2. Cell Biology and Metabolism

Cell Structure and Components

Core Concepts

1. Cell membranes
   • composed of lipids, proteins, and carbohydrates
2. The plasma membrane
   • a selective barrier
   • controls the movement of molecules between the inside and the outside of the cell
3. The endomembrane system
   • interconnected system of membranes
   • e.g., nuclear envelope, endoplasmic reticulum, golgi apparartus, lysosomes, vesicles, and plasma membrane
4. Mitochondria and Chloroplasts
   • Organelles involved in energy harvesting
   • Evolved from free-living prokaryotes

Cell Theory

• All organisms are made up of cells
• The cell is the fundamental unit of life
• Cells come from pre-existing cells

Evolution of Cellular Differentiation

Microscopy

• Cryo-EM is developed in 2017

  

Cell Membranes

Phospholipids

• Phospholipids are amphipathic
  • Polar head group (glycerol backbone, phosphate, choline) is hydrophilic
  • Fatty acid chains are hydrophobic

Lipid Structures

• Micelle: Large head and bulky with one hydrophobic tail buried

  

• Bilayer: Small head with two hydrophobic tails

  

• Liposome: Encoled bilayers composed of phospholipids

  

Cholesterol

• Component of animal cell membranes
• A buffer to lessen the impact of the temperature on membrane fluidity

  

Membrane Proteins

• Receptors: allow the cell to receive signals from the environment
• Enzymes: catalyze chemical reactions
• Anchors: attach to another proteins that help maintain cell structure and shape

  

• Integral Membrane Proteins: permanently associated with cell membranes
• Peripheral Membrane Proteins: temporarily associated with lipid bilayer or with integral membrane proteins through weak noncovalent interactions

  

• Transporters: move ions or molecules across the membrane

  

The Plasma Membranes

• Selective barrier that controls the movement of molecules between the inside and the outside of the cell (selectively permeable)

Diffusion

• The simplest movement into and out of cells

• Passive transport

• Simple Diffusion: direct transport of molecules allowed by the cell membrane

• Facilitated Diffusion: assisted transport of molecules through the action of transmembrane proteins e.g., carriers, channels

  

  Osmosis

• Diffusion of water

• Effects of osmosis

  

Hypertonic Hypotonic

Plant Cell Wall and Vacuoles

Vacuole

• Storage of water and nutrients
• Storage and disposal of waste products and
• Supported by turgor pressure: force exerted by water pressing against an object

Magnaporthe grisea and turgor pressure

• M. grisea first attach to the leaves
• Then, synthesize melanin to increase its turgor pressure
• Use the high turgor pressure to penetrate through host organism
• Subseuently occupy the host organism
• Absorb nutrients

Types of Transport

• Does not require energy
• Diffusion, Osmosis
• Through concentration gradient

Active Transport

• Requires energy
• Primary Active Transport
  • The pumps that move two molecules in the opposite directions are the antiporter

    

  • The transporters that move two molecules in the same direction are called symporters or co-transporters

    

• Secondary Active Transport
  • Movement of the coupled molecules is driven by the movement of protins, not direct ATP
  • Protons are pumped out of the cell by primary active transport
  • Electrochemical gradient from outside to inside the cell is now generated by protons
  • The antiporter move a different molecule out of the cell against its concentration gradient

    

The Endomembrane System

• an interconnected system of membranes that includes the nuclear envelope, ER, Golgi apparatus, lysosomes, vesicles, and plasma membrane

Intercellular Movement of Molecules

• Exocytosis: vesicles generated from the endomembrane system fusing with the plasma membrane to deliver its contents into the extracellular space
• Endocytosis: material from outside the cell being brought into a vesicle

  

The Nuclear Envelope

• Nuclear Pores: membrane protein openings on the nuclear envelope -> essential for the nucleus to communicate with the rest of the cell
• Small molecules (e.g., ions) can passively diffuse through the pores
• Large protines and RNA require active transport

  

The Endoplasmic Reticulum

• Largest organelle in most eukaryotic cells
• Factory of lipids and proteins
• Rough ER: lots of ribosomes (reason for its name), synthesize proteins
• Smooth ER: lacks ribosomes, synthesize lipids
• Ribosomes: site of protein synthesis, amino acids are assembled into polypeptides

  

The Golgi Apparatus

• Modify proteins and lipids produced in the ER
• Sort proteins and lipids as they move to their final destinations (providing pathway)
• Synthesize carbohydrates

  

Lysosomes

• Degrade proteins, nucleic acids, lipids, and complex carbohydrates e.g., worn-out organelle
• Fuse with macromolecule that needs to be broken down
• Maintain acidic pH through proton pumps
• Useful broken-down molecules are recycled
• Waste molecules are expelled from cell

  

Mitochondria and Chloroplasts

• Contain their own genomes
• Grow and multiply independently of other membrane compartments

Distinguishing features of plants

• Cell wall
• Vacuole
• Chloroplasts
• Autotroph

Metabolism and Cell Energy

Core concepts

1. Metabolism: the set of biochemical reactions that transform biomolecules and transfers energy
2. Kinetic energy: energy of motion
3. Potential energy: stored energy
4. The laws of thermodynamics: law that governs energy flow in biological systems

What do cells need?

