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final exam Flashcards

1
Q

chLUCA

A

the Last Universal Common Ancestor
The evolution of protobionts led to an organism(s) that is the precursor to all current life on Earth
We know it stored genetic information in DNA
Roughly 350 genes common among all life forms
We know it used proteins for catalysts
We know it used ATP as a major energy source

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2
Q

“Uncontestable” Microfossils

A

The oldest fossil evidence of life is from 3.8 byo stromatolites found in Western Australia
The first cells were Prokaryotes - a membrane surrounding cytoplasm containing loose DNA with simple metabolism

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3
Q

The Great Oxygenation Event

A

Resulted from the evolution of oxygenic photosynthesis by cyanobacteria

Oxygen first saturated the oceans and then accumulated in the atmosphere
O2 levels went from <1% to roughly 21%

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4
Q

It’s the End of the World(As We Know It)

A

This had a devastating effect on life on Earth!!
The “corrosive” O2 doomed countless anaerobic organisms
Only those organisms that had enzymes to “handle” oxygen could survive and reproduce
As oxygen levels increased slowly over time, the organisms that could remove O2 were selected for
Today we can classify species (mostly Prokaryotes) based on their oxygen requirements
Aerobic (require oxygen), facultative (can survive in presence of oxygen, but don’t require it), Anerobic (die when interacted with oxygen)

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5
Q

It’s the Beginning of the World(As We Know It)

A

The generation and persistence of oxygen allowed for an unprecedented increase in biological diversity:
The development of aerobic respiration
What better way to get rid of toxic oxygen than to reduce it to water? C6H12O6 + O2 –> CO2 + H2O + ATP
The development of an ozone layer
To protect the planet from mutagenic cosmic rays
Life could creep out of the primordial soup and colonize land…

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6
Q

Life is Predominantly Prokaryotic

A

99% of life on Earth are unicellular Prokaryotes
Prokaryote: Before the kernel (nucleus)
No membrane-bound organelles
nuclei, mitochondria, chloroplasts, ER
Divided into two groups
Bacteria and Archaea
Have adapted to every environment
Aerobic, anaerobic, acid-tolerant, salt-tolerant, radiation-tolerant

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7
Q

Eukaryotes Emerge

A

~ 1.8 bya, as Prokaryotes were optimizing photosynthesis and respiration, Eukaryotes appear in the fossil record
This occurred by the processes of Endosymbiotic Theory
Endo: Within. Sym: Together. Biotic: Life
One form of life living within another
Generated a bacteria/archaea hybrid

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8
Q

Endosymbiotic Theory

A

A small bacterium began living inside a larger archaea
Symbiosis refers to a close association between two organisms, Endo means within
The bacterium was efficient at aerobic respiration
The archaea was efficient at obtaining nutrients
Over time, the association became permanent
Neither can live without the other
The bacteria/archaea hybrid became a eukaryote
The bacterium is now an organelle = mitochondria
Also occurred with a photosynthetic bacterium = chloroplasts

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9
Q

Fireball Earth

A

With all the collisions, Earth was molten
As the collisions decreased, Earth cooled, and a crust formed
Atmosphere mainly composed of Hydrogen
Oceans formed as water cooled
Volcanoes erupted through crust dispersing simple, inorganic gases into the atmosphere

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10
Q

Primary Abiogenesis

A

Abiogenesis: Life out of no life
Simple inorganic molecules combined to become organic molecules of increasing complexity. Organisms are made of carbon
As these molecules became more stable and persisted longer in the environment, they initiated increasingly complex associations
Eventually, one gained the ability to self-replicate
Eventually, they became surrounded in a membrane
Led to the first cellular organisms
Spontaneous generation did occur, at the start when the Earth was very different

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11
Q

Anaerobic

A

no oxygen

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12
Q

Conditions of Early Earth

A

Anaerobic (no oxygen)
Oceanic
Filled with simple inorganic molecules
Hydrogen, methane, water , carbon dioxide, nitrogen, hydrogen sulfide, ammonia
High temperatures
Average global temperature of roughly 90 degrees
These conditions are almost perfect for spontaneous generation of life. The only other consideration is a source of….

