biol 108 - chp 2: chemistry
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Chemistry
BIOL 108 Intro to Bio Sci
Chapter 2
Rob Swatski Assoc Prof Biology
HACC-York 1
Learning Goals
Describe what atoms are,
their structure, & how they
bond.
Understand water’s
features that help it support
all life.
Describe the structure & function of
carbohydrates.
Describe the structure & function of
lipids.
Describe the structure & function of proteins.
Describe the structure & function of
nucleic acids.
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3
2.1–2.3
Atoms form
molecules through
bonding.
4
2.1 Everything is made of atoms.
An element is a substance that cannot
be broken down chemically into any other substances.
An atom is a bit of matter that cannot be subdivided any further
without losing its essential properties.
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Insert new figure 2.3
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Radioactive Atoms
A few atomic nuclei are not stable and break down spontaneously.
These atoms are radioactive.
They release, at a constant rate, a tiny, high-speed particle carrying a lot of energy.
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insert new fig 2.4
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Take-Home Message 2.1
Everything around us, living or not, is made
from atoms, the smallest unit into which material can be divided.
Atoms all have the same general structure.
They are made up of protons and neutrons in
the nucleus and electrons, which circle far around the nucleus.
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2.2 An atom’s electrons determine how (and whether) the atom will bond with other atoms.
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Insert new fig 2-6
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Insert fig 2-7
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Insert new fig 2-8
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Take-Home Message 2.2
The chemical characteristics of an atom depend upon
number of electrons in their outermost shells.
Atoms are most stable and least likely to bond with other atoms when
their outermost electron shell is full.
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2.3 Atoms can bond together to form molecules or compounds.
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Molecules = Products of Bonding
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Insert fig 2-11
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Take-Home Message 2.3
Atoms can be bound together in three different
ways.
Covalent bonds, in which atoms share electrons, are
the strongest.
In ionic bonds, the next strongest, one atom transfers its electrons to another and the two oppositely charged ions are attracted to each
other, forming a compound.
Hydrogen bonds, the weakest, involve the attraction between a
hydrogen atom and another polar atom or molecule.
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2.4 Hydrogen bonds make water cohesive.
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Take-Home Message 2.4
Water molecules easily form hydrogen bonds,
giving water great cohesiveness.
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2.5 Water has unusual properties that make it
critical to life.
Cohesion
Large heat capacity
Low density as a solid
Good solvent
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Cohesion
How?
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Take-Home Message 2.5
The hydrogen bonds between water molecules give water
several of its most important characteristics: cohesiveness,
low density as a solid, the ability to resist temperature changes, & broad effectiveness as a solvent
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2.6 Living systems are highly sensitive to acidic and basic conditions.
37
Hydrogen Ions & Hydroxide Ions
Ionized Hydroxide Molecule
OH -
Non-Ionized Water Molecule
H2O O O
H H H
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pH Scale
The amount of H+ in a solution is a measure of its
acidity & is called pH.
Acids
Bases
39
Acidic [H+] > [OH–]
Neutral [H+] = [OH–]
Basic [H+] < [OH–]
7
0
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H+ Ions & Acids
H+ very reactive
Acids can donate H+ to
other chemicals 41
Bases
Low H+ & high OH-
Antacids, baking soda, milk of
magnesia 42
Buffers
Can quickly absorb excess H+ ions to keep
a solution from becoming too acidic
Can also quickly release H+ ions to
counteract any increases in OH- concentration
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Take-Home Message 2.6
The pH of a fluid is a measure of how acidic or
basic a solution is and depends on the
concentration of dissolved H+ ions present.
Acids, such as vinegar, can donate protons to other chemicals while bases,
including baking soda, bind with free protons.
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2.7 Carbohydrates are macromolecules that function as fuel.
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Four Types of Macromolecules
Carbohydrates Lipids Proteins Nucleic Acids
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Carbohydrates
C, H, and O
Primary fuel for organisms
Cell structure
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Take-Home Message 2.7
Carbohydrates are the primary fuel for running all cellular machinery and also form much of the structure
of cells in all life forms.
