Week 4 Flashcards

Question

What was the deep time in relation of to the origin of life?

Answer 1

Geological evidence suggests a massive meteor hit the earth ~4.6 billion years ago (BYA), forming the moon from its debris ---From this collision, the rocky mantle melted as atmospheric temperatures exceeded 2000° C (so life must be after that) ---No rocks remain from Hadean eon (first 500-700 million years of Earth’s history.

Answer 2

CO2 levels shifted and affected temperature Early atmosphere high CO2 levels. Water slowly vaporized from the molten rock. Increased weathering converted silicate rock to soil CO2 formed carbonic acid (acid rain). Carbonic acid released bicarbonate ions (HCO3− and Ca2+ from rock. CaCO3 Precipitates in the ocean Decreases atmospheric CO2 Lowered Earth’s temperature By 3.8 BYA ocean temperatures dropped to 49-88° C

Answer 3

Evidence of life during the Archean in the form of microfossils is difficult to find and interpret Two main formations of 3.5- to 3.8-billion-year-old rocks have been found Structures in each interpreted to be biological in origin.

Answer 4

Microfossils are fossilized forms of microscopic life - --Oldest are 3.5 billion years old; seem to resemble present-day prokaryotes. - --Fossils from 3.2 BYA more closely resemble eukaryotic cells.

Answer 5

Living organisms incorporate 12C into their cells in preference to other carbon isotopes Work has been done dating and analyzing carbon compounds in the oldest rocks, looking for evidence of life; carbon fixation active as long as 3.8 BYA Ancient carbon fixation via Calvin cycle or a reductive version of the Krebs cycle Ability to fix carbon has evolved more than once

Answer 6

``` How first organic molecules formed is not known Hundreds of thousands of meteorites and comets slammed into early earth; some may have carried organic materials (but still had to be made somewhere) More likely (?), organic molecules originated on early earth ```

Answer 7

Few geochemists agree on exact composition of early atmosphere Popular view of early atmosphere. Carbon dioxide (CO2). Nitrogen gas (N2). Water vapor (H2O). Hydrogen gas (H2). Other sulfur, nitrogen, and carbon compounds. Atmosphere was chemically reducing because of availability of hydrogen.

Answer 8

In 1953, Miller and Urey did an experiment that reproduced early atmosphere Assembled reducing atmosphere rich in hydrogen with no oxygen gas. Atmosphere placed over liquid water. Temperature below 100° C. Simulate lightning with sparks.

Answer 9

Found within a week that methane gas (CH4) converted into other simple carbon compounds Compounds combined to form simple molecules and then more complex molecules. Later experiments produced more than 30 carbon compounds including amino acids Adenine also produced (so a nucleotide precursor). Concluded that key molecules of earth could have formed early Earth (assuming this was the atmosphere, some now think it was only weakly reducing, with less CH4 and less H2)

Answer 10

Sulphur-rich hydrothermal vent systems Might these also support complex carbon compound formation, and hold these in the surrounding porous rock/mineral deposits?

Answer 11

C6H12O6 + 6O2  6CO2 + 6H2O + Energy Free energy = − 686 kcal/mol of glucose Free energy can be even higher thanthis in a cell This large amount of energy must be released in small steps rather than all at once. Needs oxygen, which wasn't available, Needs sugars which hadn't been made

Answer 12

1. Anaerobic respiration | 2. Fermentation

Answer 13

Anaerobic respiration Use of inorganic molecules (other than O2) as final electron acceptor. Many prokaryotes use sulfur, nitrate, carbon dioxide or even inorganic metals. Fermentation Use of organic molecules as final electron acceptor (but these weren’t readily available early on).

Answer 14

Sulphur prokaryotes Inorganic sulphate (SO4) is reduced to hydrogen sulphide (H2S). Early sulphate reducers set the stage for evolution of photosynthesis. Methanogens CO2 is reduced to CH4 (methane). (Found in diverse organisms including in cows)

Answer 15

Oxygenic photosynthesis produced atmospheric O2 200-million-year lag between the origins of photosynthesis and substantial levels of O2 O2 in the atmosphere interacted with ultraviolet (UV) radiation from the Sun and formed O3(ozone). Ozone absorbs UV, protects from damage to nucleic acids, living gets easier….

Answer 16

Stromatolites are mats of cyanobacterial cells that trap mineral deposits Indirect evidence for ancient life. Oldest are 2.7 billion years old. Modern forms are also known.

Answer 17

1.Ability to store chemical energy in ATP 2.Evolution of glycolysis Pathway found in all living organisms. 3.Anoxygenic photosynthesis (using H2S) 4.Use of H2O in photosynthesis (not H2S) Begins permanent change in Earth’s atmosphere. 5.Evolution of nitrogen fixation 6.Aerobic respiration evolved most recently

Answer 18

Prokaryotes not easily classified according to forms Early systems relied on staining characteristics and observable phenotypes 1. Photosynthetic or nonphotosynthetic 2. Motile or nonmotile 3. Unicellular, colony-forming, or filamentous 4. Formation of spores or division by transverse binary fission 5. Importance as human pathogens or not

Answer 19

Bacillus: Rod-shaped Coccus: Spherical. Spirillum: Helical-shaped

Answer 20

- Peptidoglycan forms a rigid network. - --Maintains shape. - ---Withstands hypotonic environments. - ---Archaea have a similar molecule (pseudomurein). - Gram stain. - --Gram-positive bacteria have a thicker peptidoglycan wall and stain a purple color. - --Gram-negative bacteria contain less peptidoglycan and do not retain the purple-colored dye – retain counterstain and look pink.

Answer 21

Thick, complex network of peptidoglycan. | Also contains lipoteichoic and teichoic acid

Answer 22

Thin layer of peptidoglycan. Second outer membrane with lipopolysaccharide. Resistant to many antibiotics

Answer 23

S-layer Rigid paracrystalline layer found in some bacteria and archaea. Outside of peptidoglycan or outer membrane layers in gram-negative and gram-positive bacteria. Diverse functions – often involves adhesion. Capsule Gelatinous layer found in some bacteria. Aids in attachment. Protects from the hosts immune system.

Answer 24

Based on whole genome or “barcoding” sequences, several prokaryotic groupings have been proposed: Large scale sequencing of random samples indicates vast majority of bacteria have never been cultured or studied in detail

Answer 25

