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I. What does “alive” mean?
II. The Chemistry of Life
III. Biological Molecules (biomolecules)
I. Properties of Life
Biology is the study of life. But what is alive? Below are some criteria for being alive:
A. cellular organization – all living things are composed of cells
cell– tiny chamber covered in a membrane
smallest unit capable of all life functions
organisms are singlecelled or multicellular
B. metabolism sum of all chemical reactions an organism carries out
takes in energy and uses it to grow and live
C. homeostasis maintenance of stable, internal conditions, often different
from the environment ex: 37 0C, 98 0F
D. reproduction the ability to produce offspring from one generation to the next
E. heredity passage of a set of instructions from parent to offspring
II. The Chemistry of Life Perspective
Living things are composed of cells, which contain organelles, which are made of
biological molecules, which are made of atoms, which are made of subatomic particles…
A. Atoms
All matter (alive or not) is composed of atoms. An atom contains a nucleus. The nucleus
contains protons and neutrons. The electron cloud consists of a huge amount of empty
space with some electrons floating in it.
Atom Drawing Here:
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Fill in The Atom Chart
Particle Charge Location
proton
neutron
electron
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B. Elements
Different kinds of atoms are called elements and have different numbers of protons in
their nuclei. Elements that we will talk about a lot in biology include carbon (C),
hydrogen (H), oxygen (O), nitrogen (N), phosphorous (P), sodium (Na), potassium (K)
and chlorine (Cl). Living organisms are largely composed of these elements. The number
of protons in each element’s nucleus is the red number on The Periodic Table. Use this
information to fill in the chart below. The first has been completed for you.
Fill in the element chart
C. Ions
Most elements are neutral because they have equal numbers of protons and
electrons. Since each proton has a +1 charge and each electron has a –1 charge, an atom
with equal numbers of protons and neutrons has a total charge of zero.
Sometimes, however, an atom gains or losses electrons (protons are never lost or
gained to make ions). This creates a charged atom, called an ion. An ion with a positive
charge is called a cation. An ion with a negative charge is called an anion.
For example, P3 is a phosphorous atom that has gained 3 more electrons than
protons. Na+ is a sodium ion. Na lost one electron to become a cation.
D. Compounds
Compounds are groups of atoms held together by chemical bonds. For example, H2O is
the compound water. CO2 is the compound carbon dioxide. O2 is the compound oxygen.
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E. Chemical Bonds
Chemical bonds hold atoms together in a compound. There are different types of
chemical bonds.
1. ionic bond – In an ionic bond, electrons are TRANSFERRED between component
atoms. Ionic bonds form in salts, like NaCl, table salt. There are many other kinds of
salts that you will learn about in chemistry. Ionic bonds form between a cation and an
anion. For example: Na+ and Cl form NaCl. In watery environments like body fluids and
cells, these bonds dissolve leaving the component ions (for example, Na+ and Cl) floating
in the solution. Solutions with ions, like our bodies, conduct electricity very well.
2. covalent bond – In a covalent bond, electrons are SHARED between component
atoms. These are strong bonds that don’t come apart easily. Sugar, fats, proteins, DNA
and water are held together with covalent bonds. These bonds can be nonpolar or polar as
we will discuss below
Bonds may also form between molecules to hold them together. For example, the bonds
that hold all of water molecules together in your water glass are hydrogen bonds.
Depiction of Bonding in Water Molecules
Concepts: molecular water, polar covalent bonds, hydrogen bonds
F. Water and Hydrogen Bonding
Water is the medium of life. Not only do many life forms live in water, but the inner
environment of our bodies is watery. The vast array of hydrogen bonds in water gives
water its unique lifesupporting properties.
1. Water is “sticky.” Hydrogen bonds that result from water’s polar nature tend to make it
stick to itself and to other polar substances. Substances that readily dissolve in water are
considered polar substances.
cohesion – water sticks to itself
adhesion – water sticks to other substances
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capillary action – the combination of cohesion and adhesion that make water
climb up narrow tubes like those that run from the root to the leaves of plants.