Carbohydrates contain carbon, hydrogen, and
oxygen, and generally have the same number of carbon atoms as they do H2O units.
The C-H bonds of carbohydrates store a great
deal of energy and are easily broken by organisms.
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2.8 Simple sugars are the most effective source of
energy.
Monosaccharides
3-7 carbon atoms
Glucose & fructose
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Glucose
Most carbohydrates are ultimately converted into
glucose
Glucose provides energy for the
body’s cells
Stored temporarily as glycogen
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What is “carbo-loading”?
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Take-Home Message 2.8
The simplest carbohydrates are called monosaccharides
or simple sugars. They contain from 3-7 carbon
atoms.
The sugar glucose is the most important carbohydrate to
living organisms.
Glucose in the bloodstream can be used as an energy source, can be stored as glycogen in the muscles and liver for later use, or can be converted to fat.
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2.9 Complex carbohydrates are
time-released packets of energy.
More than 1 sugar unit:
monosaccharide
Disaccharides: sucrose, lactose
Polysaccharides: starch, cellulose
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Starch
100’s of glucose molecules
joined together
Barley, wheat, rye, corn, & rice
Glycogen: “animal starch”
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Take-Home Message 2. 9
Multiple simple carbohydrates sometimes
link together into more complex carbohydrates.
Types of complex carbohydrates include starch, the primary form of energy
storage in plants, and glycogen, a primary form of energy storage in animals.
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2.10 Not all carbohydrates are digestible.
Cellulose
Chitin
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Fiber
“Roughage”
Colon cancer prevention &
reduction
Termites ecological
role 61
Take-Home Message 2.10
Some complex carbohydrates, including
chitin and cellulose, cannot be digested by
most animals.
Such indigestible carbohydrates in the diet,
called fiber, aid in digestion and have
numerous health benefits. 62
2.11–2.13
Lipids store
energy for a rainy
day.
63
2.11 Lipids are macromolecules with several functions, including energy storage.
64
Why does a salad dressing made with
vinegar and oil separate into two
layers shortly after you shake it?
Hydrophilic
Hydrophobic
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Take-Home Message 2.11
Lipids are non-soluble in water and greasy to the
touch.
They are valuable to organisms in long-term
energy storage and insulation, membrane
formation, and as hormones.
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2.12 Fats are tasty molecules too
plentiful in our diets.
Glycerol: “head” region
Fatty acid “tails”
Triglycerides
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Saturated & Unsaturated
Fats
# of bonds in the hydrocarbon chain
in a fatty acid
Health considerations
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Carotid artery plaque
Take-Home Message 2.12
Fats, including the triglycerides common in the food we eat, are
one type of lipid.
Characterized by long hydrocarbon tails, fats effectively
store energy in the bonds connecting the molecules.
Their caloric density is responsible for humans’ preferring fats to other
macromolecules in the diet, and is also responsible for their
association with obesity and illness in the modern world.
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2.13 Cholesterol and phospholipids are used to build
sex hormones and membranes.
Not all lipids are fats
Sterols
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Cholesterol
Important component of most
cell membranes.
Can attach to blood vessel walls and cause them to
thicken.
Cells in our liver produce almost 90%
of the circulating cholesterol.
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Steroid Hormones
Estrogen
Testosterone
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Phospholipids & Waxes
Phospholipids are the major component of
the cell membrane.
Waxes are strongly
hydrophobic. 80
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Take-Home Message 2.13
Cholesterol and phospholipids are lipids
that are not fats.
Both are important components in cell
membranes.
Cholesterol also serves as a precursor to steroid
hormones, important regulators of growth and development.
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2.14–2.18
Proteins are
versatile
macromolecules
that serve as
building blocks.
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2.14 Proteins are versatile macromolecules that serve as building blocks.
