Introductory Comments chapter 1

1
Introductory Comments (chapter 1)
2

• Why study Biology?
• In order to gain an understanding of life.
• But what is life?
• Life is more easily understood by looking at the
  characteristics of living organisms, which are as
  follows

3
The possession and inheritance of DNA from parent
to offspring.
4
The ability to get and use energy E.g.
photosynthesis aerobic respiration
5
Homeostasis - the maintenance of a fairly
constant environment.
6
Reproduction or the production of offspring
7
Adaptation to the environment
8
The ability of populations of living organisms to
evolve
9
Response to stimuli
10
A higher level of organization than non-living
objects and composed of one or more cells.
11

• In order to understand how scientists conduct
  research

12

• Levels of organization

13
Molecules
14
Subcellular structures
15
Cell
16
Tissue
17
Organ
18
Organ System
19
Organism
20
Population
21
Community

• The cats, mice, grass, insects etc. that all live
  in a given area

22
Ecosystem

• The living organisms of the community the
  abiotic factors that affect them

23
Biosphere
24
Regardless of the area of interest, scientists
make their discoveries by

• observations where they document some phenomenon
  (e.g., Jane Goodalls work with chimpanzees)
• controlled experiments which often involve
  hypothesis testing. Steps
• Observation(s)
• Propose a question
• Propose hypotheses
• Alternative
• Null
• Test the hypotheses
• Apply the appropriate statistical tests
  (determined a priori )
• Make inferences based on the results and reject
  or fail to reject the null hypothesis. Never
  prove
• Objectively report the results and inferences
  (write a paper)

25

• In order to understand how biology applies to
  you.
• 1. Medical applications, human genome project,
  the search for a vaccine for AIDS, and genetic
  engineering.
• 2. Understanding our impact on current and
  future biodiversity and ultimately on our own
  species. Human induced extinctions and decreases
  in genetic variability are occurring.
• 3. Understanding our impact on the environment
  (and again on biodiversity) and ultimately the
  survival of our own species.

26

• Biodiversity and Kingdoms

27
Definitions

• Biodiversity - number of species of living
  organisms in a given area
• A species is composed of organisms that appear to
  be similar (in looks) and that are capable of
  interbreeding with other like individuals. This
  is the Biological Species Concept proposed by
  Ernst Mayr.
• Autotrophs are organisms that are capable of
  building their own large organic molecules by
  using CO2 and energy from their environment.
• a. Photosynthetic autotrophs use sunlight energy
  
• b. Chemosynthetic autotrophs use energy from
  chemical reactions involving inorganic molecules.
• Heterotrophs are organisms that are not capable
  of synthesizing their own food and thus obtain
  their nourishment from autotrophs, other
  heterotrophs or from organic wastes (e.g.,
  decomposers).
• A theory is generated by a related set of
  insights supported by evidence. It explains some
  aspect of nature and is a valued entity (e.g.,
  evolution).

28

• Biodiversity

29
Viruses. Not considered to be living (they
cannot reproduce on their own) by many
biologists, they are worth mentioning. A virus
is a noncellular infectious agent possessing a
nuclei acid core that cannot reproduce itself.
Viruses may be composed of DNA or RNA within the
protein coat (but
30
The Kingdoms of Life

• Kingdom Archeabacteria and Kingdom Bacteria -
  bacteria, all are prokaryotic (meaning that they
  do not possess membrane-bound organelles),
  autotrophs (photosynthetic and chemosynthetic)
  and heterotrophs. Archeabacteria is the kingdom
  of greatest metabolic diversity.

31

• Kingdom Protista - mostly single-celled
  eukaryotes but there are some colonial forms as
  well as some that are truly multicellular (the
  algae). Some are heterotrophs some are
  photosynthetic autotrophs.

32

• Kingdom Fungi (Myceteae) - predominantly
  multicellular eukaryotes. They have external
  digestion and all are heterotrophs.

33

• Kingdom Plantae - plants. All are eukaryotic and
  the vast majority are photosynthetic autotrophs

34

• Kingdom Animaliae - animals ranging from sponges
  to humans. They are multicellular eukaryotes and
  all are heterotrophic

35
Classification

• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• species
• Genus species (maybe subspecies) makes up the
  Scientific name

36
How to write a scientific name

• Felis catus
• Or
• Felis catus
• After first use (but not at the beginning of a
  sentence)
• F. catus or F. catus

37

• Cells Structures and Functions
• A cell is the smallest living unit
• The Cell Theory states that all organisms are
  composed of one or more cells, which are the
  basic units of organization and which, arise from
  preexisting cells.