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2. Because of the hydrogen bonding, water sticks to itself and doesn’t evaporate quickly.
Thus, the oceans don’t evaporate on a hot day.
3. Water absorbs a lot of heat from the environment in hot weather and releases heat into
the environment in cold weather. This prevents massive, rapid temperature change.
4. Water is a powerful solvent, meaning that many molecules dissolve in water. This is
because water’s polar nature. You know that salt dissolves in water. Below, draw what
happens to salt when it encounters water.
Depiction of NaCl in Water
G. Acids and Bases
1. Acid tastes sour
pH < 7
2. Base tastes bitter
pH > 7
3. Neutral –neither acidic nor basic
pH = 7
Most body fluids are close to neutral, but stomach acid, for example, has a pH of about
2.1. Blood has a pH of 7.4.
pH scale
Draw a pH scale below that runs from 0 to 14. Label it with the even numbers only. On
top of the scale, indicated which part of the scale is acidic, which part is neutral and
which part is basic. Based on the readings of your probes, locate each substance on the
scale. Also include stomach acid and blood (above).
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III. Biological Molecules (biomolecules): sugars, fats, proteins and nucleic acids
A. Sugars or carbohydrates
Some sugars provide quick energy while others build structures. Sugars are polar
molecules and dissolve easily in water. Another name for sugar is “saccharide” and
sugars are classed into groups:
1. Monosaccharide (Sugar made of one sugar unit.)
glucose – quick energy sugar
fructose – sugar in fruit
galactose – a sugar that provides a large amount of energy. It is less sweet than glucose.
How monomers differ from each other:
Each monomer has a particular shape. Monomers with similar shapes differ by the order
of atoms they contain. Draw each monomer here:
Glucose Fructose Galactose
2. Disaccharides (Sugars made of two sugar units linked together.)
sucrose table sugar – made of glucose plus fructose
lactose milk sugar – made of galactose plus glucose
Draw the disaccharides here:
Sucrose Lactose
3. Polysaccharides (Sugars made of many sugar units linked together).
starch – Plant sugar used for energy storage made of a chain of glucose molecules.
cellulose – Plant sugar used for structural support made of a chain of glucose molecules.
Draw an example of a polysaccharide made from glucose:
B. Fats
Fats provide energy storage and insulation. Fat energy is stored in fat cells, called
adipose cells, and provides energy when the body’s short term supplies run out. They
provide more energy per unit than any other biological molecule. Fats include oils, wax,
and animal fat.
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Fats are also important insulators. In animals like whales that must dive in cold water, fats
form an insulating layer called blubber. In humans and other animals, fats insulate
neurons so the nervous system can efficiently deliver nerve signals. Fats are nonpolar and
do not readily interact with water.
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III. Biological Molecules . . . continued
C. Proteins
Proteins are the “tools” of the body and form many structures. Proteins called enzymes
make chemical reactions happen correctly in the body. Hair and fingernails are built from
a protein called collagen, while muscles are built from actin and myosin proteins.
1. Amino acids – the subunits of proteins
All proteins are built from 21 subunits called amino acids. Below are two examples
of real amino acids. We will not learn the real structures; we will represent amino
acids as polygons.
2. Polypeptides – chains of amino acids
Each unique protein is a made of one or many chains of the 21 amino acids combined
in different orders much like each word in English is made of different combinations
of letters. These amino acid chains are called polypeptides. Most polypeptides range
in length from 50 to 2000 amino acids. Amino acids are joined to each other by a
special covalent bond called a peptide bond. Each polygon below represents an
amino acid, joined to the next amino acid by a peptide bond, to make a polypeptide
chain.
3. Proteins – folded polypeptide chains
A polypeptide becomes a protein once it folds into a 3 dimensional shape. Proteins
would not be very useful biological tools if they were all straight lines. Please see the
wiki to see various protein structures.
