Chapter 4

Genetics
The Genetic Material
DNA
DNA stands for Deoxyribose Nucleic Acid. That is, a nucleic acid with two sugars.
DNA is the hereditary material of cells and is considered the blueprint of life. DNA is
found in all kingdoms of life. Even most viruses have DNA. When someone says DNA,
they may be referring to one's genetic material on multiple levels: They may be
speaking about a single deoxyribose nucleic acid molecule, a section of a double helix,
a section of a chromosome, or one's entire hereditary composition.
DNA Structure
Nucleic acids are large polymers made of many repeating units called nucleotides. Each
nucleotide is composed of a sugar molecule, a phosphate group, and a molecule called
a nitrogenous base.
DNA nucleotides contain one specific sugar, deoxyribose, and one of four different
nitrogenous bases: adenine (A), guanine (G),cytosine (C) and thymine (T).

Protein Synthesis
DNA and RNA are both important in the protein-making process. In the cell, the DNA
nucleotides are used as a genetic alphabet, arranged in sets of three (e.g., ATC , GGA ,
TCA , CCC ) to form code words in the DNA language. It is the sequence of these code
words in DNA that dictates which amino acids are used, and the order in which they
appear in a protein. DNA molecules are very long and code for many proteins along
their length. Proteins are synthesized in two steps; transcription and translation .

Step One: Transcription—Making RNA

Transcription is the process of using DNA as a template (stencil) to synthesize RNA.
The enzyme RNA polymerase “reads” the sequence of DNA nitrogenous bases and
follows the base-pairing rules between DNA and RNA to build the new RNA molecule .
RNA polymerase attaches to the DNA and moves along the grooves scanning for base
sequences that act as markers, or signs, that a gene is nearby. The enzyme looks for a
Step Two: Translation—Making Protein
Translation is the process of using the information in RNA to direct protein synthesis
by attaching amino acids to one another. The mRNA is read linearly in sets of three
nucleotides called codons . A codon is a set of three nucleotides that codes for the
placement of a specific amino acid. In the context of an mRNA molecule, For example,
the codon UUU corresponds to only the amino acid phenylalanine (Phe). There are 64
possible codons and only 20 commonly used amino acids, so there are multiple ways to
code for many amino acids. For example, the codons UCU, UCC, UCA, and UCG all
code for serine.
A ribosome is made of proteins and a type of RNA called ribosomal RNA ( rRNA ).
Ribosomes usually exist in the cell as two pieces or subunits.There is a large subunit
and a small subunit. During translation, the two subunits combine and hold the mRNA
between them. With the mRNA firmly sandwiched into the ribosome, the mRNA’s
codons are read and protein synthesis begins.The cell has many ribosomes available for
protein synthesis. The process of translation can be broken down into three basic steps:
(1) initiation, (2) elongation, and (3) termination.
Initiation
Protein synthesis begins with the small ribosomal subunit binding to a specific signal
sequence of codons on the mRNA. The small ribosomal subunit moves along the
mRNA and stops at the first AUG codon on the length of the RNA. This AUG codon is
where translation begins. If an AUG is not found, translation does not occur. At the first
AUG codon, the first amino acid (methionine, or MET) is positioned on the mRNA.

Termination
The ribosome will continue to add one amino acid after another to the growing protein
unless it encounters a stop signal .The stop signal, in the mRNA, is also a codon. The
stop codon can be either UAA, UAG, or UGA. When any of these three codons appears
during the elongation process, a chemical release factor enters the ribosome. The
release factor causes the ribosome to detach from the protein. When the protein releases,
the ribosomal subunits separate and release the mRNA. The mRNA can be used to
make another copy of the protein or can be broken down by the cell to prevent any more
of the protein from being made. The two pieces of the ribosome can also be reused.
Elongation
Once protein synthesis is started, the ribosome coordinates a recurring series of events.
Each time the ribosome works through this series of events, a new amino acid is added
to the growing protein. In this way, a ribosome is like an assembly line that organizes
the steps of a complicated assembly process. For each new amino acid, a new tRNA
arrives at the ribosome with its particular amino acid. The ribosome adds the new amino
acid to the growing protein