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13
Q

Panspermia

A

Could life have evolved in outer space?
Murchison Meteor (7 byo) and found that it contained amino acids and nucleic acids

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14
Q

The Primordial Soup

A

The formation and persistence of simple organic molecules occurred in the Earth’s early oceans = the “primordial soup”

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15
Q

“primitive pizza”

A

The formation and persistence of simple organic molecules occurred in the Earth’s early oceans = the “primordial soup”
These molecules splashed onto volcanic clay “beaches”, which allowed polymerization into the four common biological macromolecules
Producing a “primitive pizza”

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16
Q

Polymerization:

A

Poly (many) mer (bodies). The joining of small building blocks into large molecules

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17
Q

Carbon dioxide

A

“captured” by photosynthesis, glucose is used in metabolism. Goals of metabolism: Energy and structure creation

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18
Q

Animals

A

require 25 elements

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19
Q

plants

A

require 17 elements

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20
Q

Cellular structure and metabolism

A

is based on carbon-containing (organic) molecules
50% of body mass is carbon (excluding water)
Other elements play important roles as well

Oxygen, hydrogen, nitrogen, phosphorus and calcium

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21
Q

Carbohydrates

A

(Carbon water) – (CH2O)n
Simple sugar - monomer + dimers
Complex sugar - polymers

Monosaccharides–3-7 carbons(Simple sugars)
Glucose, fructose, sucrose (disaccharide), etc.
Form of carbohydrate fed into metabolic pathways

Polysaccharides – 100-1000 monosaccharides
Glycogen, starch, cellulose
Form of carbohydrate used for long-time storage + building cells

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22
Q

Nucleic Acids

A

(C10H14N5O7P)n – ish!
Monomers – ATP, GTP, etc.
Complex polymers – RNA + DNA

DNA
Polymers of deoxyribonucleic acid nucleotides (monomer) that “fold” into a double helix
Used to store genetic information
RNA
Polymers of ribonucleic acid nucleotides that “fold” into complex three-dimensional shapes
Used to turn genetic information into proteins
Used as energy molecules (ATP, GTP)

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23
Q

DNA

A

Polymers of deoxyribonucleic acid nucleotides (monomer) that “fold” into a double helix
Used to store genetic information

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24
Q

RNA

A

Polymers of ribonucleic acid nucleotides that “fold” into complex three-dimensional shapes
Used to turn genetic information into proteins
Used as energy molecules (ATP, GTP)
RNA has an extra oxygen over DNA

