Cells as the basis of life

• homeostasis

• metabolism

• growth

• reproduction

• response

• nutrition

• excretion

• movement

the maintenance of constant internal conditions (e.g. temperature, water concentrations, solute concentrations), despite changes in their external environment

the sum of chemical reactions that take place within the cell(s) of an organism; these chemical reactions can be used to synthesize new molecules, digest food, generate energy, etc

• growth is quantified by an increase in size and mass of an organism

• development is the transformation or change in an organism as it ages

• in multicellular organisms, growth can also refer to an increase in the number of cells that make up an organism

• all life has the capability to create more life

• reproduction is either sexual or asexual

• all life can recognize and respond to changes in the external environment

• organisms will have special adaptations to detect these environmental changes

• specialized receptors can then initiate the appropriate response from the organism

• the intake or production of nutrients

• heterotrophic organisms obtain nutrients from the external environment

• autotrophic organisms are able to produce nutrients from inorganic material

• the removal of metabolic waste products

• in humans, excretion primarily occurs through the respiratory system and kidneys

• in many plants, excretion occurs via leaves, roots, and stems

• in unicellular organisms, excretion occurs through the cell membrane

• organisms can be stationary (sessile) or mobile (motile)

• all living things have some control over their place and position

• he classified organisms into species based on shared morphological (physical) characteristics

• developed a naming convention for species known as binomial nomenclature

• species are named using both their genus and species names

• the genus name comes first—and the first letter is capitalized—followed by the species name in all lowercase

• the entire name is put in italics

• for example, Homo sapiens

• domain

• kingdom

• phylum

• class

• order

• family

• genus

• species

• it consists of a series of opposing questions about an organism

• each question has only two possible answers, stating whether a feature or characteristic is present in the organism or not

• each description leads to either another pair of descriptions or an identification

• discrete (typically qualitative)

• continuous (quantitative)

• all living things are made of individual units called cells

• cells are the basic unit of life

• all cells arise from other cells

• they are not made of cells

• they cannot keep themselves in a stable state

• they do not grow

• they cannot replicate outside the host cell

• they cannot perform independent metabolism

• plasma membrane

• cytoplasm

• DNA

• ribosomes (70S in prokaryotes, 80S in eukaryotes)

• electron microscopes pass a beam of electrons through a specimen

• electrons will be absorbed by the denser parts of the sample, and scattered or able to pass through less dense areas, after which they are picked up by an electron detector and used to form an image

• because electrons have a shorter wavelength than light, electron microscopes have a much higher resolution

magnification = image size / actual size

• freeze fracture microscopy

• cryogenic electron microscopy

• immunofluorescence

• fluorescent dyes

• a technique to visualize structures of biological samples which have been frozen, and then broken into small pieces.

• this is useful to visualize structures that are not normally visible under the microscope, such as the internal plasma membrane

• a technique in which samples are frozen to cryogenic temperatures to fix the molecules to make them more firm

• this method improves resolution and reduces damage that may occur from the electron beam.

• a technique in which a fluorescent tag is attached to antibodies, which bind to antigens on a structure being viewed

• when a certain wavelength of light is shone onto the fluorescence tag, the tag will emit light of a different wavelength that can appear as brightly coloured spots, allowing the visualization of the location of target molecules

• dyes that preferentially attach to certain structures and appear as brightly coloured spots

• the labelled areas will appear as brightly coloured spots, allowing visualization of the target molecule throughout the specimen

• early Earth was subjected to bombardment by comets and asteroids, which brought water and other compounds to the planet

• methane and ammonia gases were released in these collisions and in the many volcanic eruptions that were occurring; as a result, these two gases formed the majority of the Earth’s early atmosphere

• since the early Earth’s atmosphere lacked free oxygen, there was no ozone layer present in the atmosphere.

• early Earth was compressed with gravity and experienced radioactive decay; proto-Earth was extremely molten

• increased motion within the liquid core would have resulted in a smaller protective magnetic field, which exposed the planet to much higher levels of cosmic and solar radiation

• conditions on early Earth would have created extreme weather events, including electrical storms.

