Transcript UNIT I - BIOCHEMISTRY

UNIT I – UNITY & DIVERSITY OF LIFE
Hillis – Chp 1, 19, 20 (pgs. 392-406), 22
Big Campbell ~ Ch 1, 18, 27, 28, 31
Baby Campbell ~ Ch 1, 10, 16, 17
Biology is . . .
I. “THE STUDY OF . . . “ – EXPERIMENTAL DESIGN
Inquiry-based
I. EXPERIMENTAL DESIGN, cont
• Types of Experiments
o Comparative, Observational, Controlled
• Setting up a Controlled Experiment
o Clearly defined purpose
o Valid, clear hypothesis
 Testable statement or prediction
 Do not use “I think …”, “My hypothesis is …”, etc!
 Often written in “If …, then …” format but not required
o Control Group
 Benchmark or standard for comparison
o Experimental or Test Group(s)
 Only one factor can be changed in each test
 Independent (Manipulated) Variable
 Dependent (Responding) Variable
I. EXPERIMENTAL DESIGN, cont
• Important Considerations
o Controlled variables (aka control variables, constants) must be
monitored
 Additional factors that could change from one set-up to another
o Sample Size
o Potential sources of error
o Is it repeatable?
• Presentation of Data
o Concise & Organized
 Tables
I. EXPERIMENTAL DESIGN, cont
o Graphs
 Format
 Descriptive title
 Key
 Units must be evenly spaced (line break) and labeled
 Use at least half of available space
 Use a RULER!!!
 DRY MIX

 Types of Graphs
 Continuous Independent Variable (time) → _Line_ Graph
 Discrete Independent Variable → _Bar__ Graph
 Part of a Whole → ___Pie___ Graph
I. EXPERIMENTAL DESIGN, cont
o Graphs, cont
 For Height Lab …
 Mean
 Median
 Mode
 Range
 Histogram

 Normal Distribution?
I. EXPERIMENTAL DESIGN, cont
o Data Analysis
 Null Hypothesis
“Statement of No Effect”
 States that any differences in data sets are due to random errors that
cannot be eliminated in experimental design/protocol
For example,
 There are no significant differences between predicted and
observed data.
 There are no significant differences between control group data
and test group data.
 Alternate Hypothesis – it is formulated to describe the effect that we
expect our data to support.
 Statistical Analysis – Supports or refutes null hypothesis
I. EXPERIMENTAL DESIGN, cont
 Standard Deviation

I. EXPERIMENTAL DESIGN, cont
 Standard Error of the Mean
I. EXPERIMENTAL DESIGN, cont
Examine the data below showing two different experiments
in which the heart rate of 10 different individuals was
measured in beats/minute.
Study A
Study B
68
68
70
84
76
90
62
60
70
92
72
58
74
64
67
66
68
78
70
86
I. EXPERIMENTAL DESIGN, cont
Calculate the standard deviation for each data set.
Study A
Study B
68
68
70
84
76
90
62
60
70
92
72
58
74
64
67
66
68
78
70
86
I. EXPERIMENTAL DESIGN, cont
• Is there is a significant difference between the average heart beat/minutes
in the two data sets? Construct a graph to illustrate.
I. EXPERIMENTAL DESIGN, cont
• Conclusion
o Evaluate hypothesis
 Was it supported, refuted, or were results inconclusive?
o Assess experimental design
 Was there only one independent variable?
 Were sources of error minimized?
 Controlled variables/constants
 Repeatable?
• Theory
II. UNITY OF LIFE
• Form vs. Function
• Characteristics of Life
o All living things are made of
_cells_.
 Prokaryotic
 Eukaryotic
II. UNITY OF LIFE, cont.
• Characteristics of Life, cont
o Living things obtain and use energy.
o Living things respond to their environment.
o Living things grow and develop.
o Living things maintain homeostasis.
o Living things are based on a universal genetic code.
o Living things reproduce.
o As a group, living things evolve.
III. HIERARCHY OF LIFE
o Organization of Life