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25
Nucleoside
Monomer
26
Nucleotide
Polymerized
27
Lipids
(C39H75O10P)n – ish! triglycerides + phospholipids Water insoluble molecules composed mostly of carbon and hydrogen atoms (hydrocarbons) The two major biological lipids are triglycerides + phospholipids
28
Saturated fats
do NOT have fatty acids that contain double bonds completely saturated with hydrogen. CH3 - CH2 - CH3
29
Unsaturated fats
have fatty acids with one or more double bonds CH2 = CH - CH3
30
fatty acids
Fatty acid molecules can vary in the: Number of carbon atoms in the hydrocarbon chain Presence of double bonds between carbon atoms
31
Triglycerides
Fats mainly serve as energy-rich storage molecules Consist of 3 fatty acid (hydrocarbon) chains bound to a glycerol “anchor” The C-C and C-H bonds store lots of energy, that can be released when needed
32
Phospholipids
Glycerol 2 fatty acid “tails” 1 phosphate “head” Attached to an organic molecule
33
Phospholipid Bilayers
In aqueous solutions, phospholipids form bilayers Man-made bilayer vesicles are called liposomes
34
Biological Membranes
Compartmentalize the cell The plasma (cell) membrane separates “out” from “in” Internal membranes create additional cellular regions Membranes are selectively permeable membranes, meaning not everything can pass through Membranes are important for cell-cell communication. Site of biological reaction
35
The Lipid Bilayer is Fluid
Most phospholipid molecules are independent Not bound to anything Each is free to move along the plane of the membrane Not all membranes have the same degree of fluidity… Type of phospholipid affects the fluidity Mixed with the phospholipids are proteins and sugars
36
The Lipid Bilayer is a Barrier
Large and/or charged molecules have a hard time squeezing between the phospholipids EX. Glucose, sucrose, Cl- Small and/or uncharged molecules can cross the membrane EX. Water, glycerol Fluid mosaic model
37
Diffusion and Osmosis
The tendency of dissolved molecules to evenly distribute themselves in a solution Molecules move from areas of high concentration to areas of low concentration Diffusion works across membranes, IF the molecule can cross the membrane If not, water will move to dilute the concentrated side
38
Transport of Molecules
Most biologically important molecules are large and/or charged Cannot diffuse across the membrane without help… Cells have transport proteins, shaped like tunnels, that allow these molecules to cross the membrane
39
Proteins
NH3CHRCOOH)n Short polymers – used as a food source Complex polymers – polypeptides Polymers of amino acids that “fold” into complex three-dimensional shapes Oligopeptides (4-10 amino acids) Used for Food Used in cell-to-cell communication Polypeptides (100s of amino acids, sometimes 1000's) Multiple uses determined by the overall 3D shape of the molecule
40
Amino Acids
Central (a) carbon Amino group Carboxyl group R group This is the part of the molecule that varies There are “20” unique amino acids Amino acids are linked together into peptides
41
Common Cellular Features
Cell membranes Phospholipid bilayers that compartmentalize stuff Cytosol the fluid that fills a cell The central dogma DNA --> RNA --> Protein
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Nucleus
Separates genetic information from rest of cell
43
Mitochondria/Chloroplasts
organic molecules synthesis energy generation (ATP)
44
Endomembrane system
Lipid/protein synthesis – Endoplasmic Reticulum Trafficking and excretion - Golgi Apparatus Digestion and detoxification - Lysosomes Storage - Vacuoles
45
Cytoskeleton
Internal and external structural support
46
Cell wall
External cell structural support Plants and algae use cellulose, pectin, chitin
47
Centrosome
cell replication
48
Flagella/cilia
cell movment
49
Nucleoid
Area in the cytosol where genetic info is stored
50
Bacterial Cell Walls: Peptidoglycan
The carbohydrates NAG and NAM are bound to one another in an alternating sequence Form long glycan (sugar) chains NAM has a protein side chain that links adjacent glycan chains together Forms a cellular lattice that surrounds the cell
51
Bacterial Cell Walls: Gram Reaction
Bacteria can be grouped into two main classes based on the thickness of their cell walls Gram-positive bacteria have thick cell walls Stain purple in a Gram reaction Gram-negative bacteria have thin cell walls Stain red in a Gram reaction
52
Lysozyme
Produced by multiple animal species including Homo sapiens… Found in secretions like tears and saliva Breaks the bonds between NAG and NAM in peptidoglycan Without a cell wall, the cell lose structural support and will die
53
Penicillin