38

• Prokaryotic
• versus
• Eukaryotic Cells

39

• Characteristics
• Types
• Organization
• Cell size
• Membrane-bound organelles
• Reproduction
• DNA

40
Components of Cells

• Cell Membranes (found in both prokaryotes and
  eukaryotes

41
Cell membrane

• Structure
• Components - lipids (primarily phospholipids),
  cholesterol, and proteins (transport, adhesion,
  receptor, or recognition)
• these lipids form a bilayer which is fluid (the
  fluid mosaic model describes the structure of
  these membranes). The polar (containing O2 for
  hydrogen bonding) heads are hydrophilic and the
  nonpolar tails are hydrophobic.

42
Cell membrane

• Function - basically these membranes serve as
  barriers which allow some substances to move in
  and out and prevent other substances from such
  movements, also they function in recognition
  (e.g., self for the immune system). Movement of
  substances can be classified under the following
  categories

43
Cell membrane

• TRANSPORT

44

• Diffusion the movement of substances from an area
  of higher concentration to an area of lower
  concentration (or down a concentration )gradien
  across a selectively permeable membrane (pore
  size and polarity are important in this type of
  movement).

45

• Osmosis is the movement of water across a
  selectively permeable membrane in response to the
  relative concentrations of solutes on the inside
  and outside of the membrane. The external
  environment of cells may be isotonic (same solute
  concentration), hypertonic (higher solute
  concentration), or hypotonic (lower solute
  concentration)

46

• passive transport - the movement of molecules
  with a concentration gradient but using a
  membrane protein which functions as a channel or
  as a carrier (facilitated diffusion). This type
  of transport does not require energy (nor do the
  others described above).

47

• Active transport involves the movement of
  substances against a concentration gradient and
  it requires an energy expenditure

48

• Nucleus (plural nuclei)
• (not found in prokaryotes)

49
Nucleus

• Structure
• lipid bilayer membrane (like the cell membrane)
  surrounding the interior of the nucleus and
  containing nuclear pores
• nucleolus (plural nucleoli)- a small dense area
• chromosomes - the DNA and associated proteins
• nucleoplasm

50
(No Transcript)
51
Function

• Membrane - functions as a barrier (see discussion
  of plasma membrane)
• Nucleolus - the formation of ribosomes
• chromosomes - contain genes whose expression
  leads to the formation of proteins which in turn
  control all aspects of an individual either
  directly or indirectly (e.g., through the ability
  to learn).
• nucleoplasm - the cytoplasm or fluid medium of
  the nucleus
• Remember that prokaryotes do not have their
  chromosomes packaged within nuclei, but instead
  the DNA of prokaryotes is found in a nuclear area.

52
Ribosomes

• found in both prokaryotes and eukaryotes but
  with structural differences.
• Structure - small consisting of a large and a
  small subunit (chemically made up of rRNA and
  proteins)
• Function - the sites of protein synthesis

53
(No Transcript)
54
Endoplasmic Reticulum (ER) (found only in
eukaryotes)

• 1. Structure - basically a system of membranous
  tunnels and sacs
• Smooth ER is devoid of ribosomes
• Rough ER is associated with ribosomes (they are
  attached to the surface)
• 2. Function
• Smooth ER - lipid synthesis
• Rough ER - protein synthesis

55
(No Transcript)
56
Golgi Apparatus or complex

• (found only in eukaryotes)
• Structure - flattened connected sacs that look
  like a stack of pancakes.
• 2. Function - the processing of lipids and
  proteins

57
(No Transcript)
58
Lysosomes

• and other vesicles (found only in eukaryotes)
• Structure of lysosomes - membrane bound sacs
  containing hydrolytic enzymes associated with the
  Golgi (actually formed from the Golgi)
• 2. Function - digestion of substances

59
(No Transcript)
60
Mitochondria

• Structure cigar-shaped, double membrane-bound
  organelle
• Function Energy transfer by ATP synthesis

61
(No Transcript)
62
Chloroplast

• Structure
• Also cigar or spindle shaped, double
  membrane-bound, green
• Function
• Site of photosynthesis

63
(No Transcript)
64
Vacuoles

• Structure - a fluid filled sac that may take up
  50-90 of the cell (e.g., central vacuole of
  plants)
• Function - storage