Biosphere
Ecosystem
Community
Population
Organism
 organ system
 organ
 tissue
 cell
 Organelle
 Molecule
 Atom
III. HIERARCHY OF LIFE, cont
• Classification of Life
 Domain
 Kingdom
 Phylum
 Class
 Order
 Family
 Genus
 Species
III. HIERARCHY OF LIFE, cont
• A Closer Look at Classification
 Domain _Archaea_
 Kingdom __Archaebacteria__
 Domain _Bacteria_
 Kingdom _Eubacteria__
 Domain __Eukarya__
Kingdom _Protista___
 Kingdom __Fungi___
 Kingdom __Plantae___
 Kingdom __Animalia___

IV. CHALLENGING THE BOUNDARIES OF LIFE
• Viruses . . . Living or Non-living?
 Discovery of Viruses
 First isolated by Ivanowsky in 1890s from
infected tobacco leaves
 Crystallized by Stanley in 1935 – proved
viruses were not cells
 Not capable of carrying out life processes
without a host cell
 Parasites
IV. BOUNDARIES, cont
• Viruses, cont
 Structures found in all viruses:
 Viral genome
 DNA or RNA.
 May be single-stranded or double-stranded
 Protein coat
 Known as a capsid
 Made up of protein subunits called
capsomeres.
IV. BOUNDARIES, cont
• Viruses, cont
 Structures/adaptations that may be present:
 Viral envelope
 Typically derived from host cell membrane
o Exception is Herpes virus, synthesized from nuclear envelope of host
cell
 Aid in attachment. Envelope glycoproteins bind to receptor molecules on
host cell
 Most viruses that infect animals have envelope
 Tail – Found in some viruses to aid in attachment
IV. BOUNDARIES, cont
IV. BOUNDARIES, cont
• Viruses, cont.
 Bacteriophage
 Infect bacteria
 Bacterial Defense Mechanisms
Restriction Enzymes
Coexistence
IV. BOUNDARIES, cont – Viral Replication
1. Virus enters; is uncoated;
releases viral genome and
capsid proteins
2. Host enzymes
replicate the viral
genome
3. Host enzymes
replicate viral genome
4. Viral genomes and
capsids self-assemble
into new viral particles;
exit the cell
IV. BOUNDARIES, cont – Viral Replication
Viral Entrance into Host Cell
IV. BOUNDARIES, cont – Viral Replication
LYTIC CYCLE
1. Lytic Cycle – Results in death of host cell.
IV. BOUNDARIES, cont – Viral Replication
LYSOGENIC CYCLE
IV. BOUNDARIES, cont – Human Viruses
• DNA Viruses
o No envelope
 Papilloma Virus
 Warts, cervical cancer
o With envelope
 Smallpox Virus - cowpox
 Herpesvirus
Herpes simplex I and II – cold sores, genital sores
Epstein-Barr virus – mono, burkitt’s lymphoma
Varicella zoster – shingles, chicken pox
IV. BOUNDARIES, cont – Human Viruses
RNA Viruses
IV. BOUNDARIES, cont – Human Viruses
• RNA Viruses
o No envelope
Rhinovirus – common cold
o Envelope
Coronavirus - SARS
Filovirus – Ebola (hemmorrhagic fever)
Influenza virus - flu
HIV
 Belongs to a group of viruses known as _Retroviruses__
 Contain RNA, reverse transcriptase
Converts _RNA_ to _DNA_
IV. BOUNDARIES, cont – HIV
 A Closer Look at Human
Immunodeficiency Virus
 Infects WBCs known as Helper T
cells