Mutations
A mutation is any change in the DNA sequence of an organism. They can occur for
many reasons, including errors during DNA replication. Mutations can also be caused
by external factors, such as radiation, carcinogens, drugs, or even some viruses. It is
important to understand that not all mutations cause a change in an organism.
Genetic engineering
Genetic engineering involves manipulating specific genes by cutting and rearranging
DNA. A restriction endonuclease cleaves DNA at a specific site, generating in most
cases two fragments with short single-stranded ends. Because these ends are
complementary to each other, any pair of fragments produced by the same
endonuclease, from any DNA source, can be joined together.
One of the first recombinant genomes produced by genetic engineering was a bacterial
plasmid into which an amphibian ribosomal RNA gene was inserted. Viruses can also
be used as vectors to insert foreign DNA into host cells and create recombinant
genomes.
Genetic engineering generally involves four stages:
1-cleaving the source DNA.
2- making recombinants; cloning copies of the recombinants.
3- screening the cloned copies for the desired gene. Screening can be achieved by
making the desired clones resistant to certain antibiotics and giving them other
properties that make them readily identifiable.

Gregor Mendel and biological

inheritance
Charles Darwin1, for all he contributed to the science of biology, never knew about the
mechanism by which living things inherit traits from previous generations, or how new
traits arise.
Mendel
• Discovered principle of genetic segregation via numerous experiments utilizing pea
plants
Human genetic disorders
Down's Syndrome(Mongolism)
Down's Syndrome is usually produced by the nondisjunction of chromosome 21 during
oogenesis and sometimes during spermatogenesis. The individual suffering from this
type of syndrome has 47 chromosomes instead of the normal 46. The extra chromosome
is not a sex chromosome but an autosome.
Most cases of mongolism were found to occur in children born by women in their
forties. The affected children, called mongoloids, show mental retardation and have a
shorter life expectancy. Their most prominent feature is the Mongolian folds in their
eyes; hence, the term mongolism.

Klinefelter's Syndrome
Gregor Mendel and biological inheritanceWhen an XY-bearing sperm unites with an
X-bearing egg, the resulting condition is called Klinefelter's Syndrome, or sexually
undeveloped male. Individuals having the syndrome show the following characteristics:
• testes are small
• sperms are never produced
• breasts are enlarged
• body hair is sparse
• individuals are mentally defective
The same abnormal meiotic division may occur in females. They produce eggs with XX
or no sex chromosomes. Such egg, when fertilized by a Y-bearing sperm, will not
develop (YO). This is because YO is lethal--it will cause death to the offspring.
Thinking Critically
 Chapter5