Produced by the soil fungus Penicillium chrysogenum Binds to the enzyme that forms the protein cross-link between glycan chains Without the cross link, the cells will die Penicillin does not harm us because we do not have peptidoglycan
54
The Outer Membrane
Only found in Gram-negative bacteria Similar structure to other biological membranes Permeable compared to the plasma membrane Lipopolysaccharides (LPS) make up ~40% of the external leaflet
55
Lipopolysaccharide (LPS)
O-specific side chain (O antigen) Various polysaccharides Helps stick to surfaces Species-specific Core Polysaccharide More polysaccharides Genus-specific Lipid A (glycolipid) A toxin that causes inflammation when found in the blood
56
Heredity/Inheritance
The transmission of traits from one generation to the next (parental generation to offspring generation)
57
A trait
is any characteristic of an individual that is heritable
58
Gregor Mendel
Studied inheritance in garden peas (1865) Tracked changes in flower colour (and other characteristics) in thousands of pea plants Worked out a mechanism showing how traits from one generation could be passed down to the next
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genome
All the genes of a species make up its genome
60
genotype
All the alleles of an individual make up its genotype
61
phenotype
the physical, observable trait
62
allele
one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.
63
the principle of segregation
The two alleles of every gene separate in each parent and a new combination comes together in offspring Each parent contributes one allele for each gene
64
principle of independent assortment
Every gene separates independently from one another Different genes (i.e., flower colour and seed shape) are not linked
65
Gametes
a reproductive cell of an animal or plant. have 1 copy of each chromosome
66
Zygotes
zygote is a eukaryotic cell formed by a fertilization event between two gametes are a random combination of 2 gametes
67
karyotype
the number and visual appearance of the chromosomes in the cell nuclei of an organism or species.
68
Morgan
studied inheritance patterns in fruit flies He crossed fruit flies with various eye colours to determine if he could identify patterns that followed the predictions of Mendel’s model They didn’t. All his models assumed that the eye colour gene would occur twice – once for each copy of a chromosome Morgan realized that if the gene for eye colour was on the X chromosome (but not the Y), the inheritance pattern supported Mendel’s ideas
69
Nettie Stevens
discovered that the sex chromosomes determine gender (females are XX and males are XY) X is a normal looking chromosome, but Y is kind of piddling and simple…
70
Chromosomes
are composed of both proteins and DNA Proteins:Composed of 20 amino acids Millions of possible 3D structures Complex enough to store heritable information DNA: Composed of 4 nucleic acids (nitrogenous bases) Simple and limited 3D structures Thought to play a structural role Today we know that DNA is storing genetic info and proteins are there for structural support.
71
Streptococcus pneumoniae
Bacterium that causes pneumonia, ear infections, and meningitis A significant cause of child mortality before the development of antibiotics and vaccines
72
Griffith et al.
In 1928, Griffith published a paper of observations he made while trying to develop a vaccine
73
AVERY et al.
Kill S cells, lyse the cells, remove the lipids and sugars (RNA, DNA and protein is left) Add DNAase Breaks down DNA Add living R cells to each tube Look for S cells (transformation)
74
discovering DNA
Franklin produced an X-ray crystallograph of DNA Wilkins (Franklin’s supervisor) showed the images to James Watson Watson and Crick pieced together the structure based on Franklin’s data and Chargaff’s rules
75
double helix
DNA molecules exist as two “strands” coiled into a
76
Chromatin
is the normal form of DNA, this is how it exists in our cells most of the time The “normal” state of our genetic material During DNA replication and transcription, it “opens” During cell division, chromatin condenses further to form a chromosome
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Transcription
(DNA to RNA) A particular DNA sequence (a gene) will specify an RNA sequence
78
Translation
(RNA to protein) A specific RNA sequence will specify an amino acid sequence
79
codon
Every 3 nucleotides form a codon Each codon codes for a specific amino acid.
80
Messenger RNA
RNA, transcribed from DNA, that acts as a template for translation of specific proteins
81
Ribosomal RNA (rRNA)
RNA that folds into a ribosome and catalyzes translation
82
Transfer RNA (tRNA)