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Keratin: structural
protein
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Amino Acids
20 different amino acids
Strung together to
make proteins
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Nonpolar Amino Acids
Glycine (Gly or G)
Alanine (Ala or A)
Valine (Val or V)
Leucine (Leu or L)
Isoleucine (Ile or I)
Methionine (Met or M)
Phenylalanine (Phe or F)
Tryptophan (Trp or W)
Proline (Pro or P)
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Take-Home Message 2.14
Unique combinations of 20 amino acids give rise to
proteins, the chief building blocks of physical structures that make up all organisms.
Proteins perform myriad functions, from assisting
chemical reactions to causing blood clotting to building
bones to fighting microorganisms.
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2.15 Proteins are an essential dietary
component.
Growth
Repair
Replacement
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Complete Proteins
Have all essential amino
acids
Incomplete proteins
Complementary proteins
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Insert new fig 2-38
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Take-Home Message 2.15
Twenty amino acids make up all the proteins
necessary for growth, repair, and replacement of tissue in living organisms.
Of these amino acids, about half are essential for
humans: they cannot be synthesized by the body so must be consumed in the
diet.
Complete proteins contain all essential amino acids,
while incomplete proteins do not.
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2.16 Protein functions are influenced by their three-dimensional shape.
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97 Silk = pleated sheet
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too freakin’ cute…
…it has eyelashes for crying out loud!
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Why do some people have curly hair and others have straight hair?
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Take-Home Message 2.16
The particular amino acid sequence of a protein determines how it folds into a particular shape.
This shape determines many of the protein's
features, such as which molecules it will
interact with.
When a protein's shape is deformed, the
protein usually loses its ability to function.
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2.17 Enzymes are proteins that initiate and speed up chemical reactions.
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Substrates
Active Site
Enzyme
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Enzymatic proteins = Catalysts
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Activation Energy
Chemical reactions occurring in organisms can either release energy or consume energy.
In either case, the reaction needs a little “push” in order to initiate the reaction―called activation energy.
Enzymes act as catalyst by lowering the activation energy.
108
Take-Home Message 2.17
Enzymes are proteins that help initiate and
speed up chemical reactions.
They aren't permanently altered in the process but rather can be used again and
again. 109
2-18 Enzymes regulate reactions in several ways
(but malformed enzymes can cause problems).
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“Misspelled” Proteins
Incorrect amino acid sequence
Active site disruptions
Phenylketonuria
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Take-Home Message 2.18
Enzyme activity is influenced by physical factors such as
temperature and pH, as well as chemical factors, including
enzyme and substrate concentrations.
Inhibitors and activators are chemicals that bind to enzymes, and by blocking the active site or altering the shape or structure of the enzyme can change the rate at which the enzyme catalyzes
reactions. 118
2.19–2.21
Nucleic acids
store information
on how to build and run a body.
119
2.19 Nucleic acids are macromolecules that store information.
120
Two Types of Nucleic Acids
Ribonucleic acid (RNA)
Deoxyribonucleic acid (DNA)
Both play central roles in directing the production of
proteins. 121
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Information Storage
The information in a molecule of DNA is determined by its
sequence of bases.
Adenine, Guanine, Cytosine, &
Thymine
CGATTACCCGAT
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Take-Home Message 2.19
The nucleic acids DNA and RNA are macromolecules that store information by having unique sequences
of molecules.
Both play central roles in directing protein
production in organisms.
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2.20 DNA holds the genetic information to build an organism.
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Base-Pairing
A & T
C & G
What is the complimentary
strand to this strand: CCCCTTAGGAACC?
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Take-Home Message 2.20
DNA is like a ladder in which the long vertical element of the
ladder is made from a sequence of sugar-phosphate-sugar-
phosphate molecules and rungs are nucleotide bases.
The sequence of nucleotide bases contains the information
about how to produce a particular protein.
127
2.21 RNA is a universal translator, reading DNA and directing protein production.
128
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RNA differs from DNA in three
important ways.
The sugar molecule of the
sugar-phosphate backbone
Single-stranded
Uracil (U) replaces thymine (T)
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Take-Home Message 2.21
RNA acts as a middleman molecule—taking the instructions for protein production from DNA to another part of the cell where,
in accordance with the RNA instructions, amino acids are
pieced together into proteins.
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