Nutrition

Photosynthesis
photosynthesis, organisms such as green plants, algae, and certain bacteria trap radiant
energy from sunlight. They are then able to convert it into the energy of chemical bonds
in large molecules, such as carbohydrates.
Organisms that are able to make energy-containing organic molecules from inorganic
raw materials are called autotrophs. Those that use light as their energy source are more
specifically called photosynthetic autotrophs or photoautotrophs.
chlorophyll, a green pigment that absorbs light energy. Through photosynthesis, light
energy is transformed to chemical-bond energy in the form of ATP. ATP is then used to
produce complex organic molecules, such as glucose. It is from these organic molecules
that organisms obtain energy through the process of cellular respiration. Chloroplasts
have two distinct regions within them: the grana and the stroma. Grana consist of
stacks of individual membranous sacs, called thylakoids, that contain chlorophyll. The
stroma are the spaces between membranes .
The following equation summarizes the chemical reactions photosynthetic organisms
use to make ATP and organic molecules:
light energy _ carbon dioxide _ water → glucose _ oxygen
light energy _ 6 CO 2 _ 6 H 2 O → C 6 H 12 O 6 _ 6 O 2.
photosynthetic pathway:
Light Reactions
• Part of the electromagnetic spectrum
• Consists of units of energy called photons
• Photons at UV end of spectrum have more energy than those at the red end
• Occur on the surface of thylakoid disks
• Chlorophyll and other plant pigments differentially absorb photons
• Chlorophyll a: light to chemical energy
• Chlorophyll b: accessory chlorophyll
• Chlorophylls absorb primarily blue and red (green reflected back, hence the green
color of plants)
“Dark” reactions
• ATP drives endergonic reactions
• NADPH provides hydrogens for reduction of CO2 to carbohydrate (C-H bonds)
• Occur in the stroma
• First step in carbon fixation
What the Dark Reactions Do:
The dark reactions build sugar from carbon dioxide gas (CO2), water (H2O), and
energy from ATP molecules that were charged up during the light reactions. The dark
reactions occur in the stroma of a chloroplast. Dark reactions usually occur in the light,
but they don't have to. They'll occur in the dark until the chloroplast's supply of ATP
runs out (usually about 30 seconds).
The Calvin Cycle:
The Calvin Cycle is the fancy name for the metabolic pathway that builds sugar. This
means that it involves a whole lot of chemical reactions, and it uses a lot of different
enzymes to catalyze the reactions.
Carbon dioxide gas is stable, therefore the bonds that hold the carbon and oxygen atoms
are strong. Therefore it takes a lot of energy to break the bonds and separate the carbon
atoms from the oxygen atoms. The energy needed to do this comes from ATP
molecules.
When inorganic carbon (like from CO2) is being added to an organic molecule (such as
sugar), this is called carbon fixation. It takes 2 complete turns of the Calvin Cycle to
make a glucose molecule.
Energy and Organisms
There are hundreds of different chemical reactions taking place within the cells of
organisms. Many of these reactions are involved in providing energy for the cells.
Organisms are classified into groups based on the kind of energy they use.
Organisms that are able to use basic energy sources, such as sunlight, to make energy-
containing organic molecules from inorganic raw materials are called autotrophs ( auto
_ self; troph _ feeding). There are also prokaryotic organisms that use inorganic
chemical reactions as a source of energy to make larger organic molecules. This process
is known as chemosynthesis. Therefore, there are at least two kinds of autotrophs:
Those that use light are called photosynthetic autotrophs and those that use inorganic
chemical reactions are called chemosynthetic autotrophs.
All other organisms require organic molecules as food and are called heterotrophs
( hetero _ other; troph _ feeding). Heterotrophs get their energy from the chemical
bonds of food molecules, such as carbohydrates, fats, and proteins, which they must
obtain from their surroundings.
Within eukaryotic cells, certain biochemical processes are carried out in specific
organelles. Chloroplasts are the sites of photosynthesis, and mitochondria are the sites
of most of the reactions of cellular respiration . Because prokaryotic cells lack
mitochondria and chloroplasts, they carry out photosynthesis and cellular respiration
within the cytoplasm or on the inner surfaces of the cell membrane or on other special
membranes. provides a summary of the concepts just discussed and how they are related
to one another.
cellular respiration, organisms control the release of chemical-bond energy from
large, organic molecules and use the energy for the many activities necessary to sustain
life. All organisms, whether autotrophic or heterotrophic, must carry out cellular
respiration if they are to survive. Because nearly all organisms use organic molecules as
a source of energy, they must obtain these molecules from their environment or
manufacture these organic molecules, which they will later break down. Thus,
photosynthetic organisms produce food molecules, such as carbohydrates, for
themselves as well as for all the other organisms that feed on them. There are many
variations of cellular respiration. Some organisms require the presence of oxygen for
these processes, called aerobic processes. Other organisms carry out a form of
respiration that does not require oxygen; these processes are called anaerobic.
Glycolysis
Glycolysis ( glyco _ sugar; lysis _ to split) is a series of enzymecontrolled, anaerobic
reactions that takes place in the cytoplasm of cells, which results in the breakdown of
glucose with the release of electrons and the formation of ATP. During glycolysis, the
6-carbon sugar glucose is split into two smaller, 3-carbon molecules, which undergo
further modification to form pyruvic acid or pyruvate. 1 Enough energy is released to
produce two ATP molecules. Some of the bonds holding hydrogen atoms to the glucose
molecule are broken, and the electrons are picked up by electron carrier molecules
(NAD_) and transferred to a series of electron-transfer reactions known as the electron-
transport system (ETS).
The Krebs Cycle
The Krebs cycle is a series of enzyme-controlled reactions that takes place inside the
mitochondrion, which completes the breakdown of pyruvic acid with the release of
carbon dioxide, electrons, and ATP. During the Krebs cycle, the pyruvic acid molecules
produced from glycolysis are further broken down. During these reactions, the
remaining hydrogens are removed from the pyruvic acid, and their electrons are picked
up by the electron carriers NAD _ and FAD. These electrons are sent to the electron-
transport system. A small amount of ATP is also formed during the Krebs cycle. The
carbon and oxygen atoms that are the remains of the pyruvic acid molecules are released
as carbon dioxide (CO 2 ).
growth regulation in plant
Plant Hormones. Hormones are grouped into seven classes.
Auxin. Auxin is involved in the elongation of stems.
Cytokinins. Cytokinins stimulate cell division.
Gibberellins. Gibberellins control stem elongation.
Brassinosteroids and Oligosaccharins. There are several recent additions to the plant
hormone family.
Ethylene. Ethylene controls leaves and flower abscision.
Abscisic Acid. Abscisic acid suppresses growth of buds and promotes leaf senescence.
 Chapter 6

