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 incrase its turgor pressure
• Use the high turgor pressure to penetrate through host organism
• Subseuently occupy the host organism
• Absorb nutrients

Types of Transport

Passive Transport

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

Active Transport

• Requires energy
• Primary Active Transport
  • Move molecules in the opposite direction of the concentration gradient
  • The pumps 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

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
• 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 -> 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

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

Gibbs Energy in different reactions

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

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:
  • binds to the active site of the enzyme, competing with the substrate to reduce the rate of reaction
  • 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

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

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

Pyruvate Oxidation

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

  

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

Citric Acid Cycle

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

Products of Citric Acid Cycle

$$2 \times 1 ATP$$ $$2 \times 3 NADH$$ $$2 \times 1 FADH_2$$ $$2 \times 2 CO_2$$

Electron Transport Chain

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

Proton transport and ATP synthesis

• 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

• 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

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

  

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

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

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)

  

• Some live in extreme environment e.g., hot spring, glacier

Uncommon Photosynthetic Players

• Nostoc sp.: example of a symbiosis

  

• Geosiphon pyriforme

  

• 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 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

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

• $$5\times 3C \rightarrow 3 \times 5C$$

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 through chlorophyll in an electorns and sent to reaction center

Reaction Center

• Possess 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)
• Result in pumping more protons

  

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
• Antioxidants can neutralize ROS
• Xanthophylls can slow the formation of ROS
  • By reducing excess light energy
  • Yellow-orange pigmenst

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 cannto photosynthesize -> steal from fungi Note: red maple leaves still can perform photosynthesis through other yellow/brown coloured pigments

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