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biology is
the study of life, primarily cellular life
what is life?
property that distinguishes living and dead organisms and inanimate matter, manifested in functions such as metabolism, growth, reproduction, and response to stimuli
a system in which proteins and nucleic acids interact in ways that allow the structure to grow and reproduce
how many different eukaryotic species are there on Earth?
5-10 million → 30,000 are discovered each year
how many different species of microbes are there?
1.6 million - 1 trillion
what are the characteristics of life?
display order
harness and utilize energy
reproduce
respond to stimuli
exhibit homeostasis
grow and develop
evolve
how many characteristics of life are there?
7
display order
all forms of life are arranged in highly ordered manners
the cell being the fundamental unit that exhibits all properties of life
harness and utilize energy
acquire energy from the environment and use it to maintain their highly ordered state
reproduce
ability to make more of their own kind
cells dividing into daughter cells
respond to stimuli
make adjustments to their structure, function, and behaviours in response to the changes to their external environment
exhibit homeostasis
regulate internal environment such that conditions remain relatively constant
evolve
populations of living organisms adapt over generations to their environment
grow and develop
increase their size by increasing the size and/or number of cells
the seven characteristics of life are emergent
they emerge from simpler interactions that individually would not have the emergent property
organisms are more than the sum of their parts
is a virus alive?
no
why are viruses not considered to be living?
they cannot harness energy from the environment
they lack cellular machinery and metabolism
they cannot break down chemical compounds and transform energy on their own
they require host cells in order to replicate as they take their genetic information
they do not maintain homeostasis
when was the Earth and the rest of the solar system formed?
4.6 billion years ago
when did the first prokaryotes form?
3.5 billion years ago
when did oxygen become a significant part of the atmosphere?
2.5 billion years ago
when did the first eukaryotes form?
2 billion years ago
when did animals appear?
525 million years ago
when did dinosaurs go extinct?
65 million years ago
how long have humans been around?
150,000 years
what was found on Earth when it was first formed?
hydrogen (H2)
carbon dioxide (CO2)
ammonia (NH4)
methane (CH3)
lots of water vapour
how long did it take for the Earth to cool down to temperatures to tolerate life?
500 million years
what are the biologically important macromolecules?
nucleic acids
proteins
lipids
carbohydrates
what is abiotic synthesis?
the production of organic compounds in the absence of life
if macromolecules are an absolute requirement of life, then simple forms of these molecules must have been produced early on in the absence of life
Oparin-Haldane Hypothesis
from the 1920s
organic molecules that formed the building blocks of macromolecules could have been formed abiotically given conditions of primitive Earth
reducing atmosphere that lacked oxygen favoured the formation of organic molecules
there was no ozone layer so the ultraviolet light and lightning provided energy for the formation of biologically important molecules
highly reducing conditions are good for promoting the synthesis of large and complex molecules such as organic molecules
Miller-Urey Experiment
simulated primitive Earth conditions
demonstrated that abiotic synthesis is possible
15% of the carbon in the “atmosphere” was converted to organic compounds such as amino acids, urea, lactic acid ect
added HCN (hydrogen cyanide) and CH2O (formaldehyde/methanol)
basic requirements of life
biologically important molecules and macromolecules
system for storing, replicating and passing on info
ability to capture and use energy (transform)
separate these systems and processes from surrounding environment in distinct compartments
polymers from monomers
proteins and nucleic acids are polymers that were no formed by the Miller-Urey expt
unlikely that polymers would form in aqueous environments; instead, it is thought that polymerization reactions could have occurred on solid surfaces
example: RNA molecules can be formed spontaneously from simple precursors such as hot sand, clay and rock
why could a virus be considered to be living?
they have the ability to store and transmit info
has a plasma membrane that separates living material inside the cell from the non-living environment around it
evolves over time
how does a clay surface catalyze polymerization?
the charged microscopic layered structure of clay allows for the formation of relatively short polymers of protein and nucleic acid, that would be long enough to impart a specific function
clays can also store potential energy- requiring polymerization reactions
clay consists of very thin layers of minerals separated by layers of water only a few nanometers thick
the layered structure is charged, allowing for molecular adhesion forces to bring monomers together in precise orientation that could more readily lead to polymer formation
the central dogma
the flow of information from DNA to RNA is common to all forms of life
information in DNA is used to synthesize proteins though an RNA intermediate
all organisms contain DNA
info in DNA copied onto molecules to RNA
how does the info stored in DNA direct the synthesis of proteins?