The Life

What Is Life?
Before we can address this question, we must first consider what qualifies something as
“living.” What is life? This is a difficult question to answer, largely because life itself is
not a simple concept. If you try to write a definition of “life,” you will find that it is not
an easy task, because of the loose manner in which the term is used.
Imagine a situation in which two astronauts encounter a large, amorphous blob on the
surface of a planet. How would they determine whether it is alive?
Movement. One of the first things the astronauts might do is observe the blob to see if
it moves. Most animals move , but movement from one place to another in itself is not
diagnostic of life.
Most plants and even some animals do not move about, while numerous nonliving
objects, such as clouds, do move. The criterion of movement is thus neither necessary
(possessed by all life) nor sufficient (possessed only by life).
Sensitivity. The astronauts might prod the blob to see if it responds. Almost all living
things respond to stimuli (figure 4.3).. Plants grow toward light, and animals retreat
from fire. Not all stimuli produce responses, however. Imagine kicking a redwood tree
or singing to a hibernating bear. This criterion, although superior to the first, is still
inadequate to define life.
Death. The astronauts might attempt to kill the blob. All living things die, while
inanimate objects do not. Death is not easily distinguished from disorder, however; a car
that breaks down has not died because it was never alive. Death is simply the loss of
life, so this is a circular definition at best. Unless one can detect life, death is a
meaningless concept, and hence a very inadequate criterion for defining life.
Complexity. Finally, the astronauts might cut up the blob, to see if it is complexly
organized. All living things are complex. Even the simplest bacteria contain a
bewildering array of molecules, organized into many complex structures. However a
computer is also complex, but not alive. Complexity is a necessary criterion of life, but
it is not sufficient in itself to identify living things because many complex things are not
alive.