• A membrane to separate the inside of the cell from the outside
• A way to encode and transmit information
• ENERGY

Adenosine Triphosphate (ATP)

• ATP stores potential energy using the bonds connecting the phosphate groups
• The energy level stored in each bond is different
• The highest energy bond is at the outer layer
• ATP is used in cellular activities e.g., antiporter activation
• ATP is used in organismal activities e.g., muscle contractions

Metabolism

• The set of biochemical reactions that transforms biomolecules and transfers energy

Metabolic Classification

Types of Reactions

• Catabolism: breakdown of a molecule e.g., breakdown of macromolecules (carbs, proteins, fats, nucleic acids) into subunits (sugars, amino acids, fatty acids, nucleotides)
  • Energy is released
  • ADP -> ATP + H2O

• Anabolism: construction of a molecule e.g., construction of macromolecules (carbs, proteins, fats, nucleic acids) from subunits (sugars, amino acids, fatty acids, nucleotides)
  • Energy is consumed
  • ATP + H2O -> ADP

Kinetic Energy

• Energy of motion

Potential Energy

• Stored energy

Chemical Energy

• A form of potential energy held in the chemical bonds between pairs of atoms in a molecule
• Strong bonds have less potential energy
• Weak bonds have more potential energy -> outermost bond of ATP has the highest energy

Packaged Energy

• ATP, a currency of energy
• Cells do not use all the available energy at once
• Cells package the energy into a chemical form that is readily accessible to the cell
• Chemical energy of ATP is held in the bonds linking the phosphate groups
• Break of each bond releases energy

The Laws of Thermodynamics

• Governs energy flow in biological systems

First Law of Thermodynamics

• Conservation of energy

  

Second Law of Thermodynamics

• Energy transformation

  

Entropy

• Describes the amount of disorder

  

Microbiome

• Consists of microbes that are helpful or harmful
• The microbiome associated with the human body has more cells than human cells
• Most are mutualists and commensals
• In smaller numbers are pathogens (promoting disease)

Metabolism and Energy Efficiency of Human Host

• Human provides nutrient
• Microbiota regulate metabolism through hormone signals

Age

• Different age provides different microbiome profile
• That way, age of the host can be predicted using microbiome
• Also the health conditions of the host can be measured

  

Chemical Reactions an Enzymes

Core Concepts

1. Chemical Reactions: involve the breaking and forming of bonds
2. Energetic Coupling: spontaneous reactions drive a non-spontaneous reactions
3. Enzymes: protein catalysts that can increase the rate of biochemical reactions
4. Allosteric Enzymes: an enzyme that is activated or inhibited when binding to another moecule changes its shape

Chemical Reactions

• Catabolic reactions + Anabolic reactions

Free Radicals (Reactive Oxygen Species)

• Free radicals steal electrons
• Normal cells get damaged under oxidative stress due to free radicals
• Consumption of antioxidants can prevent it e.g., Selenium
• Selenoprotein translation generates proteins with selenocysteine that contain abundant selenium

  

Gibbs Free Energy ($\Delta G$)

• Energonic reaction: reactions with a positive $\Delta G$, require input of energy

  

• Exergonic reaction: reactions with a negative $\Delta G$, release energy

  

Energy Available $$\text{Total Energy (enthalpy)} (H)=\text{energy available to do work} + \text{energy lost to entropy}$$ $$\implies \Delta G = \Delta H - T\Delta S$$

• G: Gibbs free energy
• H: Enthalpy
• T: Absolute temperature (K)
• S: Entropy

Gibbs Energy in different reactions

• Catabolic reaction: $$\downarrow\Delta G = \Delta H \downarrow - T\Delta S \uparrow$$
• Anabolic reaction: $$\uparrow\Delta G = \Delta H \uparrow - T\Delta S \downarrow$$

Energetic Coupling

• A process in which spontaneous reactions ($\Delta G<0$) drive a non-spontaneous reaction ($\Delta G > 0$)

e.g.,

Intermediate Free Energy

• ATP: energy provider

  

Rate of a Reaction

• Transition state: unstable, has large energy
• Note that reactants require an activation energy, denoted $E_A$, to enter the transition state

Enzymes

Protein catalysts that can increase the rate of biochemical reactions

• Enzyme-Catalzed Reactions $$\text{Substrate} (S) \leftrightarrow \text{Product} (P)$$ $$S + \text{Enzyme} (E) \leftrightarrow ES \leftrightarrow EP \leftrightarrow E + P$$

Enzyme Shape

• Active site binds the substrate and converts it to the product

  

• Interaction between the substrate and the active site decreases the activate energy required

Active Site Formation

• The amino acids that form the active site are often composed of non-linear sequence of the unfolded enzyme
• Often specific for substrates (Enzyme Specificity)

Activators & Inhibitors

• Activators: activate/promote enzyme activities
• Inhibitors:
  • Competitive inhibition: inhibitors bind to the active site of the enzyme, competing with the substrate to reduce the rate of reaction
  • Allosteric inhibition: binds to the allosteric site of the allosteric enzymes to alter the shape of the enzyme and prevent substrate bindings

Why are some mushrooms toxic to human beings?