central dogma - this s the basic flow of info in a cell
RNA
specialized molecular structures within the cell then read the RNA molecule to determine which building blocks to use to create a protein process called translation
converts info stored in the language of nucleic acids to info in the language of proteins
central dogma - pathway from DNA to RNA to protein
what does each step of information flow require?
the involvement of a group of proteins called enzymes which catalyze the transcription of DNA to RNA and translation of RNA into proteins
what is the use of term “transcription”?
for the generation of ribonucleic acid (RNA) from DNA to RNA
emphasizes that DNA and RNA use the same language of nucleic acids
DNA is the template for RNA
what is the use of the term “translation”
for this step to indicate a change in the language used
from nucleic acids to amino acids
what are ribozymes?
ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction
RNA molecules that catalyze reactions
discovered by Thomas Cech and Sidney Altman
like the action of protein enzymes
can catalyze reactions on precursor RNA molecules that lead to their own synthesis, as well as on unrelated RNA molecules
increases the rate of phosphodiester bond cleavage and peptide bond synthesis
potential conformations of ribozymes/RNA
RNA molecules are single-stranded, but not always elongated like mRNA
some RNA molecules can fold up on themselves, and in some cases, take on elaborate, complex conformations
the specific shapes they take fold into allow some of them to be able to act as catalysts
not nearly as elaborate as proteins, but dozens of different ribozymes are now known
“RNA World” Hypothesis
RNA was originally the primary substance of life
DNA eventually replaced RNA as information storage molecule and proteins mostly replaced RNA as structural and catalytic molecules
possible scenarios for evolution of flow of information
the first cells may have contained only RNA which was self replicating and catalyzed a small number of reactions for survival
some RNA molecules evolved to catalyze the production of proteins
the evolution of DNA followed next
it is hypothesized that a small population of RNA molecules then evolved that could catalyze the formation of very short proteins before the development of ribosomes
in contemporary organisms, ribosomes are required for protein synthesis
cell that evolved the ability to use the information present in RNA to direct the synthesis of even small proteins would be a tremendous advantage bc proteins are more versatile than RNA
why are proteins more dominant structural and functional macromolecules of all cells?
greater diversity
much higher rate of catalysis than ribozymes
proteins are evolutionarily advantageous compared to RNA
aa of proteins interact chemically with each other in bonding arrangements which is not possible between nucleotides
why is DNA better than RNA as a repository of genetic information?
DNA is double stranded and more stable than RNA and evolved better
there are still many ribozymes that are relevant like crispr cas 9
the evolution of biological energy sources
Life requires energy
The earliest forms of life may have derived energy from geochemical activity at hydrothermal vents in ocean floor
Sources of energy in the vent environment:
H+ concentration gradient is used to produce ATP by ATP synthase
Oxidation-reduction reactions
today, how does Earth derive all energy?
from photons coming from the sun,
redox reactions
REDOX reactions-evolution of energy releasing electron transfer reactions in the earliest cells (protobionts).
The fact that electron transfer systems are such common and indispensable mechanisms for releasing energy in living things today may be a relic of the evolution of life in an alkaline vent chemical environment.
what are organic molecules?
complex molecules that contain the element carbon bonded with other elements
Carbon is a versatile element that can form bonds with hydrogen, oxygen, and nitrogen, or other carbon atoms, to form huge carbon chains.
Some small C-containing molecules such as CaCO3 (mineral) and CO2 (gas) are inorganic
inorganic molecules
do not contain carbon
evolution of metabolism
metabolic processes today catalyzed by enzymes
they speed up rxns that can also take place on their own and are reversible
Can work in forward (oxidative) and reverse (reductive) modes
krebs cycle / Citric Acid Cycle is a fundamental metabolic pathway; one of the simplest set of metabolic reactions
Experiments suggest that before enzymes evolved, reactions in the citric acid cycle could have been catalyzed by iron–sulfur (Fe–S) clusters, an abundant output product of alkaline hydrothermal vents.
the first cells
Honeycombed, microscopic pores of hydrothermal vent chimneys provide a model for the evolution of early cells.
