atoms have no charge)
Polar covalent bonds
(atoms have partial charge)
Transfer of
electrons
Ionic bonds
(atoms have full charge)
WaterHydrogen Methane Ammonia Sodium chloride
© 2017 Pearson Education, Inc.
Chemical bonds polarity and electron sharing summary

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13
A chemical bond in which a hydrogen atom of one
molecule is attracted to an electronegative atom,
especially a nitrogen, oxygen, or flourine atom, usually
of another molecule
HYDROGEN ‘BOND’
https://www.quora.com/On-passing-slowly-through-water-ph3-phosphine-forms-bubbles-but-nh3-ammonia-dissolves-Why
HYDROGEN BONDS
Individual H bonds are weak, many H bonds together are strong
Charge attraction
between oppositely
charged parts of polar
molecules

2/7/2024
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Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
2.2 Properties of Water and the Early Oceans
• Life is based on water:
• 75% of cell is water
• Water is an excellent solvent:
• Solute dissolved into solvent makes a solution
• Substances more likely to react when they are dissolved
in solvent like water

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© 2017 Pearson Education, Inc.
• Every organism we know of needs water to survive
• Essential for cells or body to function
• Humans use water to dissolve and transport nutrients, flush
out toxins, regulate body temperature and aid our
metabolism...
• Sustains civilization
• Agriculture, industry, transportation, home for aquatic
organisms, energy source...
Why is water vital to life?
© 2017 Pearson Education, Inc.
Of all the limits on life, water is the least negotiable!
All cells need water as a medium for their chemical
reactions to take place in, and to keep their
membranes intact. Exception...
https://www.newscientist.com/article/mg20827862-200-extreme-survival-dreaming-
through-drought/
Tardigrades have survived without water for 120 years
https://www.youtube.com/watch?v=SUC0_HjNFBs

2/7/2024
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© 2017 Pearson Education, Inc.
What Properties Are Correlated with Water’s Structure?
• Water is unique due to its structure
• Small size
• Bent shape
• Highly polar covalent bonds
• Overall polarity
© 2017 Pearson Education, Inc.
Water has unusual properties that make it
critical to life.
Good solvent
Cohesion/Adhesion
Surface tension
Large heat capacity/ High heat of vaporization
Low density as a solid
Neutral pH 7

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© 2017 Pearson Education, Inc.
classconnection.s3.amazonaws.com
DIPOLE/ POLAR MOLECULE
Figure 2.11
(a) Water is polar.
Electrons
are pulled
toward
oxygen
(b) Hydrogen bonds form
between water molecules.
© 2017 Pearson Education, Inc.
Properties of water
Figure 2.11 Water Is Polar and Participates in Hydrogen Bonds.

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© 2017 Pearson Education, Inc.
Why Is Water Such an Efficient Solvent?
• Hydrophilic (“water-loving”) atoms and molecules
• Are ions and polar molecules that stay in solution
• They interact with water’s partial charges
• Makes it possible for almost any charged or polar
molecule to dissolve in water
Figure 2.12b
(b) Table salt (NaCl) dissolved in water
© 2017 Pearson Education, Inc.
Hydrogen bonds can also form between a water molecule and
any other polar molecule
Water as a Solvent

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19
© 2017 Pearson Education, Inc.
Hydrophopbic vs hydrophillic
• Hydrophobic (“water-fearing”) molecules
• Are uncharged and nonpolar compounds
• They do not dissolve in water
• Hydrophobic molecules interact with each other through hydrophobic
interactions
Figure 2.13
© 2017 Pearson Education, Inc.
Cohesion, Adhesion, and Surface Tension
• Water also has several remarkable properties, largely
due to its ability to form hydrogen bonds:
• Cohesion
• Adhesion
• More dense as a liquid than a solid
• Ability to absorb large amounts of energy