Theories about the Origin of Life

When life first appeared on earth, the environment was very hot. All of the spontaneous
origin hypotheses assume that the organic chemicals that were the building blocks of
life arose spontaneously at that time. How is a matter of considerable disagreement.
The question of how life originated is not easy to answer because it is impossible to go
back in time and observe life’s beginnings; nor are there any witnesses. There is
testimony in the rocks of the earth, but it is not easily read, and often it is silent on
issues crying out for answers.
There are, in principle, at least three possibilities:
1. Special creation. Life-forms may have been put on earth by supernatural or divine
forces.
2. Extraterrestrial origin. Life may not have originated on earth at all; instead, life may
have infected earth from some other planet.
3. Spontaneous origin. Life may have evolved from inanimate matter, as associations
among molecules became more and more complex.
Ecology
the study of biotic (living) and abiotic (nonliving) interactions in an environment.
All organisms have the ability to grow and reproduce. To grow and reproduce,
organisms must get materials and energy from the environment. Plants obtain their
energy from the sun through photosynthesis, whereas animals obtain their energy from
other organisms.
Either way, these plants and animals, as well as bacteria and fungi, are constantly
interacting with other species as well as the non-living parts of their ecosystem. An
organism’s environment includes two types of factors:
1-Abiotic factors are the parts of the environment that are not living, such as sunlight,
climate, soil, water, and air.
2-Biotic factors are the parts of the environment that are alive, or were alive and then
died, such as plants, animals, and their remains. Biotic factors also include bacteria,
fungi and protists.
Ecology studies the interactions between biotic factors, such as organisms like plants
and animals, and abiotic factors. For example, all animals (biotic factors) breathe in
oxygen (abiotic factor). All plants (biotic factor) absorb carbon dioxide (abiotic factor)
and need water (abiotic factor) to survive.

Ecosystems can be studied at small levels or at large levels. The levels of organization
are described below from the smallest to the largest:
A population is a group of organisms belonging to the same species that live in the
same area and interact with one another.
Individuals are members of the same species (a group of individuals who are
genetically related and can breed to produce fertile offspring), if their members cannot
produce offspring that can also have children. The second word in the two-word
specific epithet name given to every organism is the species name. For example, in
Homo sapiens, sapiens is the species name and Homo genus.
A community is all of the populations of different species that live in the same area and
interact with one another.
An ecosystem includes the living (biotic) organisms (all the populations) in an area
and the non-living (abiotic) aspects of the environment and their interactions.
A niche is the role an organism plays in its ecosystem. Essentially, what services it
provides and does in an ecosystem. For example, a sardines’ niche would be to eat
algae and phytoplankton and serve as a food source for many different fish species.
The biosphere :the highest level of ecological organization, it is the part of the earth,
including the air, land, surface .
Ecologists study ecosystems at every level, from the individual organism to the whole
ecosystem and biosphere.
Food chains and food webs : diagrams that represent feeding relationships of
different species) show who eats whom. In this way, they model how energy and matter
move through ecosystems. Food chains always begin with producers, organisms that use
a primary energy source (most commonly the sun) and photosynthesis, to make their
own food / energy. The plants in the figure above are an example of producers.
Consumers (organisms that cannot make their own food and must get energy from
other living organisms) can be herbivores, carnivores, or omnivores. Food chains might
also include decomposers (organisms that get nutrients and energy by breaking down
the remains of dead organisms or animal waste) such as bacteria and fungi. Through the
process of decomposition, they recycle nutrients like carbon and nitrogen back into the
environment so producers can use them.
A food chain represents a single pathway by which energy and matter flow through an
ecosystem.
A food web represents multiple pathways through which energy and matter flow
through an ecosystem. It includes many intersecting food chains. It demonstrates that
most organisms eat, and are eaten, by more than one species.