Suggestion that earliest cell membranes were an inorganic casing composed of metal sulfides (NiS, FeS)
Would trap and concentrate organic molecules and allow complex chemical reactions
An environment conducive to an early metabolic process mimicking the reverse citric acid cycle
the first cells
Lipids form liposomes (vesicles) spontaneously in aqueous environment
Abiotically produced organic molecules trapped by a lipid membrane or membrane-like structure would form cell-like structure
May have been precursors of cells
Membrane-defined compartment
Defined space, protected from external environment, for metabolic reactions to take place
Explain which properties of protobionts are associated with life.
ANSWER: Their lipid bilayer membrane is selectively permeable. They undergo osmotic swelling/shrinking when placed in solutions of different solute concentrations. Some store energy as a membrane potential—a voltage across the surface—and some maintain simple reproduction. Furthermore, if enzymes are included in the solution from which the droplets self-assemble, some protobionts can carry out simple metabolism.
the tree of life fifty years ago
All life was divided into two groups: eukaryotes and prokaryotes
Eukaryotes—animals, plants, fungi
•Organisms with cells that contain a nucleus and membrane-bound organelles (single-celled or multicellular)
Prokaryotes—bacteria
•Single-celled organisms of metabolic simplicity without a nucleus or membrane-bound organelles
the tree of life updated
For centuries, organisms had been grouped based primarily on how they looked (morphology).
A more objective approach to building phylogenetic trees was proposed: Use differences in DNA sequences.
Need to pick a gene that all organisms have
Gene needs to be relatively long in sequence
Basically, if there aren’t many DNA sequence differences between two species, they’re probably closely related and likely diverged somewhat recently.
Carl Woese suggested using ribosomal RNA (rRNA) genes to investigate organismal differences and develop a more accurate tree of life.
His research team showed that life could be grouped into three domains:
Bacteria
Archaea
Eukarya
the three domains in the tree of life
rRNA sequence comparisons suggest that Bacteria, Archaea, and Eukarya are three domains of living organisms, and that Eukarya are more closely related to Archaea than Bacteria.
Despite of the morphological similarities of the bacteria and archaea, molecular evidence tells us that the eukarya and archaea are more closely related
The three-domain tree of life showed that there were actually two major groups of organisms with prokaryotic cell structures: Bacteria and Archaea
impact of the three-domain tree of life
showed the power of molecular data
allowed the classification of microbes
showed that archaeans are more closely related to eukaryotes than to bacteria
which domain tree is correct?
Since it was first published, the three-domain tree has been well supported by many studies.
In 2010, DNA sequencing of sediment samples from the Arctic Ocean led to the discovery of a new group of archaeans referred to as Asgard.
Asgard archaeans contain genes previously thought to be present only in eukaryotes
Analysis of Asgard DNA suggests that the three-domain tree of life may be incorrect.
Eukaryotes may not have had an independent origin as the three-domain tree suggests.
•May have evolved from within the Archaea.
Growing expectation that the two domains of life (Bacteria and Archaea) view will be most widely accepted in future.
what is LUCA
last universal common ancestor
A common ancestor from which all present-day organisms are descended
likely features of LUCA
Lived in the absence of O2 (anaerobic)
Fixed CO2 into organic molecules (autotrophic!)
Possessed a metabolic pathway similar to reverse citric acid cycle
Depended on H2 as its source of H+ and electrons
Converted N2 into ammonia
Lived in hot environments
Biochemistry depended on FeS
where did the oxygen come from in oxygenation of the atmosphere?
cyanobacteria
evolved ability to oxidize water instead of H2S (hydrogen sulfide) or FE2+ as the source of electrons for photosynthesis
explosion of cynobacterial growth turned the planet green
oxygenation lead to aerobic respiration
theory of endosymbiosis
2 bya
Energy-transducing organelles, chloroplasts and mitochondria, thought to have been derived from free-living prokaryotic cells
Mitochondria developed from ingested prokaryotes capable of using oxygen for aerobic respiration
Chloroplasts developed from ingested photosynthetic prokaryote
Prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells, in a symbiotic relationship
The theory of endosymbiosis suggests that mitochondria and chloroplasts evolved from ingested prokaryotic cells
All eukaryotic cells contain mitochondria, whereas only plants and algae contain both mitochondria and chloroplasts.