• due to the lack of oxygen, and the high proportion of reducing gases, including methane and ammonia, the early Earth had a reducing atmosphere

• reducing gases in the atmosphere would have been able to donate electrons to other molecules, enabling chemical reactions to take place

• reactions resulted in the formation of more complex carbon compounds, including simple amino acids and hydrocarbons

• attempted to imitate primordial Earth conditions, as it was theorized that early Earth provided the conditions (which do not exist today) necessary for the formation of carbon compounds

• water (the “ocean”) evaporated to combine with methane, ammonia, hydrogen gases (the “prebiotic atmosphere”), and sparks (“lightning”) chemically react with the compounds

• condenser turns the steam back to water, and the new molecules formed were able to settle

• a variety of carbon compounds, including amino acids, were formed from the inorganic compounds; carbon compounds were capable of spontaneously forming on prebiotic Earth

• this experiment did not prove that carbon compounds originated in this way, only that it could have happened this way

1. formation of simple organic molecules from inorganic compounds

2. assembly of carbon compounds into polymers

3. the formation of a polymer that can self replicate

4. packaging of molecules into compartments

• cells spontaneously originated a very long time ago, which makes the evolution of cells difficult to study; evidence may become destroyed or distorted

• the very first protocells did not fossilize

• cells may have originated deep in the ocean, making it challenging to reach and collect samples for analysis

• uncertainty surrounding the exact conditions on prebiotic Earth, which means scientists cannot replicate the exact conditions that would have existed

1. RNA was formed from inorganic sources

2. RNA was able to replicate using ribozymes (RNA molecules capable of acting as catalysts and increasing the rates of chemical reactions)

3. RNA was able to catalyze protein synthesis

4. Membrane compartmentalization occurred

5. Inside the cell, RNA was able to produce both protein and DNA

6. DNA took over as the main genetic material because it is more stable due to:

   • deoxyribose makes DNA more chemically stable than chains of RNA

   • hydrogen bonds in DNA adds stability

   • use of thymine rather than uracil; thymine is less susceptible to mutation

7. Proteins took over as the catalytic form (enzymes) because they are more capable of variability

• short RNA sequences have been shown to be able to duplicate other molecules of RNA (sometimes with slight mutations), demonstrating that RNA can self-replicate

• RNA has some catalytic activity, so it may have acted initially as both the genetic material and enzymes of the earliest cells

• ribozymes in the ribosome are still used to catalyze peptide bond formation during protein synthesis

• Miller-Urey hypothesis: spontaneous generation of simple organic molecules (e.g. amino acids, carbohydrates, lipids) occurred due to conditions on prebiotic Earth

• metabolism first hypothesis: life began with simple metabolic reactions that led to the formation of metabolic pathways, which formed complex molecules, forming the basis of cells

• sulfur world hypothesis: the first forms of life were based on iron-sulfur chemistry

• lipid world hypothesis: lipid bilayers evolved before RNA, providing a protective layer to encapsulate the RNA

• early cell membranes may have formed from fatty acids, which are structurally much simpler than phospholipids and may have formed more readily in a prebiotic environment

• each fatty acid is a hydrophobic hydrocarbon chain with a hydrophilic carboxyl group attached to one end

• in a watery solution, fatty acids will spontaneously form spherical structures called micelles; the shape of the micelle tucks hydrophobic tails together

• because of the physical separation, the interior of the membrane would then have been able to provide a chemical environment with a different chemistry to the external environment

• it is likely that more than one life form spontaneously originated under the conditions present on early Earth, but only one of these life forms gave rise to all of the species existing since and today

• it is theorized that LUCA was a simple, unicellular autotrophic microbe with an RNA genome that existed between 2.5 and 3.5 billion years ago

• by looking at the half lives of particular isotopes, we can find the earliest evidence of life

• for example, when examining the remains of prehistoric autotrophs, if traces of carbon-12 are found, we know that the organism must have been photosynthetic, and therefore existed during or after the Great Oxygenation Event

• stromatolites are structures created by photosynthetic bacteria that live in shallow water; as they become covered in clay and particles, the bacteria move upward toward the light

  • movement traps and binds sediments into layers

• biomarkers are the molecular fossils of macromolecules and organic compounds

• encased in sedimentary rocks, these molecules can remain intact over hundreds of millions of years