• Amatoxins are selective inhibitors of RNA polymerase II, which is a vital enzyme in the synthesis of mRNA, microRNA, and snRNA

Allosteric Enzymes

Regulation of Chemical Reactions

• Allosteric Enzyme: an enzyme activated or inhibited by the change of shape resulting from the bindings of other molecules

Cellular Respiration I

Core concepts

1. Cellular Respiration: a seris of catabolic reactions that convert the energy in fuel molecules into ATP
2. Glycolysis: the partial oxidation of glucose, results in the production of pyruvates, ATP, and reduced electron carriers
3. Pyruvate Oxidation: pyruvate is oxidized to acetyle-CoA, connecting glycolysis to the citric acid cycle
4. The Citric Acid Cycle: results in the complete oxidation of fuel molecules, the generation of ATP and reduced electron carriers
5. The Electron Transport Chain: transfers electrons from electron carriers to oxygen using the energy released to pump protons and synthesize ATP by oxidative phosphorylation

Cellular Respiration

A series of catabolic reactions that convert the energy in fuel molecules into ATP

• Break down carbohydrates, lipids, and proteins
• Convert energy in fuel molecules into ATP
• Allow the cell to do work

Stages of Cellular Respiration

1. Glycolysis (cytoplasm)
2. Pyruvate Oxidation (Mitochondria)
3. Citric Acid Cycle (Mitochondria)
4. Oxidative Phosphorylation (Mitochondria)

Generating ATP

• Substrate-Level Phosphorylation: ATP synthesis through hydrolysis reaction assisted forming an enzyme/substrate complex
• Oxidative Phosphorylation: Majority of ATP production

Oxidation-Reduction Reactions

• Oxidation: loss of electrons
• Reduction: gain of electrons
• The oxygen atom oxidizes the glucose, it can be called the oxidizing agent
• Glucose is the electron donor and is considered the reducing agent

Electron carriers

• $$NAD^+, NADH$$
• $$FAD, FADH_2$$
• The oxidized forms of these carriers are NAD+ and FAD
• The reduced forms of these carriers are NADH and FADH_2

Glycolysis (Cytoplasm)

The partial oxidation of glucose and results in the production of pyruvate, as well as ATP and reduced electron carriers

Phase 1: Preparatory phase

• Consumption of 2 ATP
• The phosphorylation of glucose traps the molecule inside the cell and de-stabilizes it making it ready for phase 2

Phase 2: Cleavage phase

• 6-carbon sugar is separated into two 3-carbon molecules

Phase 3: Payoff phase

• Production of 4 ATP and 2 NADH

Reactants of Glycolysis $$1 Glucose$$

Products of Glycolysis $$4 ATP - 2 ATP = 2 ATP \text{ (net gain)}$$ $$2 NADH$$ $$2 Pyruvate$$

Pyruvate Oxidation (Mitochondrial Matrix)

Pyruvate is oxidized to acetyle-CoA, connecting glycolysis to the citric acid cycle

• The pyruvate is transported into the mitochondrial matrix from the cytosol
• Then converted to acetyle-CoA within the mitochondria

  

Reactants of Pyruvate Oxidation $$2 Pyruvates$$

Products of Pyruvate Oxidation $$2 \times 1 CO_2=2CO_2$$ $$2 \times 1 NADH=2NADH$$ $$2 \times 1 \text{Acetyle-CoA}=2\text{Acetyle-CoA}$$

Citric Acid Cycle (Mitochondrial Matrix)

Results in the complete oxidation of fuel molecules and the generation of ATP and reduced electron carriers

• The citric acid cycle is known as the Kreb’s cycle and the TCA cycle
• Takes place in mitochondrial matrix
• Fuel molecules are completely oxidiezed in this stage

Reactants of Citric Acid Cycle

$$2 \text{Acetyle-CoA}$$

Products of Citric Acid Cycle

$$2 \times 1 ATP=2ATP$$ $$2 \times 3 NADH = 6NADH$$ $$2 \times 1 FADH_2=2FADH_2$$ $$2 \times 2 CO_2=4CO_2$$

Electron Transport Chain (Mitochondrial Matrix & Intermembrane Space)

Transfers electrons from electron carriers to oxygen, using the energy released to pump protons and synthesize ATP by oxidative phosphorylation

• Electrons in NADH enter the ETC via complex I
• Electrons in FADH2 enter the ETC via complex II

Electron transport

• Coenyzme is reduced to CoQH2 and transfers electrons from complex I and II to complex III
• Oxygen acts as a final electron acceptor
• 2 Water molecules are produced per 4 electrons from complex IV

Proton transport and ATP synthesis

• Transport of electrons in Complex I, III, and IV is coupled with the transport of protons to the intermembrane space
• The proton gradient has two components
  • A chemical gradient resulting from the different concentration of hydrogen ions
  • An electrical radient resulting from the difference in charge between the two sides

ATP Synthase

• Utilizes the electrochemical proton gradient for ATP synthesis
• The rotation of the $F_0$ subunit -> roation of the $F_1$ subunit
• The rotation of the $F_1$ subunit -> conformational changes that allow it to catalyze the synthesis of ATP

Cellular Respiration II

Core Concepts

1. Anaerobic Metabolism: breakdown of glucose through fermentation, produces a modest amount of ATP
2. Fermentation: a process for extracting energy from fuel molecules without relying on oxygen or ETC, use an organic molecule
3. Metabolic Integration: metabolic pathways are integrated, allowing control of the energy level of cells

The Flow of Energy in Cellular Respiration

• 4 ATP produced by substrate-level phosphorylation per glucose
• Some energy transferred to 10 NADH and 2 FADH2 per glucose
• ATP Synthase converts the gradient to rotational energy to produce 28 ATP per glucose $$2.5 \times 10 NADH = 25ATP$$ $$1.5 \times 2 FADH_2 = 3ATP$$

