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The Origins of Life and Organic Evolution

04/15/2013

A brief history of the earth


Formed 4.6 billion years ago
Formed life: 3.8 billion years ago
Why was there no life during the gap?
How did life start?
The primitive Earth (pre-life)
Strongly reducing (oxygen-less) atmosphere
o Common gases: methane, hydrogen, carbon dioxide, ammonia, etc.
Energy: Volcanic eruptions, storms, lightning charges
o Temperature increased similar to global warming
Oceanic world
These, along with sufficient time, provided the requirements for chemical
evolution
First stirrings of life
Oporin-Haldane (Prebiotic/Primordial Soup) Hypothesis
Reducing gases + heat and electricity = organic molecules (amino acids, sugars,
fatty acids, etc.)
Molecules settled in the water or on rock or clay surfaces
What is/are the evidence/s for this?
Alternative: Iron-Sulfur World Hypothesis: organic molecules produced at
hydrothermal vents (deep parts of the ocean)

Chemical evolution
Prebiotic soup hypothesis
o Organic molecules formed near Earths surface in sea of organic soup or
on rock or day surfaces
Iron-Sulfur world hypothesis
o Organic molecules produced at hydrothermal vents in deep ocean floor
The Miller and Urey experiment
H2O, NH3, H2, CH4 in the spark chamber
Organic molecules are produced
Not quite living yet
Organic molecules are precursors of life, but
they lacked a replication machinery and evolutionary tendencies
Macromolecules: produced through polymerization
o Example of a polymer: carbohydrates (sugars), nucleic acids (DNA and
RNA), proteins (coming from amino acids), triglycerides (fatty acids and
glycerols)
Protobionts (Proto-cells): formed from macromolecules; began to use enzymes
for replication, transcription, and translation
But how can have proteins been first produced without a protein enzyme?
Primary enzyme: RNA
Summary of origin of cells
The origin of cells
o Macromolecules
Assembled from small organic molecules
o Protobionts (macromolecules assemblages)
Formed from macromolecules
o Cells
Arose from protobionts
Microspheres produced by adding water to abiotically formed polypeptides
Natural Selection at the Molecular Level
Survival of the fittest
Charles Darwin

Natural Selection at the Molecular Level


Molecular level
o Organic molecules
o RNA molecules for protein synthesis
The first living forms
Primary heterotrophs (prokaryotes)

o Heterotrophic: does not produce its own food; depend on other molecules
o Autotrophic: can produce own food (ex. Plants)
Evolution of ability to produce own food (photosynthesis) autotrophs
o Autotrophs release oxygen
Contribution of autotrophs: oxygen in the atmosphere
o CO2 + H2O C6 H12 O6 + O2 + H2O
Did all organisms utilize oxygen?
o Yes
o For aerobic respiration
What cells undergo aerobic respiration (in organisms)?
o Needs C6 H12 O6 + O2 CO2 +H2O + ATP
o Only living cells undergo aerobic respiration (not nails, for when cut, the
person cannot feel a thing; hair strands, for when pulled, they are released
from its root)

The rise of eukaryotes (2.2 billion years ago)


Eukaryotes: organisms with cells equipped with organelles and a membranebound nucleus
Serial Endosymbiosis Theory
What is/are the evidence/s for this?
The Endosymbiotic Theory
First proposed by Lynn Margulis and others
Suggests that double-membrane bound organelles such as mitochondria and
chloroplasts evolved from a symbiotic relationship between a bacterium (the
endosymbiont) and a host cell

Serial Endosymbiosis
Material is suspended in the cytoplasm
Endocytosis
o This process will allow the particles outside the cell to enter into the cell
o The bacteria will be allowed to enter the cell
Aerobic bacteria will become a mitochondria, after undergoing aerobic respiration
o 1) The aerobic bacteria will enter into a prokaryotic host cell (with DNA
inside); multiple invaginations of the plasma membrane
o 2) Aerobic bacteria become mitochondria; endoplasmic reticulum and
nuclear envelope form from the plasma membrane invaginations (not part
of the serial endosymbiosis)
o 3) Prokaryotic bacteria become chloroplasts
o 4) Eukaryotic cells plants some protists
Any evidence?
Both mitochondria and chloroplasts have their own DNA and ribosomes
The outer membranes of these organelles originated from invaginations of the
host cells plasma membrane
A look through evolutionary history
Ediacaran Period
600-542 million years ago
Key trend: multicellularity
Dominant: small-bodies invertebrates