• lipids generally preserve better compared to other macromolecules

• perhaps the most telling piece of evidence

• the genetic code is universal as it is shared by all living organisms and viruses on Earth due to common ancestry of all living organisms from one LUCA

• universality and conservation means that scientists can use the genetic code as a tool to study when differences in the genome of groups of organisms evolved

• the number of differences in the genomes of two species is proportional to the time since they diverged from a common ancestor

• existed between 2.5 and 3.5 billion years ago

• existed deep in the ocean in alkaline hydrothermal vents that were rich in hydrogen and dissolved minerals (including sulfur, methane, iron) which could have been used by LUCA as an energy source

  • hydrothermal vents are fissures in the ocean floor through which mineral rich water escapes; hydrothermal vents are thought to have provided LUCA physical protection from the external ocean

  • hydrothermal vents have high temperatures, which could have provided energy necessary for formation of organic molecules required for cellular formation

• was anaerobic (does not require oxygen for cellular respiration), which fits with the lack of oxygen in the early atmosphere of the Earth

• was autotrophic, combining inorganic carbon with hydrogen, to produce carbon dioxide and formic acid, which could then be used for other processes

• PILI: enables the cell to attach to surfaces, swap DNA with other cells and harpoon DNA in the environment

• CAPSULE: helps the cell keep from dehydrating and adhere to surfaces

• FLAGELLUM: long extensions used in cell locomotion

• NUCLEOID: the main DNA of the cell, found in a single loop in the cytoplasm; “naked” as the DNA is not associated with histone proteins

• PLASMID: extra pieces of DNA (not in all prokaryotic cells)

  • circular and naked

  • smaller and replicates independently of the nucleoid

  • can be shared between bacteria through horizontal gene transfer

  • since DNA is more accessible, more prone to damage and mutation

• 70S RIBOSOMES: where translation (protein synthesis) occurs

nucleus

rough ER

smooth ER

Golgi apparatus

lysosome

mitochondria

free ribosomes

chloroplast

vacuole

• vesicles

• in secretory cells, they can be distinguished from lysosomes by the fact that they may be clumped towards one side

centriole

cytoskeleton

cilia

flagella

microvilli

• OBLIGATE AEROBES: require continuous oxygen supply, so only live in oxic environments 

• OBLIGATE ANAEROBES: inhibited or killed by oxygen, so only live in anoxic environments 

• FACULTATIVE ANAEROBES: use oxygen if available, so can live in either oxic or anoxic environments

• organisms that produce ATP through aerobic cellular respiration

• oxygen serves as the final electron acceptor in the electron transport chain

• organisms that produce ATP via anaerobic cellular respiration or fermentation

• killed by atmospheric levels of oxygen, as they lack the enzymes needed to break down toxic forms of oxygen

• ANAEROBIC RESPIRATION: uses an electron acceptor other than oxygen (e.g. sulfate, nitrate, iron) in the electron transport chain 

• FERMENTATION: doesn’t use an electron transport chain; e.g. lactic acid fermentation, alcoholic fermentation

• many anaerobic bacteria are important for human digestion for breakdown of materials.

• produce ATP via aerobic cellular respiration, anaerobic respiration, and/or fermentation

• since they can survive in many different environments, facultative anaerobes can easily adapt to changing conditions

• grow better in aerobic conditions as they give much higher yields of ATP than fermentation

• most life-threatening pathogenic bacteria are facultative anaerobes.

• cell membrane has branched fatty acids with unique bonding of the fatty acid to glycerol

• peptidoglycan is the component of bacterial cell walls whereas polysaccharides make up the archaeal cell walls

• their genomes are larger and more complex than those of bacteria

• many are extremophiles (living in conditions hostile to most other forms of life on Earth)

• PHOTOAUTOTROPHS: obtain energy from light 

  • pigments other than chlorophyll are used 

  • in this form of “photosynthesis” their photosynthesis does not generate oxygen 

  • rather than an electron transport train, light-activated ion pumps generate ion gradients

• CHEMOAUTOTROPHS: obtain energy from the oxidation of inorganic chemicals 

  • often inhabit extreme habitats 

  • can use inorganic energy sources, including hydrogen sulfide, iron (II) compounds, molecular hydrogen, and ammonia to produce energy 