65
(No Transcript)
66
Cytoskeleton

• Structure - a net-like continuation of various
  protein filaments
• microtubules - thickest filaments which also make
  up cilia, flagella, and centrioles
• Intermediate filaments
• microfilaments - made up of actin
• Function in Support

67
(No Transcript)
68

• Some cells also possess locomotor and/or
  non-locomotor appendages (e.g., flagella, cilia,
  and pili)

69
(No Transcript)
70
Cell walls

• Structure a layer outside of the cell membrane
  that is made of different materials depending on
  the species
• Function is support and protection

71
(No Transcript)
72

• See Table 4.2 and note differences between the
  members of the different kingdoms concerning
  structures that are present

73
Cool video

• http//video.google.com/videosearch?gbv2hlenq
  nervous20tissueieUTF-8saNtabivqlifeina
  cellharvardhlenemb0

74
The Organization of CellsRemember that a group
of similar cells is a tissue

• There are four basic types of animal tissues
• 1 epithelial - coverings and linings
• 2 connective - support and storage
• 3 nervous - the conduction of electrical
  impulses, and the coordination of the bodys
  activities and responses to stimuli
• 4 muscle - contraction (heartbeat, voluntary and
  involuntary movements)
• There are three basic types of plant tissues
• 1 epidermis - coverings
• 2 vascular tissue - transport
• 3 ground tissue - support

75
Epithelial tissue
76
Connective tissue
77
Muscle Tissue
78
Nervous Tissue
79
Plant tissue
80

• CHEMISTRY

81
Chemical elements

• Elements are substances that cannot be broken
  down to other particles by ordinary means.
  Chemical elements are composed of atoms, which
  are the smallest units of elements that retain
  the elements properties.
• There are over 100 known elements but four of
  them oxygen (O2), hydrogen (H), carbon (C), and
  nitrogen (N) make up most of your body

82
Subatomic particles

• protons have a positive charge and are found in
  the nucleus of the atom
• electrons have a negative charge and are found
  orbiting the nucleus in orbits called electron
  shells
• neutrons have no charge and are also found in the
  nucleus of the atoms
• 4. Isotopes are atoms of elements that have
  differing numbers of neutrons (e.g., carbon 12,
  carbon 13, and carbon 14) and radioisotopes are
  atoms with dissimilar numbers of protons and
  neutrons, which are unstable and consequently
  emit electrons and energy. The latter can be
  used for radioactive dating, tracking chemicals
  etc.

83
(No Transcript)
84

• Types of bonds

85

• Ionic bonds -an association between a positive
  ion (an atom that has lost one or more electrons)
  and a negative ion (an atom that has gained one
  or more electrons). These ions are bonded
  together by a mutual attraction between the
  opposite charges. Example NaCl-

86
(No Transcript)
87

• Covalent bonds - an association between two or
  more atoms involving the sharing of electrons.
  This ability to share electrons is related to the
  position of the electrons in the shells
  surrounding the nucleus. Each shell can hold a
  certain number of electrons and unfilled shells
  facilitate covalent bonding.
• Nonpolar covalent bonds occur when both atoms
  exert the same pull on the shared electrons
• 2. Polar covalent bonds occur when the atoms do
  not exert the same pull on the shared electrons.
  The most attractive atom is slightly negative and
  the other is slightly positive.

88
(No Transcript)
89
(No Transcript)
90
(No Transcript)
91

• Hydrogen bonds - a weak association between an
  atom of a molecule with a neighboring hydrogen
  atom that is already involved in a polar covalent
  bond. These bonds are more easily broken and
  this is good (we will talk about this when we
  talk about DNA)

92
(No Transcript)
93
Water is a very special molecule because of the
following properties

• Cohesion (when like substances hold together) and
  adhesion (the attachment of different
  substances). Cohesion results in Surface
  tension.

94

• High specific heat - water heats up slowly and
  then holds that heat (it acts as a heat sink)

95

• Thermal conductivity - heat spreads rapidly when
  applied to one part of a body of water

96

• High boiling point - water requires a great deal
  of heat energy to break the hydrogen bonds
  (holding the water molecules together) and change
  the liquid water into a gas.

97

• Evaporative cooling - for example sweating or
  panting.