2/7/2024
20
Figure 2.14
(a) A meniscus forms where water meets a solid surface,
as a result of two forces.
Adhesion: Water
molecules that
adhere to the glass
pull upward at the
perimeter.
Cohesion: Water
molecules at the
surface form
hydrogen bonds
with nearby water
molecules and resist
the upward pull of
adhesion.
(b) Water has high surface tension.
Because of surface
tension, light
objects do not
fall through the
water’s surface
© 2017 Pearson Education, Inc.
Cohesion,
Adhesion,
and Surface
Tension
Adhesion is binding
between unlike
molecules
Cohesion is binding
between like molecules
Hydrogen bonding of water
results in high surface tension
Figure 2.15
(a) In ice, water molecules
form a crystal lattice.
(b) In liquid water, no crystal
lattice forms.
(c) Liquid water is denser than
ice. As a result, ice floats.
© 2017 Pearson Education, Inc.
Water Is More dense as a Liquid than as a Solid

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21
© 2017 Pearson Education, Inc.
https://i.ytimg.com/vi/OsXIyY8b7Bc/maxresdefault.jpg
Water has a very high specific heat
https://image.slidesharecdn.com/specific-heat-capacity-151015095108-lva1-app6892/95/specific-

Learning objectives
• Explain the properties of Carbon that makes it the backbone
of biological organic molecules.
• Explain the key role of functional groups in reactivity and the
behavior of organic molecules

8/30/2024
2
Why do we study Organic Macromolecules?
They are the building blocks of cells
H
H
N
MACROMOLECULES
Monomer Polymer
Amino Acid Protein
CH3
C C
O
H
OH
Ala Val Ser Val
Ala
Alanine
Nucleotide Nucleic acid (DNA)
O−
−O P O
O
CH2
H
H
C
C
C N
C
N
H
H H
H
HOH
NH2
G T
A
C
G
T
O
A
C
O A
T
T
A
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
CH2 OH
H
HO
H
OH
OH
HO
H
OH
HO
O H H H H H H H H H H
H H H H H H H H H H H
C C C C C C C C C C C H
Monosaccharide Carbohydrate (starch)
Fatty acid Lipid (fat molecule)
C
H
TABLE 3.1
H
CARBON: LIFE’S CHEMICAL BACKBONE
The typical cell’s dry mass after removal of water

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3
• Most naturally occurring nonliving things are made of inorganic
molecules while living things are made of organic molecules.
• Molecules with carbon in them were assumed to be associated
with organisms, and so were called organic molecules.
ORGANIC MOLECULES
Carbon’s valence electrons allow it to be versatile!
Versatility
Adaptability, flexibility, elasticity

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4
The Importance of Organic Molecules
• Carbon is the most versatile atom on Earth
• Because of its four valence electrons
• Because it can form many covalent bonds
• Organic compounds are molecules that contain carbon
bonded to other elements
• An almost limitless array of molecular shapes
• With different combinations of single and double bonds
• The formation of carbon–carbon bonds was an important
event in chemical evolution
Figure 2.23
(a) Carbons linked in a chain (b) Carbons linked in a ring
C8H18 Octane
C6H12O6
Glucose
© 2017 Pearson Education, Inc.
Carbon skeletons can vary in length, branching, and ring structure

8/30/2024
5
https://byjus.com/biology/biomolecules/
1. Proteins
(amino acids)
2.Carbohydrates
(sugars)
3. Lipids(fatty
acids)
4.Nucleic acids
(nucleotides)
Structure and
Function
Organic molecules important for life include relatively small monomers as well as large polymers
Biomolecules are molecules that are involved in the maintenance and metabolic processes of living organisms
Learning goals for today’s class
• Explain the properties of Carbon that makes it the backbone of
biological organic molecules.
• Outline the part functional groups play in polarity, reactivity
and the behavior of organic molecules

8/30/2024
6
Functional groups
Confer specific behavior to the molecules to which they are attached!
http://www.katiejurek.com/si/Functional%20groups%2
02.jpg
The functional
groups of organic
molecules are the
parts involved in
chemical reactions.
Table 2.3
© 2017 Pearson Education, Inc.