 Can reside in lysogenic-like cycle
for years
 Active, symptomatic = AIDS
IV. BOUNDARIES, cont – HIV, cont
IV. BOUNDARIES, cont
• Viroids
o Single, circular RNA molecule; lack protein
o Parasitize plants
• Prions
o
o
o
o
Infectious proteins; lack nucleic acid
Cause Mad Cow Disease, Creutzfeldt-Jakob Disease
Very long incubation period
No treatment
V. THE DIVERSITY OF LIFE
Kingdom
Type of Cell
Cell Structures
Nutrition
Description
Archaebacteria
•
•
Cell wall not made
of _____________
Mostly
_______________
“______________
bacteria”; require
______ conditions
Eubacteria
•
•
Cell wall made of
_______________
Mostly
_______________
Ubiquitous;
__________; may
be pathogenic
Protista
•
•Mostly ________
May have cell wall, Auto or hetero
chloroplasts,
flagella
Fungi
•
•Mostly ________
Cell wall made of
____________; no
______________!
Strictly
All non-motile;
_______________ _______________
(______________)
Plantae
•
•
Cell wall made of
____________;
all have
chloroplasts
Strictly
All non-motile
_______________
(______________)
Animalia
•
•
Never have _____
____________;
Strictly
_______________
“______________
_________”; very
diverse
“kingdom”
All ___________
during life cycle;
IV. THE DIVERSITY OF LIFE
Kingdom
Type of Cell
Cell Structures
Nutrition
Description
Archaebacteria
•Prokaryotic
•Unicellular
Cell wall not made
of peptidoglycan
Mostly
heterotrophic
“Ancient
bacteria”; require
harsh conditions
Eubacteria
•Prokaryotic
•Unicellular
Cell wall made of
peptidoglycan
Mostly
heterotrophic
Ubiquitous;
decomposers; may
be pathogenic
Protista
•Eukaryotic
•Mostly uni
May have cell wall, Auto or hetero
chloroplasts,
flagella
“Junk Drawer of
Life”; very diverse
“kingdom”
Fungi
•Eukaryotic
•Mostly multi
Cell wall made of
chitin; no
chloroplasts!
Strictly
heterotrophic
(absorption)
All non-motile;
decomposers
Plantae
•Eukaryotic
•Multicellular
Cell wall made of
cellulose; all have
chloroplasts
Strictly
autotrophic
(photosynthesis)
All non-motile
Animalia
•Eukaryotic
•Multicellular
Never have cell
walls or
chloroplasts
Strictly
heterotrophic
(ingestion)
All motile during
life cycle
VI. PROKARYOTES – A CLOSER LOOK
VI. PROKARYOTES, cont
• Archaebacteria
 Examples include methanogens, thermoacidophiles, halophiles
 Taq DNA polymerase
VI. PROKARYOTES, cont
Eubacteria
 Ubiquitous
 May be pathogenic
 Most are harmless
• Classification
 Shape
 Cocci
 Bacilli
 Spirilla
 Gram Stain Reaction
 Positive
 Negative
Gram +
Streptococcus pneumoniae
Gram -
Neisseria gonorrhoeae – gram negative;
coccus shaped
E.coli – gram negative; rod-shaped
VI. PROKARYOTES – EUBACTERIA, cont
• Nucleoid region
• Plasmids
• Asexual reproduction
Binary fission
VI. PROKARYOTES – EUBACTERIA, cont
• Adaptations
 Capsule
 Adherence
 Protection
 Associated with
virulence
 Pili
 Adherence
 Conjugation
 Endospore
 Bacterial
“hibernation”