Anaerobic Metabolism

• breakdown of glucose through fermentation, produces a modest amount of ATP

Fermentation

• a process for extracting energy from fuel molecules without relying on oxygen or ETC, use an organic molecule
• In the absence of oxygen, pyruvate molecules undergo fermentation instead of pyruvate oxidation

Lactic acid Fermentation

• Occur in anaerobic bacteria
• 2 Pyruvate is produced through glycolysis per glucose
• 2 Pyruvate is reduced to 2 lactic acid
• 2 NADH is oxidized to 2 NAD+
• 2 NAD+ is reused to produce 2 ATP in glycolysis

  

• e.g., production of yakult

  

Products of Lactic acid Fermentation $$2 ATP$$ $$2 NAD^+$$ $$2 Lactate$$

Ethanol Fermentation

• Occur in yeast
• 2 Pyruvate is produced through glycolysis per glucose
• 2 Pyruvate lose 2 CO2 and form 2 Acetaldehyde
• 2 Acetaldehyde is reduced to 2 ethanol
• 2 NADH is oxidized to 2 NAD+
• 2 NAD+ is reused to produce 2 ATP in glycolysis

  

• e.g., wine, beers, bread

Products of Ethanol Fermentation $$2 ATP$$ $$2 NAD^+$$ $$2 CO_2$$ $$2 Ethanol$$

Rising Levels of Atmospheric Oxygen

• Before the presence of atmospheric oxygen, the earliest organism used one of the fermentation pathways
• Fermentation provide quick burst of ATP
• Higher efficiency in certain environments

Metabolic Integration

• Metabolic pathways are integrated, allowing control of the energy level of cells

Glycogen Storage

• Glycogen has a core protein
• A core protein is surrounded by branches of glucose units
• Glycogen is stored in muscle cells -> muscle contraction
• Glycogen is stored in liver cells -> deliver energy and support cells
• Glucose molecules at the end of the branches can be cleaved one at a time
• Cleaved molecule is converted from glucose 1-phosphate to glucose 6-phosphate to undergo glycolysis

How other Sugars contribute to Glycolysis

• Monosaccharide, Disaccharide

  

• Polysaccharide

  

Ruminants and Microbes

• Ruminants do not have an enzyme to digest cellulose
• Rumens of herbivore ruminants are colonized by
  • Bacteria
  • Archaea
  • Fungi
  • Bacteriophages
• Microbes living in the rumen of the ruminants degrade cellulose

Evolution of Mitochondria

• Some eukaryotes lack mitochondria, possess mitosome instead

  

Hydrogenosomes in Anaerobic Fungi

• Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukarytoes
• Hydrogenosomes (H) are small (~0.5 um diameter)
• Spherical or variously elongate organelles

Regulation of Cellular Respiration

• High ADP, NAD+: Low energy state -> stimulate cellular resp.
• High ATP, NADH: High energy state -> inhibit cellular resp.

Photosynthesis I

Core Concepts:

1. Photosynthesis: the major pathway by which energy and carbon are incorporated into carbohydrates
2. The Calvin Cycle: a three-step process that synthesizes carbohydrates from carbon dioxide
3. Capturing Sunlight into Chemical Forms: the light-harvesting reactions that use sunlight to produce the ATP and NADPH required by the Calvin Cycle

Photosynthesis

• the major pathway by which energy and carbon are incorporated into carbohydrates

Energy in Biological Systems

• Photosynthesis provides an entry point to the majority of energy

Survival in Diverse Environment

• In desert, photosynthesis bacteria and unicellular algae form an easily disturbed layor on the surface (desert crust)

  

• Cyanobacteria lives in the top layer of the surface supporting the other micro organisms underneath through photosynthesis

  

• Some photosynthetic microbes (e.g., Cab. thermophilum PscA) live in extreme environment e.g., hot spring, glacier

Uncommon Photosynthetic Players

• Nostoc sp.: example of a symbiosis

  

• Fungi, Geosiphon pyriforme traps Nostoc sp. to photosynthesize

  

• Lichen: fungi + algae/cyanobacteria
  • Multiple fungal elements can be involved

    

General Equation for Photosynthesis $$CO_2 + H_2O \rightarrow C_6H_{12}O_6 + O_2$$

• Type of a redox reaction
• Oxidation of water is linked with the reduction of carbon dioxide
• Series of redox reaction to oxidize water make up the photosynthetic electron transport chain

Photosystem

• Photosynthesis begins with the absorption of light by protein-pigment complexes (photosystems)
• Absorbed light is used to drive redox reactions
• The movement of electrons through the chain is used to drive the synthesis of ATP and NADPH
• ATP and NADPH are the energy sources required for Calvin cycle

  

The Chloroplast

• Thylakoid membranes form structures that resemble flattened sacs, grouped into grana

  

Cellular Respiration vs. Photosynthesis

• Notice that the reactions are the opposite of one another
• Photosynthesis generates fuel molecules (by fixing carbons)

The Calvin Cycle

• a three-step process that synthesizes carbohydrates from carbon dioxide

Three steps

1. Carboxylation: addition of CO2 to the 5-carbon compound, RuBP (done by rubisco)

• 6-carbon molecule is broken down into two 3-carbon molecules, 3-PGA

2. Reduction: energy input form ATP and NADPH

• NADPH is the reducing agent
• The reduction of 3-PGA requires ATP and NADPH
• One 3C molecule exists (G3P)