8/30/2024
7
Functional Groups
• Important H-, N-, O-, P-, and S-containing functional
groups found in organic compounds:
• Amino groups attract a proton and act as bases
• Carboxyl groups drop a proton and act as acids
• Carbonyl groups have sites that link molecules into more-
complex compounds
• Hydroxyl groups act as weak acids
• Phosphate groups have two negative charges
• Sulfhydryl groups link together via disulfide bonds
http://imgarcade.com/1/secondary-structure-
of-protein/
http://www.annekeckler.com/nutrition-carbohydrates/
http://fish-notes.blogspot.com/2011/11/quest-for-
fat.html
http://www.nature.com/scitable/topic/nucleic-acid-structure-
and-function-9

Protein Structure and Function
Chapter 3 Freeman Biology
Bisc 207
Professor Olabisi
© 2017 Pearson Education, Inc.
Learning goals
• Describe the basic amino acid structure, know the functional groups
found on all Amino Acids
• Predict amino acid(AA) properties based on functional groups and
generally understand the side chain chemistry that differentiates each of
the 20 AA.
• Explain how amino acid monomers assemble to polymers- polypeptide
formation as an example of primary structure
• Outline the 4 different levels of protein structure(primary, secondary,
tertiary and quaternary) and explain how they determine function and
diverse roles of proteins in cells.
• Explain how protein structure influences function with examples and the
effect of denaturation in loss of structure-function.

2
Chapter 3 Opening Roadmap.
© 2017 Pearson Education, Inc.
© 2017 Pearson Education, Inc.
http://imgarcade.com/1/secondary-structure-of-protein/http://www.annekeckler.com/nutrition-carbohydrates/
http://fish-notes.blogspot.com/2011/11/quest-for-fat.html
http://www.nature.com/scitable/topic/nucleic-acid-structure-and-function-9
Carbohydrates, Proteins, Lipids, Nucleic acids all have functional groups

3
© 2017 Pearson Education, Inc.
Overview
• Cells produce tens of thousands of distinct proteins
• Vital, tremendously versatile components of cells
• They are large and very complex macromolecules or
biomolecules which perform a major part of the work
of functioning and regulating of our body's tissues and
organs.
• Amino acids are the building blocks of proteins
Figure 3.1a
Central carbon
(α-carbon)
(a) Non-ionized form
of amino acid Carboxyl
group
Amino
group
Side chain
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The Structure of Amino Acids

4
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The Structure of Amino Acids
• Most proteins are made from just 20 amino
acids
• Amino acids are composed of a central
carbon atom bonded to:
• H—a hydrogen atom
• NH2—an amino functional group
• COOH—a carboxyl functional group
• R group—a variable “side chain”
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Functional groups
http://www.katiejurek.com/si/Functional%20group
s%202.jpg

5
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Table 2.3
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Ionized form of Amino acid
• In water, the amino and carboxyl groups ionize to
NH3 and COO–, respectively
• The amino group acts as a base and attracts a proton
• The carboxyl group acts as an acid and donates a proton
• The resulting charges
• Help the amino acids stay in solution
• Make the amino acids more reactive

6
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The Nature of Side Chains
• The 20 amino acids differ only in the unique
R-group, or side chain, attached to the central
carbon
• The properties of amino acids are determined by
their R-groups
• Side chains can be grouped into three types:
1. Charged—includes both acidic (–) and basic (+)
2. Uncharged polar
3. Nonpolar
Remember functional groups, polarity
Figure 3.2
Acidic Basic
Aspartate (D)
Asp
Glutamate (E)
Glu
Lysine (K)
Lys
Arginine (R)
Arg
Histidine (H)
His
Serine (S)
Ser
Threonine (T)
Thr
Tyrosine (Y)
Tyr
Asparagine (N)
Asn
Glutamine (Q)
Gln
Glycine (G)
Gly
Alanine (A)
Ala
Valine (V)
Val
Leucine (L)
Leu
Isoleucine (I)
Ile
Methionine (M)
Met
Cysteine (C)
Cys
Phenylalanine (F)
Phe
Tryptophan (W)
Trp
Proline (P)
Pro
Electrically
charged
side chains
Charged side
chains can
form ionic
and hydrogen
bonds
Polar side
chains
Partial
charges can
form
hydrogen
bonds
Nonpolar
side chains
No charged
or electro-
negative
atoms to
form
hydrogen
bonds
© 2017 Pearson Education, Inc.

