Exam 1 Review Notes on General Biology | BIOL 1001, Study notes of Biology

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AN INTRODUCTION TO LIFE ON EARTH

What is Biology?

--- The science of living organisms and life processes.

O.K., so what is science?
SCIENCE IS AN ACVTIVITY

And

If biology is the science of “life,” what exactly is life?

We all recognize what life is, but it’s difficult to define.

The characteristics of life:
1) -Complex, organized structure

2) -Homeostasis - the ability to maintain the structure and
regulate the internal environment.

3) -Response to stimuli - a change outside (or inside) leads to another
change

4) -Ability to acquire material and energy
>The material and energy are often transformed<

5) -Growth

6) -Reproduction - either sexual or asexual
>DNA is genetic information, the “blueprint” for the offspring<

7) -Ability to evolve - to change to fit the environment


Complex, organized structure
The complexity of life is built in levels. (see fig 1-1)

Each level has ingredients or components which interact to make
something greater than the sum of the parts.


Individuals reproduce their own kind.

The genetic information for “How to build an offspring” is stored in the
DNA of the parent(s) and that information is passed on to the offspring.

Evolution

If the environment changes, then the population of organisms must change to fit the environment or possibly die out. This process of survival of the fittest is natural selection

The evolutionary changes are usually slow, taking several generations and occur by the accumulation of DNA changes known as mutations.


>>>>>All life forms have these characteristics in common, yet there is an amazing diversity in the forms of life on the planet.

All living organisms are organized into groups. Each of the major organizational
groups called 1domains
-chart

There are two prokaryotic domains; Bacteria and Archaea and a eukaryotic
domain; Eukarya.

1Within the domains are at least 6 groups known as kingdoms (See fig. 1-1). Each of the major organizational groups called kingdoms have different attributes which define them. (See table 1-1)

The first difference is cell type
Prokaryotic versus Eukaryotic

1PROKARYOTES
EUKARYOTES
No nucleus or nuclear envelope
Nucleus with a nuclear envelope
Genetic material in a “nucleoid region”
Genetic material within the nucleus
No organelles or internal membranes
Contains cytosol with membrane-bound organelles

Kingdom Cell
Type

Bacteria Prokaryotic
Archaea Prokaryotic
Protista Eukaryotic
Fungi Eukaryotic
Plantae Eukaryotic
Animalia Eukaryotic


The next property is how many cells the organism has

Single cell (unicellular) or many cells (multicellular)

Kingdom Cell Cell
Type Number

Bacteria Prokaryotic Unicellular
Archaea Prokaryotic Unicellular
Protista Eukaryotic Unicellular
Fungi Eukaryotic Multicellular
Plantae Eukaryotic Multicellular
Animalia Eukaryotic Multicellular

The third attribute in the classification of organisms at the kingdom levels is how the organism obtains nutrients

Three basic methods
Make your food using sunlight - photosynthesis
Uptake of nutrients by absorption
Uptake by eating or ingestion
hypothesis? If not then you have to change your hypothesis
If they do then you’re one step closer to a theory

A theory is an explanation of natural events which is based on a LARGE number of observations and/or experiments.

Scientific Meanings
Hypothesis
Conjecture of a possible explaination

Theory
Strongly verified explanation for a phenomenon accounts for mny facts and explains a variety of phenomena

Law
Absolute proven (rare, especially in biology
Test one Continued 09/12/2011
>> An understanding of chemistry is important because the interaction
Between atoms is one of the lowest levels of biological organization.

>>>>>The basic unit of all forms of matter is the atom

---Atom is the smallest unit of matter that retains the physical and chemical
Properties of the element.

>> Atoms are made up of subatomic particles. The 3 most stable subatomic particles are: neutrons, protons, and electrons (see fig 2.1)

---Protons are positively charged particles found at the core, or nucleus, of the atom.
These show what will be the atomic number of the element.

---Neutrons are uncharged particles found at the core, or nucleus, of the atom.

---Electrons are light, negatively charged particles that orbit around the nucleus in
electron shells.


NEUTRON
PROTON
ELECTRON
ch arge
uncharged
+1 charge
-1 charge
lo cation
at the core of the atom known as the nucleus
at the core of the atom known as the nucleus
orbiting around the nucleus in electron shells

>>>>A collection of atoms of the same type form an element.

---Element is a substance that can’t be broken down into other substances by chemical reactions. (see table 2-1)
-elements are composed of atoms

TABLE 2-1 COMMON ELEMENTS: Hydrogen, Carbon, Nitrogen, and Oxygen are the most important ones we need to know.