RNA that link specific amino acids and delivers them to ribosomes during translation
83
Mutation
A permanent change in a DNA sequence that changes an organism’s genotype Most mutations only affect one organism Mutations in gametes are passed on to offspring A mutant is an organism that has undergone one or more mutations Mutations can occur spontaneously as a mistake during DNA replication Mutations can be induced by X-rays, microwaves, UV radiation Mutations can be induced by chemical mutagens
84
point mutation
single location in DNA sequance
85
base pair mutation
change to a single nucleotide within a gene
86
substitution mutation
one nucleotide is replaced by another
87
insertion mutation
one nucleotide is added
88
deletion
a nucleotide is removed
89
silent mutation
a base pair mutation that results in the same amino acid silant mutations have no effect
90
Missense Mutations
is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid can change phenotype
91
Nonsense Mutations
a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in leading to a truncated, incomplete, and usually nonfunctional protein product
92
Frameshift Mutations
Occur when a deletion or an insertion alters the reading frame
93
Viruse
are non-cellular, infectious particles There are multiple viruses of every eukaryotic and prokaryotic organism Require living host cells for reproduction (metabolism) Can’t make ATP, ribosomes, amino acids, … Symbiosis has negative effect on host Broad (West Nile, encephalitis), or narrow (measles) host range
94
Viral Structure
All viruses consist of a nucleic acid genome covered by a protein coat called a capsid Some viral capsids are surrounded by a phospholipid bilayer envloped has membrain stolen from host Viruses have glycoprotein spikes
95
Extracellular
Extracellular the viral genome surrounded by a protective coat of protein; the resulting nucleocapsid may be surrounded by an outer lipid envelope in which viral proteins are embedded. Viral proteins confer specificity as to the range and type of host cell that may be infected.
96
Intracellular
Exist as replicating nucleic acids non-infectious
97
virulent
of a disease or poison) extremely severe or harmful in its effects.
98
lytic cycle
distroys host cells
99
Lysogenic cycle
does not destroy cells
100
Lytic Infection
Viral capsid proteins or glycoprotein spikes attach to receptors on host cell membranes Capsid proteins dissociate from genome Viral genome uses host energy, enzymes and building blocks to replicate Progeny virus particles assemble Progeny virus leave host through induces membrain fusion
101
Lysogenic Infection
Attachment/Adsorption like Viral DNA becomes integrated into host genome Viral DNA is called a provierus The host is called a lysogen As the lysogen divides, the provirus is replicated too Produces a population of host cells infected with provirus The virus is latent (dominant) The provirus can exit the host genome and the viral DNA then enters the lytic cycle
102
The Germ Theory of Disease
Soon after they were discovered, scientists began to suspect that microbes were responsible for disease * Replacing the miasma theory
103
Robert Koch
First to link specific bacteria to specific diseases * Studied anthrax and tuberculosis (consumption) * Formulated Koch’s Postulates for determining the microbial cause of infection
104
Koch’s Postulates (1876)
1.a specific organism must be associated with all cases 2. a specific organism should be isolated and grown within a lab 3. after it should spark desease within healthy individuals 4. the desease should be re-isolated from deseased individual
105
Australian scientists Marshall & Warren (1980s)
Studied gastritis, ulcers * Believed to be due to over production of stumic acid * Treated with “bland” diets and antacids daily for life *Discovered/isolated H. pylori from tissue biopsies * Couldn’t find an appropriate animal model * No one believed microbes could * 10 years later, frustration set in
106
Helicobacter pylori
Found in 50% of the human population * Leading cause of gastric inflammation (gastritis) and ulcers * Causes gastric cancer in 1% of patients * Uses helical shape and flagella to penetrate the thick mucous lining the stomach * H. pylori uses urease to generate ammonia * Produces toxins to damage epithelial cells in order to gain nutrients * Successfully resolved with specially formulated antibiotics
107
latent desease
hidden in a reservoir or host
108
isolated desease
restricted to one or a few individuals
109
endemic desease
common in a population
110
epidemic desease
rapidly spreads through a population
111
pandemic
rapidly spreads across all populations
112
virulence
