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1 - Scientific Investigation and
Microbes
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Characteristics of Life - SAES

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Characteristics of Life SAES

• List the characteristics of life
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• Explain the relationship of the characteristics discussed to life
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Without these characteristics, there is no life
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Of course, real ducks are living things
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The decoy duck doesn’t have all
the characteristics of a living thing
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It grows and develops
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It maintains homeostasis
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It consists of cells
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What happens if you step on a rock?
Nothing; the rock doesn’t respond because it isn’t alive
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This duck decoy looks like it’s alive
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Why isn’t it a living
thing?

Growth and Development

All living things grow and develop
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Animals also grow and develop
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Tadpoles go through many changes to become adult frogs
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Reproduction is the process by which living things give rise to
offspring
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Generally, however,
it is much more complicated
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Concept 1
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They keep things relatively stable
on the inside regardless of the conditions around them
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Human beings, for example, maintain a stable internal body temperature
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Instead, by shivering and other means, it
maintains a stable internal temperature
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Living things consist of large, complex
molecules, and they also undergo many complicated chemical changes to stay alive
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These functions are the organism’s metabolism
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A cell is the basic unit of the structure and function of living things
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Compare
the human cells on the left in Figure 1
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http://bio-alive
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FIGURE 1
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Onion Cells (right)
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Summary

• All living things detect changes in their environment and respond to them
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All living things are capable of reproduction, the process by which living things give rise to offspring
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All living things have complex chemistry, which they use for metabolism
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A cell is the basic unit of the structure and function of living things
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Define metabolism
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Assume that you found an object that looks like a dead twig
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How
could you determine if it is a living thing?

References
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A duck decoy looks like it’s alive, but it doesn’t have all the characteristics of a living thing
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Tadpoles go through visible changes that show growth and
development, a characteristic of life
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Humans and
onions look very different, but when comparing the cells, you might notice some similarities
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com; Onion cells: CC BY 2
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Scientific Theories - SAES15

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Scientific Theories SAES15

• Define scientific theory
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Theory vs
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Is a scientific theory different from the everyday use of the word theory?
"It’s just a theory
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But a theory in science is never "just a theory
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The theory of
evolution by natural selection is a classic scientific theory
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Keep in mind, a hypothesis is a
possible answer to a scientific question
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To become a theory, a hypothesis must be tested over and over again, and it must be supported by a great
deal of evidence
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Rather, you find evidence that supports your theory
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An example of a testable hypothesis is "Will using Miracle-Gro instead of water make radishes germinate faster?" And
an example of a non-testable hypothesis is "Is there an afterlife when you die?"
People commonly use the word theory to describe a guess about how or why something happens
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” Using the word theory in this
way is different from the way it is used in science
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There are several well-known theories in biology, including the theory of evolution, cell theory,
and germ theory, each of which is briefly described below
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Evolution is a change in the characteristics of
living things over time
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In natural selection, some living
things produce more offspring than others, so they pass more genes to the next generation than others do
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The theory of evolution by natural
selection explains how living things are changing today and how modern living things have descended from ancient
life forms that no longer exist on Earth
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You will learn more about evolution later in this course
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According to the cell theory, the cell is the smallest
unit of structure and function of all living organisms, all living organisms are made up of at least one cell, and living
cells always come from other living cells
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More on the cell theory will be presented in the next unit
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Like the other scientific theories, lots of evidence has been identified
that supports this theory, and no evidence has been identified that proves the theory is incorrect
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Experimental Variables

A quick reminder of what you learned in class recently:
• Independent variable (IV): what you are testing, what you are changing in an experiment
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It’s sometimes called the experimental variable
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On a graph, this will always go on the Y-axis
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Examples:Let’s say you set up an experiment to see if amount of light affects how many radish seeds will germinate
• The IV (independent or experimental variable) is the different amounts of light (always dark, always light, or
half dark/half light)
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It’s the results of your experiment
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Summary

• With repeated testing, some hypotheses may eventually become scientific theories
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Concept 2
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Evolution occurs by natural selection
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• The germ theory proposes that microorganisms are the cause of many diseases
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How is the word "theory" used in common language and how is it used in science?
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Prokaryotes (Bacteria +
Archaea) - SAES

Describe the structure of prokaryotes
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This shows a diagram of a prokaryote
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Bacteria are the most diverse and abundant group of organisms on Earth
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They
are found in the ocean, the soil, and the intestines of animals
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Any surface that has not been sterilized is likely to be covered with bacteria
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It’s estimated to be 5 ⇥ 1030 , or five million trillion trillion
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Prokaryotes are the simplest types
of cells
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Prokaryotes are divided into two big groups, the Bacteria and the Archaea
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Compare these images of a prokaryotic cell and a eukaryotic cell
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Prokaryote Structure (inside)