Motility (flagella,
slime,
Spore formation – adaptation seen in some bacteria that allows them to survive adverse
conditions. A hard, protective wall forms around the DNA of the bacteria – and the bacteria
can survive for centuries. When favorable conditions return, the spores revive, and the
bacteria is able to revive and germinate. Ex. Bacillus anthracis; Clostridium botulinum
Bacillus anthracis
VI. PROKARYOTES – EUBACTERIA, cont
• Adaptations, cont
 Quorum Sensing/Biofilms
 Fairly recent discovery
 Bacteria exchange chemical
communication signals
 Multicellularity???
 “Sexual Reproduction”
 Genetic Recombination
Occurs by:
 Transformation
 Transduction
 Conjugation
 Transformation – external DNA incorporated into cells – can come
from dead bacteria
• Transduction – transfer of genes between a bacteria and a virus vector – the
virus inserts new genes into the bacteria…. This method is used in
biotechnology to create bacteria that produce valuable products such as insulin.
• Conjugation – a form of sexual reproduction in which there is a direct transfer of a
plasmid from one bacteria to another (through pili) before the bacteria divides –
results in offspring with new genes/traits.
- Plasmid - smaller ring of DNA that functions in antibiotic resistance or
metabolism; replicates independently of the entire DNA
VI. PROKARYOTES – EUBACTERIA, cont
• Metabolism
o Nitrogen fixation
 Conversion of atmospheric
nitrogen (N2) to ammonium
(NH4+)
o Metabolic Cooperation
 Biofilms
o Oxygen relationships
 Obligate aerobes
 Facultative anaerobes
 Obligate anaerobes
VI. PROKARYOTES – EUBACTERIA, cont
Bacterial Pathogenesis
• Koch’s Postulates – Criteria for bacterial disease confirmation
 The microorganism is found in all individuals with the disease.
 The microorganism can be cultured from the host.
 The isolated organism will produce disease when injected into another host.
 The organism can be isolated from the newly infected host.
• “Normal Flora”
• Some bacteria are opportunistic pathogens
 Normal residents of host; cause illness when defenses are weakened
• Toxin Production
 Exotoxins - Bacterial proteins that can produce disease w/o the prokaryote
present (botulism, cholera)
 Endotoxins - Components of gram negative membranes (typhoid fever,
Salmonella food poisoning)
VI. PROKARYOTES – EUBACTERIA, cont
• Bacterial Pathogenesis, cont
 Examples
 Clostridium sp.
 Staphylococcus
 Streptococcus
 Neisseria sp.
 Mycobacterium tuberculosis
 Legionella pneumophila
EUKARYOTES
VII. KINGDOM PROTISTA
•
•
•
•
Very diverse
All _Eukaryotic_
Mostly _Heterotrophic_
Classified according to eukaryotic kingdom
protist is most like, nutrition
 Animal-like
 Ingestive
 Protozoans
 Plant-like
 Photosynthetic
 Algae, kelp, seaweed
 Very impt aquatic producers;
phytoplankton
 Fungus-like
 Absorptive
 Slime Molds
VII. KINGDOM PROTISTA, cont
Protist Phylogeny . . .
For now!
VII. KINGDOM PROTISTA, cont
• Important Protozoans
 Zooplankton
 Important component of aquatic food
chains
 Human Pathogens
 Entamoeba
o Intestinal pathogen
o Associated with dirty, stagnant water
o Moves, feeds using pseudopods
 Giardia
o Lack mitochondria, cell walls
o Live in fresh water; flagellated
o Intestinal pathogens
VII. KINGDOM PROTISTA, cont
• Important Protozoans, cont
 Plasmodium
 Belong to Apicomplexa
 All parasitic, non-motile
 Cause malaria
 Vector = Anopheles mosquito
 Resistance seen in _________
_Individuals heterozygous for
sickle cell anemia_
 Toxoplasma
VIII. KINGDOM FUNGI
VIII. KINGDOM FUNGI, cont
• Absorptive heterotrophs; release
exoenzymes
 Decomposers (saprobes)
 Parasites
 Mutualistic symbionts (lichens)
• Primarily reproduce asexually
• Classified according to reproductive
structures
• Include mushrooms, bracket fungi,
puffballs
• Yeast
 Unicellular
 Reproduce asexually; budding
 May be pathogenic
VIII. KINGDOM FUNGI, cont
• Specialized Fungi
 Molds
 Used to be classified as
Deuteromycota or “Imperfect
Fungi”
 No known sexual stage
 Penicillium
 Lichens
 Mutualistic relationship with
algae or cyanobacterium
 Sensitive to air pollution
 Mycorrhizae
 Mutualistic relationship found in
95% of all plants