7
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The Polarity and Charge of R-Groups Affects Solubility
• Charged and polar side chains are
hydrophilic: They interact readily with
water
– If the side chain has an oxygen atom, the highly
electronegative oxygen will form a polar covalent
bond and thus it is uncharged polar
• Nonpolar side chains are hydrophobic:
They do not interact with water
– C-H bonds are non polar
© 2017 Pearson Education, Inc.
Figure 3.2 Acidic Basic
Aspartate (D)
Asp
Glutamate (E)
Glu
Lysine (K)
Lys
Arginine (R)
Arg
Histidine (H)
His
Serine (S)
Ser
Threonine (T)
Thr
Tyrosine (Y)
Tyr
Asparagine (N)
Asn Glutamine (Q)
Gln
Glycine (G)
Gly
Alanine (A)
Ala
Valine (V)
Val
Leucine (L)
Leu
Isoleucine (I)
Ile
Methionine (M)
Met
Cysteine (C)
Cys
Phenylalanine (F)
Phe
Tryptophan (W)
Trp
Proline (P)
Pro
Electrically
charged
side chains
Charged side
chains can
form ionic
and hydrogen
bonds
Polar side
chains
Partial
charges can
form
hydrogen
bonds
Nonpolar
side chains
No charged
or electro-
negative
atoms to
form
hydrogen
bonds
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Side chains
determine
AA
properties

8
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CARBON-BASED MOLECULES AND
THEIR BUILDING BLOCKS
1. Proteins (amino acids)
2.Carbohydrates (sugars)
3. Lipids (fatty acids)
4.Nucleic acids (nucleotides)
Structure and
Function
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How Do Amino Acids Link to Form Proteins?
• Proteins are macromolecules
• Large molecules made of smaller subunits
• Subunits are called monomers (“one-part”)
• Monomers link together (polymerize) to form
polymers (“many-parts”)
• Amino acids are the monomers that make up
proteins

9
Figure 3.3
Growing polymer
Polymerization
(bonding together
of monomers)
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Polymerization of Proteins
• Monomers polymerize through
condensation (dehydration) reactions
– Results in the loss of a water molecule
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The Peptide Bond
• Amino acids polymerize when a bond forms
between a carboxyl group of one amino acid
and an amino group of another
• The resulting C–N bond is called a peptide
bond

10
Figure 3.4
(a) Condensation reaction:
monomer in, water out Monomer
Monomer
(Water)
(b) Hydrolysis:
water in, monomer out (Water)
Monomer
Monomer
+
+
H
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Figure 3.5
Carboxyl
group
Amino
group
Electron sharing here
gives the peptide bond the
characteristics of a double
bond
Peptide bond
formation
Peptide
bond
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The Peptide Bond
Condensation reaction
Figure 3.5 Peptide Bonds From When the Carboxyl Group of One
Amino Acid Reacts with the Amino Group of A Second Amino Acid.

11
Figure 3.7
One of the nine
amino acid
residues in this
chain
Peptide
bond
Amino
group
Carboxyl
group
Chains flex because groups on
either side of each peptide bond
can rotate about their single bonds
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Amino Acid Chains Are Flexible
R-group orientation such that
side chains extend out and can
interact with each other or water
Directionality
Flexibility
Figure 3.6
(a) Chain of amino acid residues
Amino acids joined by peptide bond
N-terminus C-terminus
Peptide-
bonded
backbone
Carboxyl
group
Amino
group
(b) Residue numbering system
N-terminus
Side chains
C-terminus
1 2 3 4 5 6 7 8
H3N+ COO–
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How many Amino acids are in this polypeptide?
Think pair share... how could you tell?
Amino terminus Carboxyl terminus