Here are the cell structures that most prokaryotes have
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• Cell membrane - like all cells, prokaryotic cells have a cell membrane
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• Cell wall - most prokaryotes have a cell wall
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(You may be familiar with the cell wall of plants, which serves the same purpose)
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You have these in your cells, too!
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Concept 3
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This image shows a prokaryotic cell on
the left and a eukaryotic (animal) cell on
the right
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In prokaryotes, the DNA is NOT enclosed within a nucleus (as it is in
eukaryotes)
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The
DNA in a prokaryotic cell is a single loop, unlike the 46 separate chromosomes in each of your cells
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Note: many bacteria also contain separate bits of DNA, also in a circular form; these are
called plasmids
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• Cytoplasm - the fluid within the cell, which contains and supports the ribosomes and DNA
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Prokaryotic DNA
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Prokaryote Structure (outside)

Many prokaryotes have an extra layer, called a capsule, outside the cell wall
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It also allows the cell to stick to surfaces and to other cells
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The sticky plaque that collects on your teeth between brushings is a
biofilm
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Most prokaryotes also have long, thin protein structures called flagella (singular, flagellum)
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Flagella help prokaryotes move
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As shown in Figure 3
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A third outside structure are small extensions called pili
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FIGURE 3
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The greatly magnified
biofilm shown here was found on a medical catheter (tubing) removed from a patient’s body
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They are similar to Bacteria, described above, but there are some
key differences
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• The cell wall of Bacteria contains peptidoglycan, composed of sugars and amino acids
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• The DNA sequences for certain structures (like ribosomes) of Archaea are very similar to those in eukaryotic
cells, and not at all like bacterial DNA sequences
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This indicates that they probably evolved very early in Earth’s history
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Use this information to help
you complete the table about Archaea in your notes
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Thermophiles live in high heat conditions, such as in hot sulphur springs in Yellowstone, and deep sea vents
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Prokaryotes (Bacteria + Archaea) - SAES

FIGURE 3
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Flagella in prokaryotes may be located at
one or both ends of the cell or all around it
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These are not what is found in oceans, which are not salty enough for them
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Methanogens thrive in low-oxygen, high-methane conditions
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They also live in YOUR large intestine, and in sewage-treatment plants
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Bacteria make our lives easier in a number of ways
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On the other hand, some bacteria can also make us sick
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For example, they are important decomposers
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There are billions of bacteria inside the human intestines
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Humans have developed many ways to use bacteria, including:
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Creating products, such as ethanol and enzymes
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Making biogas, such as methane
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Killing plant pests
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Fermenting foods (see Figure below )
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Various fermented foods

Bacteria and Disease

You have ten times as many bacteria as human cells in your body
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However, some bacteria can also cause disease
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Bacteria may spread directly from one person to another
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They may also spread via food, water, or objects
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A vector is an organism that spreads pathogens from host to host
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) Insects are the most common vectors of human
diseases
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FIGURE 3
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When people come into contact with wild populations, they may become part of natural cycles of disease transmission
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It’s caused by
bacteria (Borrelia burgdorferi) that normally infect small, wild mammals, such as mice
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The tick may then bite a human who invades the natural habitat
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Controlling Bacteria

Bacteria in food or water usually can be killed by heating it to a high temperature (generally, at least 71 C, or 160 F)
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Bacterial infections in people
can be treated with antibiotic drugs
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You will get to test some antibiotics in lab
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Antibiotics have saved many lives
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Figure below shows how antibiotic resistance evolves
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These infections are very difficult to treat
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Prokaryotes (Bacteria + Archaea) - SAES

FIGURE 3
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• Prokaryotic cells have a cell wall outside their plasma membrane
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Some prokaryotes also have small, circular pieces of DNA called
plasmids
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Bacteria provide humans with a number of services
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Be able to answer these questions

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What is the role of the cell membrane? The cell wall?
Sketch and label a typical bacterial cell, including all possible parts
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List two beneficial uses of bacteria (for humans)
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Look again at the last picture, showing the evolution of antibiotic resistance
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References

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emaze
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Location of prokaryotic DNA
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Bacterial biofilm under microscope
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User:Adenosine/Wikimedia Commons
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CC BY 3
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Various fermented foods
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Various fermented foods
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Bacterial disease vectors include ticks and deerflies
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Bacterial disease vectors include ticks and deerflies
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Evolution of antibiotic resistance in bacteria
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Evolution of antibiotic resistance in bacteria
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Classifying Prokaryotes - SAES

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Classifying Prokaryotes SAES

• Outline the classification of prokaryotes
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Bacteria are classified by their traits, some of which have to do with their shape, others with the cell wall, and even
additional traits
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Shape

One way to classify bacteria is by their shape
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These three distinct shapes are shown here
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FIGURE 4
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Cell wall composition