``` Bacterial flagella Flagella Slender, rigid, helical structures. Composed of the protein flagellin. Involved in locomotion – spin like propeller. ``` Allows some directional movement Has a flagellum motor.

Answer 26

A proton gradient

Answer 27

``` Short, hairlike structures. Found in gram-negative bacteria. Aid in attachment to surfaces Can help gliding movement Involved in conjugation (“sex”) Important in disease? ```

Answer 28

Survival Develop a thick wall around their genome and some of the cytoplasm when exposed to environmental stress Highly resistant to environmental stress Especially heat and desiccation. When conditions improve, can germinate and return to normal cell division e.g. Bacteria causing tetanus, botulism, and anthrax

Answer 29

complex internal membranes

Answer 30

Invaginated regions of plasma membrane

Answer 31

fix nitrogen

Answer 32

Specialised cells: Heterocysts Thickened cell wall Not photosynthetic Anaerobic? ``` Some can float: Can regulate their buoyancy: Control exposure to light Gas vesicles Protein barrels ```

Answer 33

Bacteria evolve They have genetic exchange But they’re haploid No gametes, No meiosis

Answer 34

3 types of horizontal gene transfer. Transformation: from the environment. Transduction: by viruses. Conjugation: cell-to-cell contact. All 3 processes also observed in archaea

Answer 35

Natural transformation Occurs in many bacterial species. DNA that is released from a dead cell is picked up by another live cell. Proteins involved in natural transformation encoded by bacterial chromosome. Not an accident of plasmid or phage biology. Artificial transformation Some species do not naturally undergo transformation. Accomplished in the lab. Used to transform E. coli for molecular cloning.

Answer 36

Generalized transduction Virtually any gene can be transferred. Occurs via accidents in the lytic cycle. Viruses package bacterial DNA and transfer it in a subsequent infection. Specialized transduction Occurs via accidents in the lysogenic cycle. Imprecise excision of prophage DNA. These phage carry both phage genes and chromosomal genes.

Answer 37

Plasmids may encode functions not necessary to the organism, but may provide a selective advantage In E. coli, conjugation is based on the presence of the F plasmid (fertility factor) F+ cells contain the plasmid. F− cells do not.

Answer 38

F+ cell produces F pilus that connects it to F− cell Transfer of F plasmid occurs through conjugation bridge F plasmid copied through rolling circle replication The end result is two F+ cells

Answer 39

The F plasmid can integrate into the bacterial chromosome F plasmid integrated into chromosome. Replicated every time host divides. It can transfer chromosomal DNA earby as well as the F region! The F plasmid can also excise itself by reversing the integration process An inaccurate excision may occur picking up some chromosomal DNA – F′ plasmid.

Answer 40

During conjugation in Hfr strains, the transfer of genes is linear and progressive genes farther from the origin of transfer will be transferred later. Different marker genes appear in the recipient cell at specific times. Gene order can be mapped based on entry time

Answer 41

Incoming DNA might include viruses or transposons Damaging to the genome The challenge: How to recognise incoming DNA from what should be there?

Answer 42

Restriction enzymes recognise particular DNA sequences and cut there Methylate the DNA of your genome to mask these sites Incoming DNA from other strains has no methylation of the sites so gets chopped This “restricts” the host range for viruses

Answer 43

Adaptive immunity

Answer 44

Screens of prokaryotic genomes revealed repeated sequences with spacer regions called CRISPR (clustered regularly interspaced short palindromic repeats) Adaptive immunity to viral infection Prokaryotes integrate short segments of viral nucleic acid into CRISPR loci, produce RNA that degrades viral nucleic acid Useful for gene editing in the lab