>>>The Atomic Nucleus

---Atomic number is the number of protons in an atom of a particular element (see
table 2-1)

-The atomic number is constant for a given element

The atomic weight of an element is the number of protons plus the number of neutrons.

The atoms of a particular element may have different numbers of neutrons
This difference results in isotopes.

---Isotopes are atoms of the same element, which have different atomic weights
ratio
-example: our atmosphere, nitrogen, helium, carbon dioxide, etc.

>>>Formation of ions

If an atom has an almost empty or an almost full outer electron shell it is more likely
to form an ion (see fig. 2-3)


---Ion is a charged atom or molecule: For an ion to be charged, it has to have a different number of protons and neutrons.

---Anion is a negatively charged atom or molecule
---Cation is a positively charged atom or molecule

---Ionic bond is formed by the attraction between oppositely charged ions after the
completion of an electron transfer

Ionic compounds are called salts and usually form crystals as a solid.
Ionic bonds are strong in crystals but break easily in water.

>>>Sharing Electrons

>>>>>>>Covalent bond is a bond formed when two atoms share electrons (see
fig 2.6

An atom may have to share only one pair of electrons to fill the outer shell.
Some atoms may have to share two (or more) pairs of electrons or may have to
share with more than one atom to fill the outer electron shell.


---Single covalent bond shares a single pair of electrons ((HYDROGEN))

---Double covalent bonds share two pairs of electrons ((OXYGEN))

---Triple covalent bonds share three pairs of electrons


>>>Non-polar Covalent Bonds versus Polar Covalent Bonds

---Nonpolar covalent bond is a covalent bond in which the sharing of the electron
pair is equal. (see fig. 2.6a)

---Polar covalent bond is a covalent bond in which the sharing of the electron pair
is unequal. (See fig 2.6b)

When polar covalent bonds form, the molecules which result may also be polar.
-positive charge at one end negative charge at the other.


>>>Hydrogen bonds form between polar molecules

---Hydrogen bond is formed by the charge attraction when a hydrogen atom which
is covalently bonded to one atom is attracted to a second atom. (see fig. 2.5)

A weak attractive force about 20 times easier to break than a covalent bond.
A charge attraction between oppositely charged polar molecules.


Weak bonds are often as important as strong bonds in biological systems.

Reversible binding
Can form between molecules or within large molecules.
Can help stabilize three-dimensional shape of large molecules.

Water has a greater surface tension than most liquids because of the
arrangement of the hydrogen bonds at the surface.

Causes water to bead
>>>Acids and bases

Water molecules can dissociate. That means that the hydrogen atom of one
water molecule leaves its electron behind and forms a hydrogen ion (H+) and a
hydroxide ion (OH-).


H
\
O H+
/ =>
H
O-
/
H


In pure water the number of H+ ions = the number of OH- ions

If the solution is acidic, then the number of H+ ions is greater than the number of
OH- ions.

Conversely if the number of OH- ions is greater than the number of H+ ions, then
the solution is basic.

---Acid is a substance which increases the concentration of H+ in a solution.

---Base is a substance which reduces the concentration of H+ in a solution.


>>>The pH Scale

The degree of acidity is expressed on the pH scale.

---pH scale is a scale used to measure the acidity of solutions. The scale ranges
from 0 to 14. (See fig. 2-9)

For a neutral solution pH =7
For an acidic solution pH =5
For a basic solution pH = 9

Because the pH scale is a logarithmic scale, a change of one pH unit represents a
tenfold change in the concentration of H+.

When pH goes up, the Hydrogen ion concentration goes down; and vice versa. It has an inverse relationship. When you change the pH of something, you’re also changing the Hydrogen ion concentration by increments of 10.

Most biological solutions are between pH 6 and pH 8


>>>Buffers Help Maintain a Constant pH

---Buffers are substances that prevent large sudden changes in pH.

Buffers are combinations of H+ donor and H+ acceptors

Buffers function by accepting H+ ions from solution when they are in excess, and
donating H+ ions to the solution when the supply is depleted.


CHAPTER 3
BIOLOGICAL MOLECULES

>>>>>>>>Aside from water, most biologically related molecules contain carbon.

---Organic molecules are molecules containing carbon.
Exceptions: All carbon molecules, graphite, diamonds, coal
Carbon dioxide
Carbon monoxide

Only living organisms can create organic molecules.

Carbon atoms are the most versatile building blocks of molecules

Carbon has a valence of 4.
Can bind to 2, 3, or 4 other atoms.

>>>Another factor which leads to the versatility of organic molecules is the
attachment of functional groups (see table 3-1)

---Functional groups are small characteristic groups of atoms which are
frequently bonded to the carbon skeleton of organic molecules.