elative ability of a pathogen to cause disease
113
pathogen
a microorganism that causes disease
114
virulance factors
– molecules produced by, or strategies used by, a pathogen to cause disease * Attach to host cells – fimbriae/pili, capsules * Evasion of host immune system – capsules, enzymes * Invasion and spread – flagella, extracellular enzymes * Acquisition of nutrients – toxins and enzymes
115
Infection * Portal of entry
Skin (wounds or bites) * Gut (need to survive acidic stomach) * Mucous membranes (nose, mouth, eyes, etc.) * Mucous is composed of mucin (glycoproteins and polysaccharides) * Most “normal” microbes cannot penetrate * Pathogens have flagella and enzymes that degrade mucin
116
hyloriadias
destroys hyaluronic acid
117
collegenace
destroys collagen
118
Endotoxin
Permanent component of outer cell membrane in Gram- negative bacteria * Properties * Heat resistant – won’t degrade at body temperature * Poor Immunogen – does not stimulate anntibodys * Symptoms * Fever, diarrhea, vomiting, low blood pressure, general inflammation(body trying to get it out) * Prognosis * Toxicity is low – immune system clears it out * Unless things get out of hand – septicemia – leads to septic shock – multi-organ system failure - death
119
Toxins
* From the Greek word for “bow” * Relating to the use of poison arrows * Properties * Heat labile – destroyed at high temp * Immunogenic – stimulate antibodys * Symptoms * Various – but all involve destroying cells * Prognosis * Toxicity is high – small concentrations can be very damaging * Numerous types * Exotoxins, enterotoxins, neurotoxins, hepatotoxins, cytotoxins, ...
120
Immunogenic
stimulation of antibody responce
121
Cytotoxins
cell killers cell poison I.e., Diphtheria * Caused by Corynebacterium diphtheriae * Inhibits * Results in organ failure * As well as suffocation * Virtually eliminated in “developed” countries with access to the * Can be treated with antibiotics
122
Neurotoxins
reacts with nerve system
123
Botulism
Food Botulism * We eat C. botulinum all the time!! * They can’t compete with our normal gut bacteria * BUT if the bacteria produce toxin in food before we eat... * Exposure via unpasteurized milk/honey/juice or improper canning * Infant Botulism * Babies don’t have gut bacteria! * Wound Botulism * Spores enter wounds, wounds “heal”, organisms grow and produce toxin * Toxin is absorbed in small intestine, enters bloodstream, and moves to motor neurons * Treatment via antibiotics and antitoxin, but there is no way to heal an affected neuron – must be replaced
124
Tetanus
Normally enters body through wounds * C. tetani is everywhere!! * Loves to grow in healing tissues * Toxin enters bloodstream and moves to motor neurons * Treatment via antibiotics and antitoxin, but there is no way to heal an affected neuron – must be replaced * Virtually eliminated in “developed” countries that have access to the
125
Enterotoxin
Affects the intestens * I.e., Cholera * Caused by Vibrio cholerae * Exposure via food/water contaminated with feces * Blocks Na+ from entering cells and pumps Cl- out of cells * Water leaves blood and intestinal cells to * * Results in severe diarrhea leading to dehydration and electrolyte loss * Treatment via rehydration therapy and antibiotics * Virtually eliminated in “developed” countries with access to
126
Disinfectants are used on
Detergents - molecules that disrupt membranes
127
Antiseptics are used on
Alcohols disrupt lipid membranes and denature proteins
128
selective toxicity
inhibit or kill only the pathogen without damaging the host
129
Narrow-spectrum
affect only specific microbes or groups of microbes
130
Broad-spectrum
affect a wide range of microorganisms
131
Sir Alexander Fleming
discovered penicillin in 1929 * The penicillins are b-lactams that inhibit the formation of peptidoglycan – Prevents new cell wall synthesis – More effective against Gram+ than Gram– – Most widely used antibiotics in the world
132
Polymyxins
insert themselves into membranes, forming a pore that causes leakage of metabolites
133
rifamycins
ifamycins inhibit the DNA-dependent RNA polymerase of mycobacteria, resulting in decreased RNA synthesis. These agents are generally bactericidal at treatment doses, but they may be bacteriostatic at lower doses.
134
tetracyclines
inhibit protein synthesis by preventing the attachment of aminoacyl-tRNA to the ribosomal acceptor (A) site.
135
quinolones inhibit
rapidly inhibit DNA synthesis by promoting cleavage of bacterial DNA in the DNA-enzyme complexes of DNA gyrase and type IV topoisomerase, resulting in rapid bacterial death

bio 205 (1 decks)

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