  • this form of energy acquisition is considered one of the oldest on Earth

the organization of different functions and processes within specific areas or structures within the cell that are separated by plasma membranes

• enzymes (reactant catalysts) and metabolites (“reactants” for metabolism) can be concentrated in a small space, increasing the chance for collision between the active site and substrate 

• substances that damage cells can be isolated within a membrane 

• conditions, such as pH, can be maintained at an optimal value for a particular reaction 

• large areas of membrane can become dense with proteins for a specific process

• not enclosed by a phospholipid bilayer solids

• ribosomes, centrioles, nucleolus

• sacs enclosed by a single phospholipid bilayer

• vesicles and vacuoles, rough ER, smooth ER, Golgi apparatus, lysosomes

• structures enclosed by two phospholipid bilayers

• nucleus, mitochondria, chloroplasts

• cell wall: as it is extracellular, it is not an organelle; also not involved in metabolic processes

• cytoplasm: not specialized to perform a specific function

• cytoskeleton: filaments and tubules that make up the cytoskeleton do not qualify it as a discrete structure; also not involved in metabolic processes

• lysosomes contain a high concentration of enzymes capable of hydrolyzing all types of biological polymers (including proteins, nucleic acids, carbohydrates, lipids)

• internal conditions of lysosomes are highly acidic, with a pH of 5; this contrasts with the neutral pH of the cytoplasm

• lysosomal enzymes are acid hydrolases; these enzymes would be rendered inactive in the case that a lysosome’s membrane broke down, thus protecting the cytosol

• particles are brought into the cell in by phagocytic vacuoles to be “consumed” by lysosomes

• the breakdown of waste in cells requires the use of potentially damaging enzymes

• isolating these enzymes in the phagocytic vacuoles protects the rest of the cell and allows the waste to be broken down safely

• the double membrane of the nucleus serves as a barrier between the genetic material inside the nucleus and the rest of the cell

• inner membrane controls entry and exit of molecules involved in regulation of gene expression

• nuclear pore complexes have selective passageways that allow small polar molecules, ions, and macromolecules to travel between the nucleus and cytoplasm; also serve as channel proteins that regulate mRNA leaving the nucleus

• during prophase, nuclear membrane breaks down into small vesicles, held together by dimers (small polymers) and lamin (structural proteins); membrane is reassembled in telophase

  • process is critical for maintaining integrity of genetic material

• has a double membrane with pores, allowing cells to separate gene transcription and translation

• contains the DNA, which stores information for making proteins via transcription and translation

• contains the nucleolus, where ribosome subunits are made

• made from dozens of proteins arranged on a scaffold of ribosomal RNA

• ribosomes have binding sites to which mRNA and tRNA bind during translation; causes the flow of information to go from DNA to mRNA to a protein

• the mRNA that codes for proteins that need to be exported outside of the cell is transcribed in the nucleus with an ER signal sequence (a short sequence on a protein that directs the protein towards the ER)

• proteins for use inside the cell do not have this sequence in their mRNA; allows the cell to direct proteins to correct locations, which depends on the protein’s function

• free (floating in cytoplasm): synthesizes polypeptides used in the cell

• bound (attached to the cytosolic side of the rough ER): synthesizes polypeptides secreted from the cell to become proteins in the cell membrane

a series of flattened membranous sacs that play a central role in the synthesis and transport of polypeptides; continuous with nuclear membrane

• composed of a series of connected flattened membranous sacs continuous with the rER

• lacks ribosomes and is not involved in protein synthesis

• synthesizes phospholipids and cholesterol; both are used for membrane repair and synthesis

The Golgi apparatus is composed of flattened membrane-enclosed sacs called cisternae.

The Golgi sorts, concentrates, and packs proteins into vesicles. Vesicles are dispatched to one of three places:

• within the cell to organelles, (e.g. lysosomes)

• plasma membrane

• secretion to outside of the cell via exocytosis

Vesicles fuse with the cis compartment membrane and release the protein inside the Golgi. Proteins for use within the cell (e.g. lysosomes) are transported to the medial compartment to undergo further modification. Proteins destined for export outside the cell are transported to the trans compartment.