3. Regeneration of RuBP: 3-carbon compounds are reorganized and combined to produce RuBP

• $$5\times 3C (\text{triose phosphate}) \rightarrow 3 \times 5C (\text{RuBP})$$

Energy Storage

• Excessively produced glucose is stored as starch granules

Sunlight into Chemical Forms

• the light-harvesting reactions that use sunlight to produce the ATP and NADPH required by the Calvin Cycle

Light Absorption

• Light is a type of electromagnetic radiation
• Pigments absorb some wavelegths of visible light
• Pigments look colored as they reflect light enriched in the wavelengths that they do not absorb

  

Chlorophyll Light Absorption

• Chlorophyll appears green as it poorly absorbs green wavelengths
• Chlorophyll molecules are bound by their tail region to integral membrane proteins in the thylakoid membrane
• Hydrocarbon tail anchors the chlorophyll to cell

  

• Light energy is absorbed by the photosystems
• Reaction center in the Photosystem II is reduced by the electrons from water
• Reaction center in the Photosystem I is reduced by the Ferredoxin
• Antenna chlorophylls (e.g., chlorophyll b) and accessory pigments (e.g., carotenoid) absorbs and transfers light to the reaction center

  

  

  • Pigments other than chlorophyll are called accessory pigments

    

• Reaction center (e.g., chlorophyll a) with the excited electron reduces the primary electron acceptor

Reaction Center

• Chlorophyll with distinct configuration
• Transfer energy to the electron acceptor

Photosynthesis II

Core Concepts

1. Photosynthesis Challenge: challenges to the efficiency of photosynthesis include excess light energy and the oxygenase activity of rubisco
2. The evolution of photosynthesis: a profound impact on life on Earth

Photosynthesis Challenge

Reaction Center

Two Photosystems

• Z Scheme describes change in energy level of the electron as it goes through the photosystems
• PS II supplies electrons to the beginning of the ETC
• PS I energizes the electrons with a second input of energy -> provide enough energy to reduce NADP+
• Electron carriers (e.g., Pq, Pc, Fd) are responsible for moving electrons between complexes

  

Proton Accumulation

• There are two sources of options
  • Through water oxidation
  • Through the cytochrome b6f complex

    

Cyclic Electron Transport

• To increase ATP production, electrons are shunted into an alternative pathway via ferredoxin (Fd)
• Fd transfers electrons to Pq, Pq transfers electrons to Cyt, Cyt pumps protons
• Result in more accumulation of protons in lumen
• Increase in ATP, but decrease in NADPH

  

Photosynthesis Challenge I: excess light energy

• If the light density is too high, the high-energy electrons will lose a safe place to go
• Increased change to create Reactive Oxygen Species (ROS)

Reactive Oxygen Species

• Releases harmful free radical
• NADP+ is in short supply
• -> Either the absorbed light energy or the energy associated electron can be transferred to O2
• -> Formation of ROS
• Mitigation stratiegies:
  • Antioxidants can detoxify ROS
  • Xanthophylls can slow the formation of ROS
    • By reducing excess light energy
    • Yellow-orange pigments in the photosystems

Photosynthetic Challenge II: the oxygenase activity of rubisco

• Photorespiration occurs when rubisco adds O2 instead of CO2 to RuBP (rubisco accepts both as substrates)
• Photorespiration can be reduced through C4 cycle (e.g., Corn)
  • Increase CO2 concentration
  • PEP carboxylase synthesizes 4-C molecules
  • CO2 is passed to the bundle-sheath cell, where the Calvin cycle occurs

Photosynthetic Efficiency

Cell-free Solar-to-starch Efficiency

• Perfom photosynthesis in lab
• Efficiency of 9%

The evolution of photosynthesis

Step 1: two phosotytems

Step 2: endosymbiosis

Horizontal Gene Transfer (HGT)

Methods prevalent in Prokaryotes

• Conjugation

  

  • DNA from a donor cell is transferred to an adjacent recipient cell
  • Pilus tethers the donor to the recipient
  • Bring the cells together
  • Once closely aligned, DNA passes through the small opening formed
  • e.g., genes that confer resistence to antibiotics
• Transformation

  

  • DNA is released to the environment by dead cells and taken up by a recipient cell
• Transduction

  

  • Transfer by a virus
  • Viruses that have infected bacterial cells can integrate their DNA into the host bacterial cell
  • Before leaving the bacterial host, the viral DNA removes itself
  • Sometimes removal of viral DNA involves the additional takeup of the host DNA

HGT between Eukaryotes

• HGT of Carotenoid genes from fungi to Aphids
• HGT of ubiquitine genes from insects to fungi

Note: ghost plant cannt photosynthesize -> steal carbon source from mycorrhizal fungi Note: red maple leaves still can perform photosynthesis through other yellow/brown coloured pigments e.g., carotenoid (in cold weather, separation happens and leaves recieve less nutrition -> not enough to synthesize chlorophylls)

Cell Cycle

Core Concepts

1. During cell division, a single parental cell divides into two daughter cells
2. Mitotic cell division is the basis of asexual reproduction in unicellular eukaryotes and the process by which cells divide in multicellular eukaryotes
3. Meiotic cell division is essential for sexual reproduction, the production of offspring that combine genetic material from two Integral_Peripheral_Membrane_Proteins