Enzymes
Enzymes are special proteins that help speed up or slow down reactions in your
body to help your body run efficiently. We study them in more detail in the
energy unit.
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III. Biological Molecules . . . continued
D. Nucleic Acids
Nucleic Acids are information and energy storage molecules including DNA, RNA and
ATP.
1. Nucleotide – all nucleic acids are made of special subunits called nucleotides. A
nucleotide consists of three components: a pentose sugar, three phosphate groups
and a nitrogenous base. Draw a nucleotide here:
a. Sugar
DNA sugar: Deoxyribose
RNA and ATP sugar: Ribose
b. Phosphates – One or two phosphate groups are often removed to release
energy. DNA and RNA only have one phosphate group per nucleotide.
Removal of the other two phosphate groups provides the energy to make the
DNA and RNA molecules.
c. Nitrogenous bases
Pyrimadines – made of one ring – Draw general shape here:
1. Cytosine – in both RNA and DNA
2. Thymine – in DNA only
3. Uracil – in RNA only
Purines – made of 2 fused rings – Draw general shape here:
1. Adenine – in RNA, DNA, and ATP
2. Guanine – in RNA and DNA
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III. Biological Molecules . . . continued
D. Nucleic Acids . . . continued
2. ATP (adenosine triphosphate)
ATP is the energy currency for cells just like dollars are a monetary currency. ATP
powers most cellular work. Examples of ATPpowered work include beating of cilia,
contraction of muscle cells and pumping substances across membranes.
Structure: c. adenine
PO3 PO3 PO3
a. 3 phosphate groups
b. ribose sugar
Energy is stored in ATP’s structure
The phosphate groups have negative charges, which repel each other. Holding them close
to each other like pushing together the repellant ends of a magnet. The bonds that hold
the phosphates together are very strong and contain a lot of energy. When the bond to the
last phosphate group is cut, a great deal of energy is released. This energy is used to do
cellular work. When ATP loses its last phosphate, the molecule becomes ADP
(adenosine diphosphate).
PO3 + energy
ATP ADP
QUESTIONS :
1. What three molecules make up ATP?
2. What does each letter in ATP stand for?
3. Why does the ATP molecule contain so much energy?
4. How does your body get energy out of ATP?
5. What is ATP called after one phosphate comes off? What about after two come off?
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III. Biological Molecules . . . continued
D. Nucleic Acids . . . continued
2. RNA (ribonucleic acid)
There are several kinds of RNA. We learn about each of them later.
mRNA = messenger RNA
tRNA = transfer RNA
rRNA = ribosomal RNA
RNA is made of ribose nucleotides stacked on top of each other. The nucleotides are held
together by covalent bonds between the phosphate of one nucleotide and the ribose sugar
of the next nucleotide. The whole strand coils. Let’s draw a 3 nucleotide RNA sequence
here:
3. Three differences between DNA and RNA. Fill in the table below:
RNA DNA
Sugar
Bases
Number of
strands
Shape
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III. Biological Molecules . . . continued
D. Nucleic Acids . . . continued
4. DNA (deoxyribonucleic acid)
DNA (deoxyribonucleic acid) stores hereditary information. Nearly every cell in an
organism’s body contains the entire set of DNA needed to build that organism. DNA
instructions contain all the information to build and grow the organism and meet the daily
demands of living.
DNA is similar to RNA except two strands are attached together by hydrogen bonding
between the base pairs. Adenine pairs to thymine and guanine pairs to cytosine. The
strands coil into a double helix.
Base pairing: Draw arrows to the hydrogen bonds.
Two strands of DNA attached by hydrogen bonding. Then they coil into a double helix.
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Questions:
One the above picture, circle one DNA strand, circle one set of hydrogen bonds between
the strands, draw arrows pointing to two phosphate groups, color in 2 ribose sugars, and
label the double helix.
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