The Paleozoic Era


Started at around 542 million years ago
Origin of many plants and animals
o All major plants (except flowering plants)
o All animal phyla
o Reptiles, fishes and amphibians
Devonian Period
Primitive jawless fishes
o Pterapsis
o Theolodus
o Jamoytius
Carboniferous Period
There were already plants during this period
Formation of other plants that served as a source of carbon and coal
Greatest mass extinction of all time:
Permian Period (end of Paleozoic era; 251 million years ago)
90% of marine species

70 % of land-dwelling vertebrate genera


Many plant species
Caused by competition, and limited resources

The Mesozioc Era


Started around 251 million years ago
Domination of dinosaurs, diversification of reptiles
Flourishing of insects
Appearance of flowering plants, birds, and early mammals
Triassic Period -Ichthyosaurs
The Cretaceous Period
66 million years ago (end of Cretaceous period): many species abruptly became
extinct
Collision of extraterrestrial body with Earth
The Cenozoic Era
From 66 million years ago to present
Diversification of plants, insects, birds, mammals
Late Miocene and Early Pliocene epochs: human ancestors appeared in Africa

Parts of the cell


Prokaryote
o Cell wall
o Cell membrane
o DNA
o Cytoplasm with ribosomes
Eukaryote
o Golgi apparatus
o Nucleolus
o Lysosome
o Nucleus
o Endoplasmic reticulum
o Mitochondrion
o Cell membrane
Cell Theory and the Evolution of Life
1. Cells are basic units of organization and function in all living organisms
2. All cells come from other cells
Basic Parts of Eukaryotic Cells
Plasma membrane
Cytoplasm
Nucleus
Plasma Membrane
Surrounds the cell
Movement Across Membranes
Simple diffusion transfer of molecules from one region to another region (ex.
Spraying of perfume)
Facilitated diffusion there is a protein molecule that serves as a carrier
Osmosis
Filtration
Active transport
Endocytosis
Exocytosis

Plasma membrane
Surrounds the cell
Separates cell from external environment
Maintains internal conditions
Allows the cell to exchange materials with outer environment

Movement Across Membranes


Simple Diffusion (ex. oxygen entering into the lungs and going into the red blood
cells)
Facilitated Diffusion
Osmosis (ex. The large intestine absorbs the nutrients from food)
Filtration (ex. Observed in the urinary system)
Active transport
Endocytosis (ex. The white bloods cells engulf pathogens)
Exocytosis
Examples in the Body of an Animal
Inhalation of air containing oxygen, which moves into the lings and then diffuse
into the bloodstream (SD)
Glucose in the gut combines with carrier proteins to pass through the gut cells
into the bloodstream (FD)
Water molecules move into a red blood cell when the concentration of water
molecules outside the blood cells is greater that it is inside (Osmosis)
Blood pressure forces water and dissolved wastes into the kidney tubules during
urine formation (Filtration)
Sodium ions move from inside the neurons of the sciatic nerve (the sodiumpotassium pump) to the outside of the neurons (AT)
Endocytosis
The kidney cells take in fluid to maintain fluid balance (Pinocytosis)
The white blood cells engulf and digest harmful bacteria (Phagocytosis)
The intestinal cells take up large molecules from the inside of the gut (Receptormediated endocytosis)

Exocytosis
The sciatic nerve releases a chemical (neurotransmitters)
Prokaryotes
Prokaryotic cells
o No internal membrane organization
o Nuclear area (not nucleus)
o Cell wall
o Ribosomes
o Flagellum and cilia
Cells arise only from preexisting cells
All cells come from cells
At the heart of the reproduction of cells and organisms is cell division
Cell Division
1. Mitosis division that results to 2 daughter cells
2. Meiosis division of reproductive cells (legamines: egg cells and sperm cells)
Two Main Roles of Cell Division

1. Makes the development of fertilized egg to embryo and to an adult organism


possible
2. Ensures the continuity of life from generation to generation (basis of asexual
and sexual reproduction)

Division Mechanisms
Eukaryotic organisms
o Mitosis
o Meiosis
Prokaryotic organisms
o Binary fission
Roles of Mitosis
Multicellular organisms
o Growth for healing and fast recovery
o Cell replacement
Some protistans, fungi, plants, animals
o Asexual reproduction
Division of cells
Before a cell starts dividing, the chromosomes are duplicated
o This process produces sister chromatids
Nuclear DNA
One chromosome (one dispersed DNA molecule + proteins; not duplicated)
Interphase