Another classification of bacteria is based on differences in their cell walls and outer membranes
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FIGURE 4
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Different types
of bacteria stain a different color when
stained with Gram stain
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Notice the color each type of stain produces
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This extra
membrane provides some protections against antibiotics
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Concept 4
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We will look at this in detail in class,
but here’s a quick overview:
• Heterotrophs (decomposers, parasites, consumers) consume other organisms or their waste
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• Autotrophs make their own food using inorganic materials
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Plants are another example of photoautotrophs
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These are very
rare!
Metabolism

And still another way to classify bacteria is by the type of metabolism they do
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Most bacteria are aerobes
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• Anaerobe - oxgyen is poisonous to these bacteria!
• Facultative aerobe - these bacteria can go either way - with or without oxygen
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One bacterial cell copies its DNA, then just separates into two equal
parts, each with one DNA chromosome
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Bacteria can also do conjugation, where one bacterium transfers some of its DNA to another bacterium of the same
species
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FIGURE 4
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However, some prokaryotes form spores for survival
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The stress could be UV radiation, high
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FIGURE 4
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Notice how a small
separate piece of DNA, called a "plasmid", is copied and ends up in both bacterial cells
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Endospores enclose the DNA and help it survive under conditions that may kill
the cell
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Endospores are most often found in
soil and water
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Summary

• Bacteria can be classified in several different ways, including shape, cell wall structure, nutrition, and metabolism
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• Some bacteria can withstand temporary poor environmental conditions by forming endospores
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Distinguish between Gram-positive and Gram-negative bacteria
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Which one(s) result in more bacteria than when it started?
What is the function of an endospore?

References
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/Centers for
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Concept 4
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Clark/Centers for Disease and Control
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C ONCEPT

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Virus Characteristics SAES

• Describe a virus
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He (or she) looks very angry
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In fact, viruses are the smallest things
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A bacteriophage (or phage
for short) is a virus that infects prokaryotes
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Phages are estimated to be the most widely
distributed and diverse entities in the biosphere, even more numerous than prokaryotic organisms
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Up to 109 viruses
have been found in a milliliter of seawater, and up to 70 percent of marine bacteria may be infected by phages
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In addition, viruses can infect the cells of eukaryotic organisms (like you and me,
unfortunately!)
Characteristics of Viruses

A virus is a sub-microscopic particle that can infect living cells
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Why? Viruses are often considered to be nonliving, because they do not have the characteristics
of life as we defined it in the first chapter
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In fact, a virus generally consists simply
of a protein coat called a capsid surrounding some genetic material like DNA
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What are some of the differences between viruses and typical living cells?
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Wow - that’s tiny!] By comparison, prokaryotic bacteria cells are typically
up to 5000 nm in length
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Concept 5
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CELL PARTS - viruses lack typical cell structures such as cell membranes, cytoplasm, ribosomes, plus more
complex organelles that are found in eukaryotic cells
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3
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So, can viruses be considered "alive?" They do share two important traits with living things
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This is why the classification of viruses has been controversial
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What do you think? How would you classify viruses?
The Largest Virus - Up until 2013, the Mimivirus, shown in the Figure 5
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Protein filaments measuring 100 nm stick out from the surface of the virus, which increases the
diameter of the virus to about 600 nm
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The virus appears hexagonal under
an electron microscope; the viral shape is icosahedral (having 20 faces or sides)
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The largest known virus up until 2013,
called mimivirus, is so large that scientists
first mistook it for a bacterium
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The
core contains DNA, with the majority of
the DNA in genes, and only 10% DNA of
unknown function
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It is an amazing 1000 nm, which is about twice the size of the
Mimivirus, and larger than many of the smaller bacteria
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Replication

Let’s look at the details of how a virus replicates
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They infect a wide variety of organisms, including both eukaryotes and prokaryotes
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There are two ways viruses can
do this
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Here is a short animation that summarizes the five steps of the lytic cycle
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http://sites
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harvard
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html
The lysogenic cycle is similar to the lytic cycle in that the virus first attaches to the cell it is going to infect, and
injects its genetic material into the cell
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It is referred to as a "prophage" in this state
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The Pandoravirus is nearly twice the size
of the Mimvirus, making it the largest
known virus as of 2015
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At some point, the virus may re-activate, and start up the lytic cycle where it
left off
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Only some viruses can enter the lysogenic cycle
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• Viruses get copied either through the lytic cycle or the lysogenic cycle
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Describe the structure of a typical virus
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How is the lysogenic cycle different from the lytic cycle?