98

• High freezing point and it is less dense as a
  solid

99

• Many substances dissolve in water and it is a
  part of many chemical reactions

100
pH

• When water partially dissociates (comes apart) it
  forms hydrogen ions (H) and hydroxide ions (OH-)
• These ions can change the pH (acidity or
  alkalinity) of a substance depending on the
  relative concentrations of the types of ions.
• 1. An acid contains more H ions
• 2. A base (or alkaline substance) contains more
  OH- ions
• 3. Substances with a pH below 7 are acidic,
  substances with a pH above 7 are basic or
  alkaline, and substances with a pH of
  approximately 7 are neutral

101
(No Transcript)
102

• Both acids and bases are very caustic and in
  general damage proteins, cells, and tissues.
  Thus pH is under homeostatic control. Buffers
  are substances that help stabilize pH by
  combining with and/or releasing H. For example
• HCO3- H -? H2CO3
  (bicarbonate hydrogen ion ? carbonic acid)

103

• Compounds are substances that are composed of
  atoms or two or more different elements. There
  are four very important types of biological
  compounds and all of these are organic (they
  contain C)

104
Lipids

• organic compounds that are not soluble in water
  (they are nonpolar). They contain mostly C and
  H, and are involved in energy storage and
  cellular structures

105

• Fatty acids are components of cell membranes that
  are made of a long hydrocarbon chain (the
  backbone - which is hydrophobic or water hating)
  with an attached carboxyl group (which is polar
  and hydrophilic or water loving). Some of these
  are trans fats (unhealthy) and others are cis
  fats (less unhealthy in moderation). A
  saturated fat contains all single bonds and is
  solid (e.g., Crisco shortening) and an
  unsaturated fat (oil) contains one or more double
  bonds is more liquid (e.g., Crisco cooking oil)
  depending on the number of double bonds

106

• Glycerides (neutral fats) are storage lipids
  (they also function in insulation against cold
  temperatures) which consist of fatty acid tails
  attached to a backbone of glycerol

107

• Phospholipids also have a back bone of glycerol,
  two (not three as in triglycerides) fatty acid
  tails and one or more phosphate groups. They
  are important components of cell membranes due to
  their structure with both hydrophilic and
  hydrophobic parts.

108

• Steroids are insoluble in water and contain
  carbon rings (they have no fatty acid tails).
  Examples include sex hormones and the
  cholesterols found in cell membranes

109

• Waxes possess long-chain fatty acids and
  long-chain alcohols or carbon rings. They repel
  water.

110
Carbohydrates

• carbon compounds involved in energy storage
  (e.g., glucose) or structural molecules (e.g.,
  cellulose found in plant cell walls)

111

• Monosaccharides are simple sugars that contain
  energy storing bonds (e.g., glucose)

112

• Disaccharides (and other oligosaccharides) are
  compounds consisting of two monosaccharides that
  are bonded together. Examples include table
  sugar (sucrose), and milk sugar (lactose).

113
Polysaccharides are large compounds often called
complex carbohydrates that are composed of many
monosaccharides bonded together. Examples
glycogen (energy storage for animals), starch
(energy storage for plants ), cellulose (plant
cell walls), chitin (exoskeletons of insects)
114
Proteins

• Amino acids are the building blocks of proteins

115

• These amino acids are linked together by special
  bonds called peptide bonds to form proteins or
  polypeptides

116

• Protein structure involves four levels
• a. primary structure - the sequence of the amino
  acids
• b. secondary structure - the shape of these
  chains of amino acids (e.g., alpha helix)
• c. tertiary structure - the three-dimensional
  shape
• d. quaternary structure or associations between
  the individual chains of proteins that are made
  up of more than one polypeptide

117
(No Transcript)
118

• Enzymes are special proteins (with few exceptions
  all enzymes are proteins), that act as catalysts
  (they speed up reactions). Each enzyme is
  specific in that it reacts with a particular
  substrate in what is called a lock and key
  mechanism. Enzymes are greatly affected by the
  concentrations of the substrate, inhibitors, pH
  changes, and temperature changes.

119
Nucleic acids

• Nucleotides are the building blocks of DNA
  (deoxyribonucleic acid) and RNA (ribonucleic
  acid).
• DNA is the heritable material that codes for
  proteins. It exists are a double helix and is
  generally double stranded, and contains the sugar
  deoxyribose
• RNA (usually single stranded and contains the
  sugar ribose) is the compound that directs the
  information encoded in DNA in the formation of
  proteins. Thus we have
• DNA gt RNA gt proteins

120
Nucleotides
121
(No Transcript)
122

• END OF NOTES FOR EXAM I