• cisternal maturation model: layers of membrane gradually mature and progressively move through the Golgi in the trans direction

• vesicle transport model: buds off at layers

• small, spherical organelles enclosed by a single membrane

• contain enzymes that work in oxygen-poor areas and lower the pH

• enzymes in lysosomes digest large molecules to degrade and recycle components of the cell’s own organelles when they are old or damaged

• lysosomes also have an immune defence function, as they digest pathogens that have been engulfed by phagocytes

• formation of vesicles is achieved through endocytosis; the most common type is called clathrin mediated endocytosis

• clathrin forms a skeleton around the newly formed vesicle, and forms with another protein, dynamin, and wraps around the base of the vesicle and pinch off a piece of the membrane to form a vesicle

• once the vesicle forms, the clathrin coat breaks down through hydrolysis, back into individual pieces

• transport vesicles: move molecules between locations inside the cell

• secretory vesicles: secrete molecules from the cell via exocytosis; this is how new phospholipids are added to the cell membrane

• transport: of integral membrane proteins (e.g. pumps channels, adhesion proteins, receptor proteins)

• cell membrane growth: phospholipids used to form vesicles are added to the accepting membrane

• surrounded by a double membrane

• adapted for production of ATP, for aerobic cellular respiration

• belong to a group of organelles called plastids

• responsible for the green colour of plants

• adapted for photosynthesis

• central vacuoles of plants occupy 30%-90% of the cell

• in addition to water storage, the main role is to maintain turgor pressure against the cell wall

• includes microtubules, actin filaments, and intermediate filaments

• helps cells maintain their shape, organize cell parts, and enables cells to move and divide

• microtubules are polymers of a protein called tubulin

• form part of the cytoskeleton

• used for intracellular transport of organelles and separation of chromosomes during mitosis

• centrosomes are composed of a pair of centrioles

• responsible for the arrangement of the mitotic spindle during cell division

• serve as an anchor point for microtubules and for cilia and flagella

• cilia and flagella are extensions from the cell surface

• formed from modified centrioles called basal bodies

• used to aid cell movement

• while cilia beat in coordination with each other, flagella move independently of each other

• multicellular eukaryotes without a cell wall, as cell walls are too rigid to allow fluid movement

• all are holozoic, meaning that they eat other organisms with internal digestion of nutrients

• the largest kingdom, with a million known species; number of known species is likely due to human bias toward studying animals

• eukaryotes with a cell wall made of chitin

• can be unicellular or multicellular

• most are saprotrophs; they don’t perform digestion inside their cell

  • rather, they release digestive enzymes in the environment and suck up the nutrition afterward

• fungi are the primary decomposers in ecological systems

• multicellular eukaryotes with a cell wall made from cellulose

• cellulose is a molecule that is hard to break down; thus, in humans, there are bacteria in the gut biome that are used to help digest cellulose

• with just a few exceptions, plants are autotrophs

• there are an estimated 300 000 known species of plants

• not in animal or fungus kingdom

• in plants, including chloroplasts for photosynthesis

• not in animal kingdom

• in fungi, composed of chitin and other molecules

• in plants, primarily composed of cellulose

• in animals, small, temporary structures that expel excess water or other waste products

• in fungi and plants, large, permanent organelle used to store water to cause turgor pressure

• in animals, used to arrange mitotic spindle during mitosis and as anchor points for cilia and flagella

• not in fungi

• in plants, present in male gametes of moss and ferns, absent in all conifers and flowering plants

• in animals, present in many animal cells, including male gamete

• in fungi, absent from most fungi, except a small number that have a swimming male gamete

• in plants, present in male gametes of moss and ferns; absent in all conifers and flowering plants

• skeletal muscle fibre

• red blood cells

• aseptate fungal hyphae

• phloem sieve tube element

multinucleated because the muscle cell has formed from many smaller myocytes (muscle cells) that have fused together

during their maturation, red blood cells discard their nucleus and mitochondria cells become small to increase surface area to volume ratio for efficient gas exchange and the ability to move through narrow capillary vessels

aseptate hyphae in fungi do not have the cellular partitions that are normally present, and so there are many nuclei in a single unit; thus, they are considered to be multinucleated