Endosymbiosis therefore occurred in stages, with the evolution of mitochondria occurring first.
evidence supporting prokaryotic origin of mitochondria and chloroplasts
Morphology—size and shape are similar to that of prokaryotic cells
Reproduction—divide by binary fission in the same way as prokaryotic cells
Genetic information—contain their own DNA with genes essential for organelle function
Transcription and translation—contain complete separate set of transcription and translational machinery
Electron transport—like prokaryotic cells, mitochondria and chloroplasts have electron transport chains
DNA sequence analysis—has shown that these organelles belong on the bacterial branch of the tree of life
rRNA
what describes the emerging thinking about the tree of life?
there are two domains of life: bacteria and archaea
what describes LUCA the best
LUCA is thought to have lived without O2 and to have been autotrphic by fixing CO2 into organic molecules by using a pathway similar to a reverse krebs cycle
the endomembrane system
another characteristic feature of eukaryotic cells
When thinking abt other structures in eukaryotic cells, you can thinks of things in the endomembrane system which contains everything but chloroplast and mitochondria
Collection of internal membranes dividing the cell into structurally and functionally distinct regions
These regions include the nuclear envelope, the endoplasmic reticulum (ER), and the Golgi complex
All inter-connected via vesicular trafficking pathway Proteins and lipids are moving thru these vesicles (interconnected)
horizontal gene transfer
genetic inheritance between unrelated species
more common than you think
critical for endosymbiosis
Some protein-coding genes once located in the chloroplast or mitochondrial genomes relocated to the nuclear genome.
Following transcription of these genes, translation occurs in the cytosol before proteins are imported into the mitochondrion or chloroplast.
vertical gene transfer
genetic inheritance from one generation to the next within a species
horizontal gene transfer and the tree of life
A tree of life incorporating the endosymbiotic events from Bacteria to Eukarya.
While the host eukaryotic cell and the nuclear genome are directly descended from the Archaea, the energy-transducing organelles the mitochondria and chloroplast are descended from free-living bacteria.
THERE ARE TWO DOMAINS OF LIFE
two major characteristics that distinguish eukaryotic cells form prokaryotic cells
the separation of DNA and cytoplasm by a nuclear envelope
the presence in the cytoplasm of membrane bound organelles with specialized functions: mitochondria, chloroplasts, the endoplasmic reticulum (ER) and the Golgi complex, among others
rise of eukaryotes is linked to increasing oxygen levels
a type of sedimentary rock called banded iron is dated to determine when oxygen levels in the atmosphere started increasing
evolution of multicellular eukaryotes
led to increased speciation
multicellularity in the species of algae appears in the fossil record starting about 1.2 bya
all cells are structurally and functionally autonomous
some cells specialized in harvesting energy whereas some are related to motility of the organism
Multicellular organisms contain cells that are structurally and functionally distinct
Multicellular eukaryotes probably evolved by differentiation of cells of the same species that congregated into colonies.
Colonies gave rise to division of labour leading to structural and functional distinction among cells.
what is a cell colony
unlike a true multicellular organism, a cell colony is a group of cells that are all of one type
there is no specialization in cell structure or function
the fossil record is incomplete
only provides direct evidence abt what life was life millions of years ago
tells us abt size and appearance of ancient animals and plants
only reps a small record of the most successful of organisms
soft bodied organisms with small geo distributions are underrepresent in fossil record
fossils for when organisms are buried by sediments of preserved in oxygen poor environments
most fossils form in sedimentary rocks
particles of sedimentary rock forming layers are called strata
fossils usually preserve details of hard structures
bones
teeth
shells of animals
wood
leaves
pollen of plants
solving an energy crisis
Ability of early eukaryotes to generate more energy led to remarkable changes—cells could become larger and more complex
Eukaryotes contain several mitochondria, each converting energy into ATP
A wider variety of genes could be supported that led to eukaryotic-specific traits: the cell cycle, sexual reproduction, phagocytosis, endomembrane trafficking, the nucleus, and multicellularity
Increase in complexity comes about by being able to support a larger genome that codes for a greater number of proteins
Relative and Absolute Fossil Dating
Relative ages of fossils are determined by the sedimentary stratum within which they are found.