Cell Division

• A single parent cell divides into two daughter cells
• The process by which cells make more cells
• Purpose
  • Growth
  • Cell replacement
  • Healing
  • reproduction
• Requirements
  • Two daughter cells must each receive the full complement of genetic material present in the single parent cell
  • The parent cell must be large enough to divide into two and still contribute sufficient cytoplasmic components to each daughter cell

Prokaryotes

Binary Fission: asexual reproduction

1. The circular bacterial DNA molecule is attached by proteins to the inner membrane
2. DNA replication begins at a specific location and proceeds bidirectionally around the circle
3. The newly synthesized DNA molecule is also attached to the inner membrane, near the attachment site of the initial molecule.
4. As replication proceeds, the cell elongates symmetrically around the midpoint, separateing the DNA attachment sites.
5. Cell division behinds with th synthesis of new membrane and wall material at the midpoint
6. Continuted synthesis completes the constriction and separates the dauther cells

   

   

Cell Cycle (Eukaryotes)

• M phase: time during which the parent cell divides into two daughter cells
• Interphase: time between two successive M phases
  • Cells make many preparations for division
  • e.g., replication of DNA and increase in the cell size

Eukaryotic DNA Organization

• DNA is organized with histones and other proteins into chromatin
• Chromatin can be looped and packaged to form chromosomes

Karyotype

• Profile of the chromosomes in a certain species

  

Haploid/Diploid

• Haploid: cells with a single set of chromosomes e.g, human gametes
• Diploid: cells with paired chromosomes

Centromeres/Chromatids

• Note that the sister chromatids are analogous to each other as they are duplicated

Mitotic Cell Division

• The basis of asexual reproduction in unicellular eukaryotes and the process by which cells divide in multicellular eukaryotes

  

Prophase

• Chromosomes condense
• Centrosomes radiate microtubules and migrate to opposite poles

Prometaphase

• Mitrotubules of the mitotic spindle attach to chromosomes

Metaphase

• Chromosomes align in center of cell

Anaphase

• Sister chromatids separate and travel to opposite poles

Telophase

• Nuclear envelope re-forms
• Chromosomes decondense
• The end of mitosis

Cytokineses (Animal)

• Contractile ring forms to divide and cleave the cytoplasm

Cytokineses (Plant)

• Cell plate forms to divide the cytoplasm

Meiotic Cell Division

• Essential for sexual reproduction, the production of offspring that combine gneetic mateirla from two parents
• Meiosis I, homologous chromosomes separate
• Meiosis II, sister chromatids separate
• Results in four daughter cells
• Each daughter cell contains a half number of chromosomes as in the parent cell
• Each daughter cell is genetically unique

  

Meiosis I

• Reductional division as the number of chromosomes in daughter cells are reduced by half (2n -> n)
• the centromeres do not split during this stage of meiosis

Prophase I

• Chromosomes become visible as thin threads (DNA replication is complete)
• Homologous chromosomes condense, undergo synapsis (gene-for-gene pairing)
• Each pair of homologous chromosomes forms a bivalent (each chromosome consists of two sister chromatids)
• Chromosomes shorten and thicken
• Nuclear envelope break down

Crossing Over

• Meiosis allows homologous chromosomes of maternal and paternal origin to undergo an exchange of DNA sements
• Contribute to the genetic variation
• Crossing over also helpes hold together the bivalents for metaphase I

  

Prometaphase I

• Spindles attach to kinetochores on chromosomes

Metaphase I

• Homologous pairs line up in center of cell, with bivalents oriented randomly with respect to each other
• Contribute to the genetic variation

Anaphase I

• Homologous chromosomes separate, but sister chromatids do not

Telophase I

• Reformation of nucleus envlope

Cytokinesis

• Separation of cytoplasm

Meiosis II

• The process resembles mitosis except phrophase II (have haploid, not diploid)
• No DNA synthesis between two meiotic divisions
• Meiosis II is called equational division (n -> n) because cells in meiosis II have the same number of chromosomes in the beginning and in the end

Mitosis vs. Meiosis

• During meiosis I, maternal and paternal homologs separate from each other
• During meiosis II, sister chromatids separate from each other (similar to mitosis)

Cytoplasmic Division

• In females, the cytoplasm is divided very unequally in both meiotic divisions to form an egg
• In males, the cytoplasm divides fairly equally, resulting in products of functional sperms

  

  Note that the original number of chrosomomes (2n) is restored through the formation of zygote as a result of combination between Oocyte and a sperm cell

Regulation of Cell Cycle and Cancer

Core Concepts

1. Nondisjunction results in extra or missing chromosomes
2. Cell cycle regulation: the cell cycle is regulated so that cell division occurs only at appropriate times and places
3. Cancer is uncontrolled cell division that results from mutations in genes that control cell division

Nondisjunction

• results in extra or missing chromosomes

First-division

• Result in gametes with an extra or missing chromosome

  

Second-division

• REsults in gametes with an extra chromosome, a missing chromosome, and normal numbers of chromosomes

  

Trisomy 21: Down Syndrome

• Three 21 chromosomes present

Nondisjunction in species with different reproduction strategies

Cell cycle regulation

• The cell cycle is regulated so that cell division only occurs when and where appropriate