The Pyramids
The Pyramid of Energy
The energy within an ecosystem can be measured in several ways. One simple way is to
collect all the organisms present at any trophic level and burn them. For example, all the
plants in a small field (producer trophic level) can be harvested and burned. The number
of calories of heat produced by burning is equivalent to the energy content of the
organic material collected.
Similarly, all the herbivores in the second trophic level could be collected and burned.
Then you could compare the amount of heat generated by producers and herbivores and
get an idea of how much energy is lost as you go from the producer to the herbivore
trophic level. Another way of determining the energy present is to measure the rate of
photosynthesis and respiration of a group of producers. The difference between the rates
of respiration and photosynthesis is the amount of energy trapped in the living
material of the plants.
When we examine a wide variety of ecosystems, we find that the producer trophic level
has the most energy, the herbivore trophic level has less, and the carnivore trophic level
has the least. In general, there is about a 90% loss of energy from one trophic level to
the next higher level. Actual measurements vary from one ecosystem to another. Some
may lose as much as 99% ,whereas other, more efficient systems may lose only 70%,
but 90% is a good rule of thumb. This loss in energy content at the second and
subsequent trophic levels is primarily due to the second law of thermodynamics.
(Whenever energy is converted from one form to another, some energy is lost to the
surroundings as heat.)
In addition to the loss of energy as a result of the second law of thermodynamics, there
is an additional loss involved in the capture and processing of food material by
herbivores and carnivores. Although herbivores don’t need to chase their food, they do
need to travel to where food is available, then gather, chew, digest, and metabolize it.
All of these processes require energy. Just as the herbivore trophic level experiences a
90% loss in energy content, the higher trophic levels of primary carnivores, secondary
carnivores, and tertiary carnivores also experience a 90% reduction in the energy
available to them.
The Pyramid of Numbers
Because it is difficult to measure the amount of energy at any one trophic level of an
ecosystem, scientists often use other methods to quantify trophic levels. One method is
simply to count the number of organisms at each trophic level. This pyramid of numbers
, This is not a very good method to use if the organisms at the different trophic levels
are of greatly differing sizes. For example, if you counted all the small insects feeding
on the leaves of one large tree, you would actually get an inverted pyramid.
The Pyramid of Biomass
One way to overcome some of the problems associated with simply counting organisms
is to measure the biomass at each trophic level. Biomass is the amount of living
material present; it is usually determined by collecting all the organisms at one trophic
level and measuring their dry weight. This eliminates the size-difference problem
associated with a pyramid of numbers, because all the organisms at each trophic level
are combined and weighed. The pyramid of biomass also shows the typical 90% loss at
each trophic level. Although a pyramid of biomass is better than a pyramid of numbers
in measuring some ecosystems, it has some shortcomings. Some organisms tend to
accumulate biomass over long periods of time, whereas others do not. Many trees live
for hundreds of years; their primary consumers, insects, generally live only 1 year.
Likewise, a whale is a long-lived animal, whereas its food organisms are relatively
short-lived.
Behavior
1-Behavioral ecology is the study of how natural selection shapes behavior.

Foraging Behavior. Natural selection favors the most efficient foraging behavior. Or
Natural selection may favor the evolution of foraging behaviors that maximize the
amount of energy gained per unit time spent foraging. Animals that acquire energy
efficiently during foraging may increase their fitness by having more energy available
for reproduction, but other considerations, such as avoiding predators, also are
important in determining reproductive success.
Territorial Behavior. Animals defend territory to increase reproductive advantage and
foraging efficiency. An economic approach can be used to explain the evolution and
ecology of reproductive behaviors such as territoriality. This approach assumes that
animals that gain more energy from a behavior than they expend will have an advantage
in survival and reproduction over animals that behave in less efficient ways.

Pollution
Human industrial and agricultural activity introduces significant levels of many
harmful chemicals into ecosystems.
Chemical pollution is causing ecosystems to accumulate many harmful substances, as
the result of spills and runoff from agricultural or urban use. Industrial pollutants such
as nitric and sulfuric acids, introduced into the upper atmosphere by factory
smokestacks, are spread over wide areas by the prevailing winds and fall to earth with
precipitation called “acid rain,’’ lowering the pH of water on the ground and killing life.