Absolute fossil ages are determined using radiometric dating, which determines how much of an unstable parent isotope has decayed to form another.
common attributes for all forms of cellular life
1.Lipid molecules form a membrane bilayer that defines the cell
2.A genetic system based on DNA
3.A system of information transfer: DNA to RNA to protein
4.A system of protein assembly using messenger RNA and transfer RNA using ribosomes to polymerize the amino acids into peptides
5.Reliance on proteins as the major structural and catalytic molecule
6.Use of ATP as the molecule of chemical energy
7.The breakdown of glucose by the metabolic pathway of glycolysis to generate ATP (chemiosmosis, substrate-level phosphorylation)
cell theory
By the mid-19th century, microscopic observations had yielded three generalizations, which constitute the cell theory
All organisms are composed of one or more cells
The cell is the basic structural and functional unit of all living organisms
Cells arise only from the division of preexisting cells.
many kinds of cells
Unicellular organisms carry out all activities necessary for life
In multicellular organisms, the activities of life are divided among numerous types of specialized cells
Cells assume a wide variety of forms in different prokaryotes and eukaryotes
size of cells
Most cells are too small to be seen by the unaided eye—ranging from about 0.5 μm (bacteria) to a few hundred micrometres (plant cells)
To see cells and the structures within them we use two types of microscopes
Light microscopes use light to illuminate the specimen
Electron microscopes use electrons to illuminate the specimen
why are cells so small
Cell size is limited by surface area-to-volume ratio
doubling diameter of cell increases its surface area by four times and increases volume by 8 times
The volume of a cell determines the amount of chemical activity that can take place within the cell.
Surface area determines the amount of substances that can be exchanged between a cell and the outside environment
the plasma membrane
All cells are surrounded by the plasma membrane, a bilayer made of lipids with embedded protein molecules
The lipid bilayer is a hydrophobic barrier to water-soluble substances
Selected water-soluble substances can penetrate cell membranes through transport protein channels
Selective transport of ions and water-soluble molecules maintain the specialized internal environments required for cellular life
Water-soluble substances cannot pass through the phospholipid part of the membrane. Instead, they pass through protein channels in the membrane; two proteins that transport substances across the membrane are shown. Other types of proteins are also associated with the plasma membrane. (Inset) Electron micrograph showing the plasma membranes of two adjacent animal cells.
internal organization
DNA molecules are concentrated in a central area of all cells; DNA stores hereditary information (genes)
Genes are segments of DNA that code for individual proteins
The cytoplasm (between the plasma membrane and the central region) corresponds to the cytosol and cytoskeleton
Cytosol is an aqueous solution containing ions, various organic molecules, and organelles
The cytoskeleton maintains cell shape and plays key roles in cell division, chromosome segregation, and transportation within the cell
prokaryotic cell
nucleoid region has no boundary membrane
many bacteria and archaea sepcies contain few of any internal membranes
Three shapes are common among bacterial prokaryotes: spherical, rodlike, and spiral
For most species, the DNA (located in the nucleoid) is a single, circular molecule (the prokaryotic chromosome)
Information from DNA is copied into messenger RNA (mRNA) molecules and carried to ribosomes in the cytoplasm, which assemble amino acids into proteins
Prokaryotic cytoskeletons maintain cell shape and also function in cell division
Many bacteria and archaeans move using long flagella—the bacterial flagellum rotates in a socket and pushes the cell through a liquid medium
Hairlike pili attach the cell to surfaces or other cells—a special sex pilus joins bacteria during mating
The plasma membrane is typically surrounded by a rigid external cell wall coated with polysaccharides (glycocalyx)
When the glycocalyx is loosely associated with the cells, it is a slime layer; when it is firmly attached, it is a capsule (as in previous figure)
The plasma membrane contains molecular systems that metabolize food molecules (or light energy) into the chemical energy of ATP
eukaryotes
have a membrane bound compartment called the nucleus
cytoplasm typically contains extensive membrane systems that form organelles
golgi complex and exocytosis
The Golgi complex “sorts” proteins to ensure they are delivered to their final destination
the golgi sorts proteins to make sure they get to their lysosome or plasma membrane
proteins that are leaving the cell move through this pathway