References
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Diagram of a large mimivirus
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Viruses and Human Disease - SAES

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Viruses and Human Disease
- SAES

• Explain how viruses cause human disease
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The flu is caused by an influenza virus
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Viruses and Human Disease

Viruses cause many human diseases
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1)
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Viruses can
cause disease via the lytic cycle, by forcing host cells to burst open and die
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They may cause illness by disrupting homeostasis in host cells
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This is called latency
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Then the virus may remain latent in nerve cells within the body for decades
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In shingles, the virus causes painful skin rashes with blisters (see Figure 6
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Some viruses can cause cancer
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Hepatitis B virus causes cancer of the liver
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There is much about this we still do not understand, but scientists continue to increase
their knowledge through research
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Cold Sore
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FIGURE 6
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Shingles is a disease caused by
the same virus that causes chicken pox
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For example, scientists believe West Nile Virus was introduced to the United
States by an infected air traveler
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Watch this 3:50-minute video Virus Crisis at https://www
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com/watch?v=91b3MCAlYSI to learn
more about the spread of West Nile Virus
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Several lethal viruses that cause viral hemorrhagic fever have been discovered, two of which are shown in the Figure
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Ebola outbreaks have been limited mainly to remote areas of the world
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The primary
hosts of the viruses are thought to be apes in west central Africa, but the virus has also been isolated from bats in
the same region
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Viruses and Human Disease - SAES

infected persons while they are sick, and in preparation for burial, since many local people do not know (or do not
believe) that Ebola is caused by an easily transmitted virus
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The Ebola virus (left), and Marburg virus (right), are viruses that cause hemorrhagic fevers that can cause multiple
organ failure and death
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A disease that can be
spread from animals to humans is called a zoonosis
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Epidemiologists are like detectives trying to solve a crime
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People get exposed to new and rare zoonoses when they move into new areas and encounter wild animals
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An outbreak in China in 2003 was linked to the handling and consumption of wild civet cats sold as food in
a market
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It is likely that the
virus spread from bats to civets, and then to humans
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Different
ones become prevalent each year, so it can be tricky to predict which vaccine will be the most useful in any given
year
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An epidemic is an outbreak of a disease within a
population of people during a specific time
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Most influenza strains can be inactivated easily by disinfectants and detergents
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https://
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• A number of these diseases may be familiar to you, including the flu, Ebola hemorrhagic fever, and West Nile
virus
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Be able to answer these questions:

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What is an epidemic? Why can the flu be considered an epidemic?

References
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Cold sore caused by herpes virus
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Preston Hunt
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CC BY 3
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Ebola virus: Courtesy of CDC/Cynthia Goldsmith; Marburg virus: Courtesy of CDC/Dr
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C ONCEPT

Concept 7
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FIGURE 7
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You can see here
that the number of measles cases dramatically declined after 1963, due to vaccination of children
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Control of Viruses

A little history - People have been able to control the spread of viruses even before they knew they existed
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Inoculation involves introducing
a small amount of virus into a person’s body to allow their body to build up immunity to the virus
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This all happened even before Edward Jenner invented the vaccine!
Vaccines

Because viruses use the machinery of a host cell to reproduce and stay within them, they are difficult to get rid of
without killing the host cell
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A vaccine is a mixture of the virus
protein capsid and other immune stimulants that will cause the body to mount an immune response, so the person
will develop immunity to the disease
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In fact, the term "vaccine" comes from Edward Jenner’s use of cowpox (vacca means
cow in Latin), to immunize people against smallpox, in 1796
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2, health clinics, and even at home
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Most new vaccines
are produced using genetic engineering
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A young student receives a vaccine
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Smallpox is a contagious disease unique to humans and is caused by two Variola viruses
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To this day, smallpox is the only human infectious
disease to have been completely eradicated from nature
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Click here if
you want to see a picture of someone who was infected with smallpox (don’t click if you don’t want to see it): http
://bit
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In 2013, only 413
children contracted polio, all of them in poor areas of three West African countries where medical resources are
scarce, so perhaps you can expect elimination of polio in your lifetime!
Herd Immunity

You may recall the measles outbreaks starting in 2014
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Compare this to just 37 cases diagnosed in 2004! What caused
this outbreak?
A number of parents, centered in Southern California, recently have chosen not to immunize their children in the
mistaken belief that vaccines cause autism
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If enough people are vaccinated, that passing of the disease is stopped
in its tracks
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Check
out the picture to see how this works:
And here’s a little video by Penn and Teller, dramatically illustrating the concept of herd immunity: https://www
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com/watch?v=RfdZTZQvuCo CAUTION: strong language is used
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Antiviral drugs are medications used
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Concept 7
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3

specifically for treating the symptoms of viral infections
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Like antibiotics, specific antivirals are used for specific viruses
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Most of the antiviral drugs now available are designed to help deal with
HIV and herpes viruses
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Summary

• Several viral diseases can be treated with antiviral drugs or prevented with vaccines
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Be able to answer these questions:

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3
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What is a vaccine made of?
How likely do you think it is for a vaccine to cause the disease it is meant to prevent?
What is herd immunity?
What are antiviral drugs and how do they do their job?

References
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McGalliard
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Public Domain

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