Seatwork/Homework
1. What is a nucleosome?
2. What is a kinetochore?
3. Differentiate a bacterial DNA from Eukaryote DNA
4. What is the function of scaffolding proteins?
5. Describe some ways in which the cell cycle is controlled
Nucleosome
A structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled
around a come of histones
Kinetochore
Another term for Centromere
The point on a chromosome by which it is attached to a spindle fiber during cell
division
The cell cycle multiplies cells
The cell cycle consists of 2 major phases:
o Interphase, where chromosomes duplicate and cell parts are made
o Mitotic phase, cell division occurs
Cytokinesis
The pinching to produce the daughter cells
Interphase
Usually the longest part of the cycle
Cell increases in mass
Number of cytoplasmic components doubles
DNA is duplicated/replicated
Mitotic Phase
1. Mitosis (period of nuclear division)
o In mitosis, the duplicated chromosomes are distributed into 2 daughter
nuclei
2. Cytokinesis (cytoplasmic membrane)
Prophase (Early)
Duplicated chromosomes begin to condense
Anaphase
Sister chromatids of each chromosome are pulled apart

Once separated

Results of Mitosis

Two daughter nuclei


Each with the same chromosome number as parent cell
Chromosomes in unduplicated form

2n = diploid 6
n = haploid 3
Cytokinesis
Division of cytoplasm
Usually occurs along with telophase
In animals cytokinesis occurs by cleavage
o This process pinches the cells in two
Most animal cells divide only when stimulated, and others not at all
Some cells normally stop in interphase
Neurons in human brain
Arrested cells do not divide
Adverse conditions can stop cycle
Nutrient-deprived amoebas get stuck in interphase

Connection: Growing out of control, cancer cells produce malignant tumors


Cancer involves a loss of control over the cycle, malfunction of the brakes
They divide excessively and can form abnormal masses called tumors
Radiation and chemotherapy are effective as cancer treatments because they
interfere with cell division
Cell Cycle Control
Cyclin-dependent kinases (Cdks)
o Protein kinases that control cell cycle
o Active only when bound to cyclins
Cyclins
o Regulatory proteins
o Levels fluctuate during cell cycle
Cylins
1. Cyclin is synthesized and accumulates
2. Cdk associates with cyclin forming a cyclin-Cdk complex, M-Cdk
3. M-Cdk phosphorylates proteins, activating those that facilitate mitosis and
inactivating those that inhibit mitosis
4. An activated enzyme complex recognizes a specific amino acid sequence in
cyclin and targets it for destruction
Key Concepts
An internal genetic program interacts with external signals to regulate the cell
cycle

Asexual Reproduction
Single parent
o Offspring have identical hereditary traits
Mitosis
o Basis for eukaryotic asexual reproduction
From 1 prokaryotic cell to 2 identical prokaryotic cells
1. DNA replication begins at single site on bacterial DNA.
2. Replication continues, as replication enzymes work in both directions from site
where replication began.
3. Replication is completed. Cell begins to divide, as plasma membrane grows
inward.
4. Binary fission is complete. Two identical prokaryotic cells result.
Mitosis
P4
M4
A4
T4
Impacts, Issues: Why Sex
Asexual reproduction is easier and faster

Sexual reproduction can be an alternative adaptation in changing environments

Sexual Reproduction
Involves
o Meiosis
o Gamete production
o Fertilization
The Human Life Cycle
Haploid gametes (n=23)
Animal Life Cycle
At

fertilization, a sperm fuses with an egg, forming a diploid zygote


Repeated mitotic divisions lead to the development of a mature adult
The adult makes haploid gametes by meiosis
All of these processes make up the sexual life cycle of organisms

Chromosomes are matched in homologous pairs

A body cell (somatic cell) has two of each chromosome


Homologous pairs carry genes controlling the same inherited characteristics

One chromosome in each pair from the mother, other from the father

Meiosis
Meiosis reduces the chromosome number from diploid to haploid
Meiosis, like mitosis, is preceded by chromosome duplication
Meiosis: Two Divisions
Two consecutive nuclear divisions
o Meiosis I
o Meiosis 2
DNA is not duplicated between divisions
o 4 haploid daughter cells
Meiosis I Stages
Prophase I
Metaphase I
Anaphase I
Telophase I
Crossing-over
Tetrad
Synapse