Proteins to be secreted from the cell are transported to the plasma membrane in secretory vesicles, which release their contents to the exterior by exocytosis
there is an aq protein that is meant to be secreted
the membrane of the vesicle fuses with the membrane of the plasma membrane
membrane proteins of plasma membranes get there the same way
The membrane of the vesicle fuses with the plasma membrane and becomes part of the plasma membrane
endocytosis
Vesicles also form by the reverse process, endocytosis, which brings molecules into the cell from the exterior
The plasma membrane forms a pocket, which bulges inward and pinches off into the cytoplasm as an endocytic vesicle
Endocytic vesicles carry materials to the Golgi complex or other destinations such as lysosomes
lysosomes
Lysosomes are small, membrane-bound compartments containing hydrolytic enzymes that digest complex molecules
Cells recycle the constituents of these molecules
Lysosomes are found in animals and plants
Lysosomes are formed by budding from the Golgi complex; their hydrolytic enzymes are synthesized in the rough ER
The pH within lysosomes is acidic (pH = 5), significantly lower than the pH of the cytosol (pH = 7.2)
Lysosomal enzymes digest food molecules, worn out organelles (autophagy), and materials engulfed by phagocytes (cells of the immune system)
In lysosomal storage diseases, one of the hydrolytic enzymes normally found in the lysosome is absent
mitochondria
membrane bound organelles in which cellular respiration occurs
two membranes - outer and inner
outer covers
inner is expanded by folds called cristae
more SA important bc more capacity for CR
cellular respiration
the process by which energy rich food molecules are broken down to water and CO2 by mitochondrial reactions, and energy is converted to ATP
mito require oxygen for CR
breathing in animals
the cytoskeleton
The cytoskeleton is an interconnected system of protein fibres and tubes that extends throughout the cytoplasm
The cytoskeleton maintains a cell’s characteristic shape and internal organization, and functions in movement
The cytoskeleton of animal cells is comprised of microtubules, intermediate filaments, and microfilaments
microtubules
Outer diameter of 25 nm
Microtubules are assembled from dimers of α- and β-tubulin proteins
Dimers are organized head-to-tail in each filament, giving the microtubule polarity (+ and – ends)
Microtubules are dynamic structures, changing their lengths by the addition or removal of tubulin dimers
Centrosome (or cell centre) serves as MTOC in many animal cells
Organizes microtubule arrays that are involved in various processes
mitosis, holding organelles in position, and others
Centrosomes are comprised of two short, barrel-shaped structures also formed from microtubules called centrioles
Microtubules provide tracks along which vesicles move between the cell interior and the plasma membrane
Microtubules separate and move chromosomes during cell division (mitosis), and are involved in moving some eukaryotic cells themselves
motor proteins
Eukaryotic cell movements are generated by “motor” proteins that push or pull against microtubules (dyneins and kinesins) or microfilaments (myosins)
One end of a motor protein is fixed to a cell structure such as a vesicle
The other end has reactive groups that “walk” along a microtubule or microfilament, using ATP for energy
Intermediate Filaments
•Intermediate filaments are intermediate in size between microtubules and microfilaments (8-12 nm)
•Assembled from a large and varied group of intermediate filament proteins
•Intermediate filaments occur singly, in parallel bundles, and in interlinked networks
•Provides structural support in many cells and tissues, and are tissue-specific in their protein composition
Microfilaments
•Microfilaments are thin (5-7 nm diameter) protein fibres assembled from actin subunits
•Microfilaments have polarity (+ and – ends)
•Microfilaments have many structural and locomotor functions:
•Components of contractile elements in muscle fibres
•Involved in cytoplasmic streaming, which transports nutrients, proteins, and organelles in animal and plant cells, and is responsible for amoeboid movement
•Divide the cytoplasm when animal cells divide
Flagella and Cilia
•Flagella and cilia are elongated, motile structures that extend from the cell surface
•
•Cilia are shorter than flagella and occur in greater numbers
•
•Movements of a flagellum propel a cell through a watery medium, and cilia move fluids over the cell surface
Eukaryotic Flagellum
The relationship between the microtubules and the basal body of a flagellum. (b) Diagram of a flagellum in cross-section, showing the 9 + 2 system of microtubules. The spokes and connecting links hold the system together. (c) Electron micrograph of a flagellum in cross-section. Individual tubulin molecules are visible in the microtubule walls.