12
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Chapter 3 Opening Roadmap.
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What Do Proteins Look Like?
• Proteins are made of single amino acids
• The specific amino acids sequences and the
order are decided or controlled by DNA.
• Proteins have unparalleled diversity of size,
shape, and chemical properties
• Proteins serve diverse functions in cells
because structure gives rise to function

13
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What Do Proteins Look Like?
• Proteins have unparalleled diversity of size,
shape, and chemical properties!
• Proteins serve diverse functions in
cells because structure gives rise
to function Structure and
Function
https://www.youtube.com/watch?v=wvTv8TqWC48
Figure 3.8
(a) Collagen Triple strands
Fibrous; provides structural support
(b) TATA box–binding protein
Saddle-shaped;
binds DNA (DNA
shown in shades
of red)
(c) Porin
Doughnut-shaped;
forms a pore
(d) Chymotrypsin
Globular; binds
substrates Target
protein
Target
DNA
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Proteins Are the Most Diverse Class of Molecules Known
No matter how complex, the underlying structure
breaks down in 4 levels of organization
What Do Proteins Look Like?

14
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Best-Collagen-Supplements-for-Healthy-Younger-Looking-Skin--Top-10-
Collagen is a structural protein in the
extracellular matrix
Collagen is a building block that: promotes
skin elasticity.
https://www.medicalnewstoday.com/articles/262881.php
https://www.youtube.com/watch?v=wvTv8TqWC48
© 2017 Pearson Education, Inc.
What Do Proteins Look Like?
• All proteins have just four basic
structures:
1. Primary
2. Secondary
3. Tertiary
4. Quaternary

15
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Primary Structure
• Protein primary structure is its unique sequence of amino
acids
• The number of primary structures is practically limitless
• 20 types of amino acids are available
• Lengths range from two amino acid residues to tens of thousands
Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved
Figure 3.4
(a) Chain of amino acid residues
C-terminus
Peptide-
bonded
backbone
Side chains
N-terminus
N-terminus
(b) Residue numbering system
Amino acids joined by peptide bond
Carboxyl
group
Amino
group
C-terminus
1 2 3 4 5 6 7 8
Gly Pro Ser Asp Phe Val Tyr Cys
Polypeptide is a chain of amino acids held by peptide bonds

16
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Primary structure is fundamental to the
higher levels of protein structure
• Secondary, tertiary, and quaternary
• The amino acid R-groups affect a polypeptide’s
properties and function
• A single amino acid change can radically
alter protein function
Proteins are the complete, functional form
of the molecule
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Secondary Structure
• Protein secondary structure is formed by hydrogen bonds
between
• The carbonyl group of one amino acid
• The amino group of another amino acid
• Can occur only when a polypeptide bends so that CO and N–
H groups are close together
• Types of secondary structure:
• -helices
• -pleated sheets
image credit: OpenStax Biology

17
Figure 3.10
(a) Hydrogen bonds can form between nearby amino
and carbonyl groups on the same polypeptide chain.
(b) Secondary structures of proteins result.
α-helix β-pleated sheet
(c) Ribbon diagrams of secondary structure
Arrowheads
point toward
the carboxyl end
of the primary
structure
α-helix β-pleated sheet
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https://www.youtube.com/
watch?v=VCUbtqw1h84
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Tertiary Structure
• The tertiary structure of a polypeptide results from
• Interactions between R-groups
• Or between R-groups and the peptide backbone
• These contacts cause the backbone to bend and fold
• Bending and folding contribute to the distinctive three-
dimensional shape of the polypeptide
https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/73-translation/protein-structure.html