Regulation

• Cell division cannot occur all the time because uncontrolled division is dangerous and can lead to cancer
• The proteins that appear and disappear cyclically are called cyclins

  

• Enzymes activated by cyclins are called cyclin-dependent kinases (CDK)
• Once the CDK are activated by cyclins, target proteins are phosphorylated by the cyclin-CDK complexes
• Cell division is promoted by the phosphorylated target proteins

Cyclin level through the Cell Cycle

Cyclin-CDK Complexes

• Cyciln D-CDK and E-CDK (at the end of G1)
  • Prepare the cell for DNA replication
  • Promotes the expression of histone proteins
• Cyclin A-CDK is involved in the initiation of DNA synthesis (throughout S)
  • Prevents the reassembling of the same proteins
  • Prevents the re-replicating of the same DNA
• Cycling B-CDK, initiates multiple events associated with mitosis (throughout M)
  • Breakdown of the nuclear envelope during prophase
  • Formation of mitotic spindles

    

Checkpoints

DNA Damage Checkpoints

• This arrests the cell at the G1/S transition, giving the cell time to repair the DNA damage

Cancer

• uncontrolled cell division that results form mutations in genes that control cell division

  

Cancer and oncogenes

• Proto-oncogenes: normal genes that are important in cell division that have the potential to become cancerous if mutated (can be mutated by cancer-causing agents)
• Oncogene: cancer-causing gene
• Tumor suppressors: encode proteins whose normal activities inhibit cell division

Cancer causing agents

• Virus

  

  • Cancerous viral RNA is injected to the host genome
• Pathogens

  

  • Helicobactor Pylori is a cancer-causing bacteria
  • HBV, HCV, and HPV are cancer-causing virus

Multiple-Mutation Model for Cancer Development

Types of Cancer Treatment

• Hormone therapy
• Surgery
• Bone Marrow Transplantation
• Chemotherapy
• Targeted theraphy
• Radiation therapy
• Immunotherapy
• Note that cancer is difficult to treat as it begins from healthy cells -> challenge is to selectively kill the affected cells

Cordyceps fungus, Cordycepin, NUC-7738

• Cordycepin from Cordyceps inhibits DEK in the cancer cell

Medicinal mushroms

• The Jack-o-Lantern fungus is bioluminescent (the glow “foxfire”)
• Poisonous but the source of a new cancer drug in clinical trials

Restriction of Isoleucine

• Dietary restriction of isoleucine decreased cancer rate

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

• CRISPR can be used to fight against cancer

  

• Modify the T-cells with CRISPR -NY-ESO-1 TCR precisely recognizes the cancer cell

Comparison of Mitosis and Meiosis

Fungal Cells

Core Concepts

1. Fungi are heterotrophic eukaryotes that feed by absorption
2. Fungi reproduces both sexually and asexually, and disperse by spores

Fungi

• Fungi are responsible for
  • the decomposition of plants and animal tissues
  • locate and break down the complex molecules and bulky tissues
  • cycle carbon
• Heterotrophs: depend on pre-existing organic molecules for carbon and energy
• Release enzymes to break down complex organic molecules e.g., starch, cellulose, and lignin
• Absorb the digested organic molecules directly through their cell walls

Fungal Hyphae

• Most fungi are multicellular
• Consist of highly branched filaments, hyphae
• No mode of locomotion
• Use growth to find nourishment
• Mycelium: a network of branching hyphae

Hyphal Growth

Material Transport

• Cell walls are made of chitin, the same compound found in the exoskeleton of insects
• Can transport food and signaling molecules across long distances in mycelia, driven by changes in turgor pressure
• Differences in turgor pressure along hyphae drive bulk flow (similar to phloem transport)

  

  • Allows hyphae to use materials in nutrient-rich locations to fuel hyphal elongation across nutrient-poor locations
• In some early-diverging groups, the hyphae have many nuclei but no cell walls to separate them
• In more advanced groups, nuclear divisions are accompanied by the formation of septa, walls partially divide the cytoplasm into separate cells

Septa variation

• Plugs are developed to regulate the nutrient flow

  

Yeast

• Yeasts are single-celled fungi (Ascomycota)
• Foundin moist nutrient-rich environments
• Divide by budding

  

• Common on the surface of plants, and to a lesser extent on the surfaces and in the gut of animals

Decomposition

• Most fungi use dead organic matter as their source of energy and raw materials
• Bacteria and some protists can also subsist on dead organic matter but it is mostly fungi that decompose them back to carbon dioxide and water

Fungal Infections in Living Tissues

• Plants are vulnerable to a diverse array of fungal pathogens
  • e.g., rusts, smuts, and molds that cause huge losses in agricultural production
• Aboveground, infection is transmitted by fungal spores
• Belowground, infection is transmitted by hyphae that penetrate the root

Fungal Infections in Invertebrates

• Insects and other invertebrates are susceptible to fungal pathogens

Fungal Infections in Vertebrates

• Rare in vertebrates
• Severe infections are more frequent among fish and amphibians than in mammals

Fungus as a pathogen

• Mucormycosis caused a fungal disease (Mucorales)
• It is difficult for the fungi to meet the virulence factors

  

Mutualistic Relationships (Mycorrhizal)

• Mycorrhizal fungi supply plant roots with nutrients e.g., phosphorus from the soil
• In return, receives carbohydrates from their host
• Two main types: ectomycorrhiza, endomycorrhiza

  