Functional groups:

-Have specific chemical and physical properties.
-Are regions of organic molecules which are frequently
chemically reactive.
-Behave consistently from one organic molecule to another.
-Can determine the chemical properties of the organic molecule in
which they are located.

There are seven general functional groups found in organic molecules:

1) Hydrogen Group (-H)
2) Hydroxyl Group (-OH)
3) Carboxyl Group (-COOH)
4) Amino Groups (-NH2)
5) Phosphate Groups (-PO4)
6) Methyl Groups (-CH3)
7) Sulfhydryl Groups (-SH)

1) Hydrogen Group (-H)


---Hydrogen group is a functional group of a hydrogen atom bonded to a carbon
atom (of the carbon skeleton).

-Is either a polar group or a non-polar group depending on the atom to
which the hydrogen is attached.

-Involved in condensation (dehydration) and hydrolysis reactions

2) Hydroxyl Group (-OH)


---Hydroxyl group is a functional group of a hydrogen atom bonded to an oxygen
atom which is bonded to a carbon atom (of the carbon skeleton).

-Is a polar group

-Involved in condensation (dehydration) and hydrolysis reactions
-Critical in stabilizing protein structure

>>>SYNTHESIZING ORGANIC MOLECULES: A MODULAR APPROACH

Biological molecules are often put together in subunits, or modules, called
monomers.

---the simple molecules condensed into more complex ones
---monomers into polymers

>polymers are chains of similar building blocks or monomers.


>>>Biological Molecules (monomer) Are Joined Together Or Broken Apart By
Adding Or Removing Water

The reaction which forms a polymer from monomers is a dehydration synthesis (or condensation reaction)


---Dehydration synthesis is a reaction in which the covalent linkage of the
monomers is accompanied by the “removal” of a water molecule.

-One monomer loses a hydroxyl group (-OH), and the other monomer loses
a hydrogen (-H).


---Hydrolysis is the breaking of the covalent bond between two monomers by the
addition of water.

-One monomer gains a hydroxyl group (-OH), and the other monomer
gains a hydrogen (-H).


Test One 09/12/2011
BIOLOGICAL MOLECULES

>>>>>>>>Aside from water, most biologically related molecules contain carbon.

---Organic molecules are molecules containing carbon.
Exceptions: All carbon molecules, graphite, diamonds, coal
Carbon dioxide
Carbon monoxide

Only living organisms can create organic molecules.

Carbon atoms are the most versatile building blocks of molecules

Carbon has a valence of 4.
Can bind to 2, 3, or 4 other atoms.

>>>Another factor which leads to the versatility of organic molecules is the
attachment of functional groups (see table 3-1)

---Functional groups are small characteristic groups of atoms which are
frequently bonded to the carbon skeleton of organic molecules.

3) Carboxyl Group (-COOH)


---Carboxyl group is a functional group in which a carbon atom is double bonded to an oxygen atom (like a carbonyl) and is also single bonded to the oxygen atom of a hydroxyl group.

-Since this group can donate a proton, it is an acid

-Involved in peptide bonds

4) Amino Groups (-NH2)

---Amino groups are functional groups in which two hydrogen atoms are bonded to a nitrogen atom which is bonded to a carbon atom (of the carbon skeleton).

-Acts as a weak base (similar to ammonia)

-Involved in peptide bonds

5) Phosphate Groups (-PO4)

---Phosphate group is a functional group which is the dissociated form of phosphoric acid (H3PO4)

-Acts as an acid because of the ability to donate protons.

-Links nucleotides

-Important in cellular energy storage and energy transfer.

Example: ATP

6) Methyl Groups (-CH3)

---Methyl group is a functional group which consists of three hydrogen atoms bonded to a carbon atom.

-Is a non-polar group.

-Makes the molecule more hydrophobic

7) Sulfhydryl Groups (-SH)

-Critical in stabilizing protein structure

>>>SYNTHESIZING ORGANIC MOLECULES: A MODULAR APPROACH

Biological molecules are often put together in subunits, or modules, called
monomers.

---the simple molecules condensed into more complex ones
---monomers into polymers

>polymers are chains of similar building blocks or monomers.


>>>Biological Molecules (monomer) Are Joined Together Or Broken Apart By
Adding Or Removing Water

The reaction which forms a polymer from monomers is a dehydration synthesis (or condensation reaction)


---Dehydration synthesis is a reaction in which the covalent linkage of the
monomers is accompanied by the “removal” of a water molecule.

-One monomer loses a hydroxyl group (-OH), and the other monomer loses