18
(b) Tertiary structures are diverse.
A tertiary
structure
composed
mostly of
β-pleated
sheets
A tertiary
structure
composed
mostly of
α-helices
A tertiary
structure
rich in
disulfide
bonds
Ionic bond
Hydrogen bond
between two side chains
Hydrophobic
interactions
+
van der Waals
interactions
Disulfide bond
Hydrogen bond
between side chain and
carbonyl group on
backbone
(a) Interactions that determine the tertiary structure of proteins
© 2017 Pearson Education, Inc. Figure 3.11 Tertiary Structure of Proteins Results from Interactions Involving R-Groups
Tertiary Structure
© 2017 Pearson Education, Inc.
Tertiary Structure
• Five important types of R-group interactions:
1. Hydrogen bonds—form between polar side
chains and opposite partial charges
2. Hydrophobic interactions—water forces
hydrophobic side chains together
3. Van der Waals interactions—weak electrical
interactions between hydrophobic side chains
4. Covalent disulfide bonds—form bridges
between two sulfhydryl groups
5. Ionic bonds—form between groups with full and
opposing charges

19
SPECIAL AMINO ACIDS
Effect of cysteine on protein Structure
Forms cross bridgesFlexibility Rigid
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Curly hair science:
https://www.youtube.com/watch?v=oCZva_6abFM
Cysteine Amino acid structure function
https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-
acids/a/orders-of-protein-structure

20
Figure 3.2
Acidic Basic
Aspartate (D)
Asp
Glutamate (E)
Glu
Lysine (K)
Lys
Arginine (R)
Arg
Histidine (H)
His
Serine (S)
Ser
Threonine (T)
Thr
Tyrosine (Y)
Tyr
Asparagine (N)
Asn
Glutamine (Q)
Gln
Glycine (G)
Gly
Alanine (A)
Ala
Valine (V)
Val
Leucine (L)
Leu
Isoleucine (I)
Ile
Methionine (M)
Met
Cysteine (C)
Cys
Phenylalanine (F)
Phe
Tryptophan (W)
Trp
Proline (P)
Pro
Electrically
charged
side chains
Charged side
chains can
form ionic
and hydrogen
bonds
Polar side
chains
Partial
charges can
form
hydrogen
bonds
Nonpolar
side chains
No charged
or electro-
negative
atoms to
form
hydrogen
bonds
© 2017 Pearson Education, Inc.
© 2017 Pearson Education, Inc.
Overview Primary to Tertiary structure
Proteins in tertiary
structure are the
complete, functional
form of the molecule

21
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Quaternary Structure
• Many proteins contain several distinct polypeptide subunits
that interact to form a single structure
• The bonding of two or more distinct polypeptide subunits
produces quaternary structure
• Some cells contain molecular machines
• Groups of multiple proteins
• That carry out a particular function
Quaternary structures may be held together by a variety of bonds (similar to tertiary structure)
https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/73-translation/protein-structure.html
Figure 3.12
(a) Cro protein, a dimer (b) Hemoglobin, a tetramer
α1 α2
β1 β2
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Quaternary Structure
• The bonding of two or more distinct polypeptide subunits
produces quaternary structure
• Some cells contain molecular machines

22
© 2017 Pearson Education, Inc. http://www.particlesciences.com/news/technical-briefs/2009/protein-structure.html
Proteins were key to understanding structure-function!
Figure 3.15
A triad of key
residues (*) can
cut a substrate
like molecular
scissors Protein
substrate
Active
site
* **
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The location on an enzyme where substrates bind and
react is the active site
Tertiary structure
Structure and
Function

23
Figure 3.7
Normal
red blood
cells
(a) Normal sequence of residues
(b) Single change in sequence of residues
Sickled
red blood
cell
Pro Glu Glu
5 6 7
Pro Val Glu
5 6 7
Structure and function matters!
Sickle cell
anemia involves
a change in
protein structure
Figure 3.13
Ribonuclease protein, folded Ribonuclease protein, denatured (unfolded)
HS
Denaturant added
S
S
HSS
S
Denaturant removed
HS
Disulfide
bonds
S S
HS
S HS
S Hydrogen
bonds
Broken disulfide and
hydrogen bonds
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Each protein has a
characteristic folded
shape that is necessary
for its function
Many proteins have a
disordered shape when they
are inactive
A denatured (unfolded) protein is unable to
function normally
Normal Folding Is Crucial to Function

24
Table 3.1
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Take home message: Combined effects of primary, secondary, tertiary,
and sometimes quaternary structure allow for amazing diversity in