• Ectomycorrhiza fungi do not penetrate
• Endomycorrhiza (Arbuscular mycorrhiza) penetrate into the root cells and produce arbuscules -> increase surface area for exchange of materials

Mutualistic Relationships (Endophytes)

• Fungi called endophytes live within leaves and grow within cell walls and in the spaces between cells -> mutualistic

  

• The insects provide the fungi with shelter, food, and protection from predators and pathogens
• Fungi are used as a food source for the insect

Mutualistic Relationships (Lichens)

• Lichens are associations between fungi and photosynthetic microorganisms e.g., green algae, cyanobacteria -> mutualistic

  

• The hyphae anchor the lichen to a rock or tree, aid in the uptake and retention of water and nutrients
• The photosynthetic partners provide a source of reduced carbon e.g., carbohydrates
• Cyanobacteria living in lichens provide a source of nitrogen e.g., ammonia
• Fungi and photosynthetic microorganisms exchange nutrients through fungal hyphae that tightly encircle or event penetrate the walls of the photosynthetic cells
• Lichens spread asexually by
  • Fragmentation
  • The formation of dispersal units consisting of a single photosynthetic cell surrounded by hyphae

    

Spore Dispersal

• Fungi face two challenges in completing their life cycles:
  • Maintaining genetic diversity: must find other individuals to mate with
  • Dispersal: must be able to disperse from one place to another
• The probability of any given spore landing on a favourable habitat is low -> produce huge number of spores
• Spores allow fungi to use resources that are patchy in time and in space

Asexual Spore Dispersal

• In many species, asexual spores are produced within sporangia that form at the ends of erect hyphae, facilitating the release of the spores into the air
• A moldy pieces of bread reveals that the surface is covered with hyphae carrying sporangia containing asexual spores

Sexual Spore Dispersal

Fruiting bodies

• Some fungi rely on external agents such as raindrops or animals to move their spores around e.g., Bird’s nest fungus

Fungal Life Cycle

• In most fungi, the sexual phase of the life cycle involves the fusion of hyphal tips rather than specialized reproductive cells, or gametes
• In fungi, the fusion of haploid cells is not immediately followed by the fusion of their nuclei
• Haploid nuclei retain their independent identities, resulting in a heterokaryotic stage
• The cytoplasmic union of two cells (plasmogamy) is not always followed immediately by the fusion of their nuclei (karyogamy)

  

Parasexual Cycle

• Parasexual fungal species lack an observable sexual cycle
• Use another mechanism of generating genetic diversity
  • The crossing over of DNA during mitosis
• The haploid chromosome number is restored not by meiotic division, but by the progressive loss of chromosomes
• The key difference is that parasexual species do not undergo meiosis

  

Fungal Diversity

Core Concept

• Other than animals, fungi are the most diverse group of eukaryotes

Fungal Phylogeny

Chytrids (Blastocladiomycota + Chytridiomyceta)

• Most chytrids are decomposers
• A few are pathogens of algae or vascular plants
• Many chytrids are single cells with walls or chitin
• Chytrids do not form a true mycelium
• Forms elongated structures rhizoids (not a hyphae)

Zygomycetes (Zoopagomycota + Mucoromycota)

Zoopagomycota

• Constitutes the earliest zygomycetes
• Contains species that are primarily parasites and pathogens of small animals and other fungi i.e., mycoparasites
• Basidiobolus can jump between its hosts

  

• Orphella: fungus growing on an insect

  

Mucoromycota

• Characterized by plant associations and plant-based ecologies
  • Mycorrhizae
  • Root endophytes
  • Decomposers
• Rizopus stolonifera: black bread mold

  

• Pilobolus: can forcibly eject the entire sporangium rather than releasing individual spores

  

• Fungal Highway Mucor: promote the growth of bacteria, mucorales species impact human beings beneficially through their use in food industry
• Glomeromycetes: a monophyletic group within Mucoromycota
  • Almost all occur in association with plant roots with tremendous ecological importance

Dikarya

• Key feature: every mitotic division is accompanied by the formation of a new septum

• e.g., All edible mushrooms, truffle, yeast, penicillin, blue cheese, cordyceps

  

• Allows fungi to control the number of nuclei within each cell

• Proliferate in the dikaryotic state

• Contains two monophyletic subgroups:

  • Ascomycetes: meiosis is followed by a single round of mitosis, resulting in asci that contain eight haploid spores

    

  • Basidiomycetes: fruiting bodies
    • Life cycle is similar to that of ascomycetes with some exceptions
      • fruiting body entirely made up of dikaryotic hyphae
      • nuclear fusion takes place in a specialized cell called a basidium

        

      • haploid products of meiosis do not undergo mitosis
      • Clamp formation: ensure that each cell is dikaryotic

        

    • Live by forming ectomycorrhizal associations or by decomposing wood and other substrates
    • The multicellular fruiting bodies produced by some fungi facilitate the dispersal of sexually produced spores
    • Fruiting bodies are highly ordered and compact structures compared to the mycelia from which they grow

• A novel floral mimicry system by Fusarium fungi

  

• Here, only D is a healthy flower

Terminologies

hypertonic: having a lower concentration of solute

hypotonic: having a higher concentration of solute

mutualist: a type of relationship between the host and symbiont where both organisms benefit and no one is harmed

commensal: a type of relationsip between the host and symbiontwhere one species obtains food or other benefits from the other without harming or benefiting the latter