Prophase I
Each duplicated chromosome pairs with homologue
Metaphase I
The spindle is fully formed
Chromosomes are pushed to the center
4 chromosomes
Anaphase I
Homologous chromosomes segregate
Telophase II
4 daughter cells
Gamete Formation
Gametes are sex cells (sperm, eggs)
Arise from germ cells
Formation of Egg
1. Oogonium (diploid) Growth
2. Primary oocyte (diploid) Meiosis I, cytoplasmic division
3. Secondary oocyte (haploid) Meiosis II, cytoplasmic division
4. Ovum (haploid) Meiosis II, cytoplasmic division
5. Egg cell
Formation of Sperm
1. Spermatogonium (diploid) Growth
2. Primary spermatocyte (diploid) Meiosis I, cytoplasmic division
3. Secondary spermatocytes (haploid) Meiosis II, cytoplasmic division
4. Spermatids (haploid) Meiosis II, cytoplasmic division
5. Sperm (mature, haploid male gametes)
Mitosis end with 4 daughter cells
Meiosis end with 2 daughter cells

Protein Synthesis
Ribosomes
Nucleus
Nucleolus
Cytoplasm
Endoplasmic Reticulum
AA
o Codon

Anticodon

RNA
rRNA
tRNA
mRNA
Results of Mitosis and Meiosis
Mitosis
o Two diploid cells produced
o Each identical to parent
Meiosis
o Four haploid cells produced
o Differ from parent and one another
o Daughter cells will be haploid in Meiosis
o Four cells produced by a woman but only one is viable, the other 3 are
called Polar bodies
Mitosis and Meiosis Compared
Mitosis
o Functions
Asexual reproduction

Growth, repair
o Occurs in somatic cells (body cells)
o Produces clones
Meiosis
o Function
Sexual reproduction
o Occurs in germ cells
o Produces variable offspring

Factors Contributing to Variation among Offspring


Crossing over during prophase I
Random alignment of chromosomes at metaphase I
Random combination of gametes at fertilization
Effect of Crossing Over
After crossing over, each chromosome contains both maternal and paternal
segments
Creates new genetic combinations in offspring
Random Alignment
Either the maternal or paternal member of a homologous pair can end up at
either pole
The chromosomes in a gamete are mix of chromosomes from the 2 parents
Possible Chromosome Combinations
As a result of random alignment, the number of possible combinations of
chromosomes in a gamete is: 2n (n is the number of chromosome types)
Fertilization
Which two gametes unite in random
o Adds to variation among offspring
Accidents during meiosis can alter chromosome number
Abnormal chromosome count is a result of nondisjunction
o Either homologous pairs fail to separate during meiosis I
Sister chromatids would not separate during Meiosis I
Results to 2 n-1s (number of chromosomes) instead of 2 n+1s
o Egg cell (n=23); Sperm cell (n=23): Fertilization; Zygote =(2n) 46
Fertilization after nondisjunction in the mother results in a zygote with an extra
chromosome
Connection: An extra copy of chromosome 21 causes Down syndrome
This karyotype shows 3 number 21 chromosomes
An extra copy of chromosomes 21 causes Down syndrome (trisomy 21)
The chance of having a Down syndrome child goes up with maternal age
Connection: Abnormal number of sex chromosomes do not usually affect survival
Nondisjunction can also produce gametes with extra of missing chromosomes
Abnormalities of Sex Chromosomes Number in Humans

Sex Chromosomes

Syndrome

XXY

Klinefelter syndrome
(male)
None (normal male)

XYY

Origin of
Nondisjunction
Meiosis in egg or
sperm formation
Meiosis in sperm
formation

Frequecy on
Population
1/2000
1/2000

A man with Klinefelter syndrome has an extra x chromosome


A woman with Turner syndrome lacks a x chromosome
Karyotype
Number and kinds of chromosomes present in the nucleus of an individual
o Enables researchers to identify various chromosome abnormalities
Key Concepts
Karyotype analysis helps detect chromosome abnormalities
Duplication
A duplication is a gene sequence that is repeated more than once
ABC EFEFGHI

Deletion
A deletion is the loss of a portion of chromosome material. May occur at one end
of the chromosome (a terminal deletion), or in the middle (interstitial deletion)
ABC -DEF
Inversion
An inversion is a segment of a chromosome that has been separated from the
chromosome and then replaced in the same location, but in reverse
ABC - DGFEH
Translocation
Translocation occurs when a broken piece from a chromosome attaches to
another chromosome
Most commonly, 2 chromosomes, exchange fragments
ABC DNOP and JKL -MEFG
Part of 1 chromosome becomes attached to another chromosome
o In Down syndrome, part of chromosome 21 may be attached to
chromosome 14
How Cells make ATP: Energy-Releasing Pathways
In aerobic respiration, which reactant is oxidized and which is reduced?
C6H12O6 + 6O2 6CO2 + 6H2O + energy
Aerobic Respiration
A catabolic process

o Fuel (glucose) broken down to carbon dioxide and water


Redox reactions
o Transfer electrons from glucose (oxidized)
o To oxygen (reduced)
Energy released
o Produces 36 to 38 ATP per glucose

4 Stages of Aerobic Respiration


1. Glycolysis
2. Formation of acetyl CoA
3. Citric acid cycle
Electron transport chain and chemiosmosis
Gylcolysis
1 molecule of glucose degraded
o To 2 molecules pyruvate
2 ATP molecules (net) produced
o By substrate-level phosphorylation
4 hydrogen atoms removed
o To produce 2 NADH

Glycolysis
Occurs at the cytoplasm
Occurs outside the Mitochondria
Breaking down of 1 glucose = 2 molecules of pyruvate 2 ATP

Citric Acid Cycle


1 acetyl CoA enters cycle
o Combines with 4-C oxaloacetate
o Forms 6-C citrate
2 C enter as acetyl CoA
o 2 leave as CO2
1 acetyl CoA
o Transfers H atoms to 3 NAD+, 1 FAD
o 1 ATP produced
o
2 acetyl CoA enters the system = 2 ATP produced
The Krebs Cycle
Overall Reactants
o Acetyl-CoA
o 3 NAD+

o FAD
o ADP and Pi
Overall Products
o Coenzyme A
o 2 CO2
o 3 NADH
o FADH2
o ATP

Electron Transport Chain


H atoms (or electrons) transfer
o From one electron acceptor to another
o In mitochondrial inner membrane
Electrons reduce molecular oxygen
o Forming water
Oxidative Phosphorylation
Redox reactions in ETC are coupled to ATP synthesis through chemiosmosis
Chemiosmosis
Energy of electrons in ETC

o Pumps H+ across inner mitochondrial membrane


o Into intermembrane space
Protons (H+) accumulate in intmermembrane space
Proton Gradient
Difference in concentration
Caused by the movement of the H ions in the mitochondrion
How does the proton gradient drive ATP synthesis in chemiosmosis?
ATP Synthase
Enzyme ATP synthase
o Forms channels through inner mitochondrial membrane
Aerobic Respiration
Glycolysis occurs in the cytosol
How do the products of protein and lipid catabolism enter the same metabolic
pathway that oxidizes glucose?
Amino Acids
Undergo deamination breaks down or removes amino acids from proteins
Carbon skeletons converted to intermediates of aerobic respiration

Lipids
Glycerol and fatty acids
o Both oxidized as fuel
Fatty acids converted to acetyl CoA by -oxidation
Carbohydrates (Glycolysis, Glucose G3P Pyruvate) (Acetyl Coenzyme A)
and CO2 Citric acid cycle Electron transport chemiosmosis
PROTEINS Amino acids Pyruvate Acetyl coenzyme A
Anaerobic Respiration
Electrons transferred
o From fuel molecules to ETC
o Coupled to ATP synthesis (chemiosmosis)
Final electron acceptor
o Inorganic substance
o Nitrate or sulfate (not molecular oxygen)
Fermentation
Anaerobic process
o No ETC
Net energy gain only 2 ATP per glucose
o Produced by substrate-level phosphorylation during glycolysis
NAD+
o Produced by transferring H from NADH to organic compound from nutrient
Fermentation
1. Alcohol fermentation
o In yeast cells
o Waste products: Ethyl alcohol, CO2
2. Lactate (lactic acid) fermentation
o Some fungi, prokaryotes, animal cells
o H atoms added to pyruvate
o Waste product: lactate
o How to avoid lactate: good circulation for cells to receive oxygen
Fermentation
Is an inefficient anaerobic redox process in which glucose becomes oxidized and
an organic substance becomes reduced
Some fungi and bacteria, as well as muscle cells under conditions of low oxygen,
obtain low yield of ATP through fermentation
Coverage for LT
Origin of Life
Cells (parts and functions)
Cell division
Aerobic and Anaerobic Respiration
(Know raw materials and products, where reactions take place, and # of ATPs in
reactions)

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