Light microscopy → interacts with visible light for contrast e.g., reflection, scattering
- Specimen prep → minutes to hours
- Specimen status → dead or alive
- Staining → colored dyes
- Resolving power → low (0.25 \mu m to 0.3 mm)
- Magnification → 500X to 1500X
- Image → using eyes/screen
Electron microscopy → use of electrons as the source of illuminating radiation
- Specimen prep → days
- Specimen status → dead or dried
- Staining → heavy metal coating
- Resolving power → high (0.001 \mu m)
- Magnification → 100000X
- Environment → vacuum
- Image → fluorescent screens/photographic plate

Relating Cell Shape to Cell Function

Why are cells so small:
- Maximize sa:v → surface area:volume
- Size is determined by purpose
Root hair cell:
- Thin cell wall → increases rate of diffusion and osmosis
- Hair-like structure sticking out of the cell → increases sa:v
- Large vacuole → increases the amount of water/mineral salts it can store and pass on
- Many mitochondria → increased release of energy during respiration to provide energy for active transport
Nerve cell:
- Dendrite → allows collection and distribution of signals so multiple sources at the same time
- Axon → elongated to send electrical impulses quicker
- Myelin sheath → acts as an electrical insulator to maintain the strength of the impulse
- Node of Ranvier → increases speed of impulse transmission and conserves energy
- Schwann cell → acts as an electrical insulator to maintain the strength of the impulse
Red blood cell:
- No nucleus → allows more space for hemoglobin molecules
- Biconcave shape → maximizes sa:v to allow oxygen to be absorbed quicker and to allow movement
- Smooth rounded edge → more through capillaries without getting stuck

Identifying Different Cell Organelles

Endomembrane System → modify, package, and transport lipids and proteins

Rough endoplasmic reticulum
Golgi apparatus
Golgi vesicle
Plasma membrane
Lysosome
Smooth endoplasmic reticulum
Vacuole
Secretory vesicle

Information Center

Nucleus
Nucleolus
Chromatin

Cytoskeleton

Intermediate filament
Microtubule
Centrosome
Microfilament

Energy Converters

Mitochondria
Peroxisome

Organelle Roles

Nucleus → protects most of the cell's DNA, controls gene expression, manages replication of DNA
Nucleolus → site of ribosome and ribosomal RNA production
Ribosome → protein synthesis - found in the cytoplasm, on rough ER, on nuclear envelope
Chromatin → DNA complexed by proteins - primary components are histones - highly basic proteins
Endoplasmic reticulum → helps modify proteins and synthesize lipids
- Rough ER → folds proteins and modifies them to incorporate into cellular membranes or from the cell
- Smooth ER → synthesizes carbohydrates, lipids, and steroid hormones, detoxes medications and poisons, stores calcium ions
Golgi apparatus → processes proteins with different enzymes
Vesicles → transport vesicles → store and transport materials, secretory vesicles → absorb and destroy toxic substances and pathogens, fuse with other cell membranes to carry out specific roles
Lysosomes → breaks down macromolecules, repairs cell membrane, responds to foreign substances
Vacuole → help of various substances, store nutrients, and waste products to protect the cell from contamination
Plasma membrane → separates cytoplasm from the external environment, controls movement substances in and out of cells and organelles, involved in cell adhesion, ion conductivity, and cell signaling
Peroxisomes → transforms reactive oxygen species into safer molecules, oxidizes fatty acids
Mitochondria → generates energy stored in ATP, contains DNA
Cytoskeleton → gives the cell its shape and mechanical resistance to deformation, gives cell movement, organizes cell
Cilia and flagella → moves cells and other molecules
Cytoplasm → fills cell

Plant vs. Animal Organelle Function

Animals

Vacuole → one or more small temporary vacuoles, much smaller than plant cells
Peroxisome → oxidizes specific molecules
Cell size → smaller
Cell shape is generally round, irregular
Nucleus → found in a central location
Plasma membrane → contains cholesterol
Golgi apparatus → single and highly complex
Cell movement → moves by changing shape
Flagellum → present in some cells
Cilia → present in some cells
Energy source → heterotroph
Storage → reserve food in the form of glycogen
Extracellular matrix (ECM)→ extremely large proteins and polysaccharides → act as connective material to hold cells in a defined space, provide structural and biomechanical support to surrounding cells, involved in cell adhesion, cell-to-cell communication, and differentiation

Plants

Peroxisomes → oxidizes fatty acids, recycle carbon
Vacuole → one large, permanent vacuole - filled with water to maintain structural integrity of plant
Chloroplast → converts light energy to chemical energy → produces oxygen and energy-rich compounds
Cell wall → provides protection, chemically buffered environment, a porous medium for circulation and distribution of molecules, rigid building blocks to build stable structure, storage site of regulatory molecules
Plasmodesma → helps regulate passage of small molecules through cell wall → responsible for cell to cell communication
Cell size → usually larger in size
Cell shape → usually fixed rectangular shape
Nucleus → found along the periphery of the cell
Plasma membrane → does not contain cholesterol
Golgi apparatus → several simple
Cell movement → limited
Flagellum → present in some cells
Cilia → absent
Energy source → autotroph
Storage → reserved in the form of starch

Membrane Structure and Function

Features and Functions

Cell membrane - double layer of lipids and proteins that surround the cell
- Separates the cytoplasm from the external environment
- Controls movement of substances in and out of cells and organelles
- Cellular processes → cell adhesion, ion conductivity, cell signaling
- Selectively permeable
- Held together by strong hydrophobic interactions
- 3 main factors influencing membrane fluidity:
  - Temperature → increase temperature = increase fluidity
  - Presence of cholesterol → high temperature - holds membrane together using both hydrophobic and hydrophilic ends → raising Tm (when the membrane changes from gel-like to fluid-like by melting)
  - Phospholipid length and saturation → increased length → increased strength of interaction → decrease fluidity - kinks in tails (double bonds → unsaturated) → reduce ability to pack tightly → reduces strength of hydrophobic interactions → increases fluidity
- Components
  - Membrane proteins → proteins that interact with or are a part of biological membranes → integral (membrane penetrating), peripheral (attached via non-covalent bonds), lipid-anchored (attached through covalent bonds)
    - Transport - transporter
    - Enzymatic activity - enzyme
    - Signal transduction - receptor
    - Cell-cell recognition
    - Inter-cellular joining - anchor
    - Attachment to cytoskeleton and extracellular matrix
  - Membrane carbohydrates → carbohydrate chains consisting of 2-60 units - can be straight or branched
    - Sometimes linked to extracellular proteins (glycoproteins) or phospholipid molecules (glycolipids)
    - Cell adhesion
    - Cell recognition

Mechanisms of Transport for Molecules → Cellular Transport

Passive → requires no energy input

Diffusion → net passive movement of molecules from regions of higher to lower concentration (must be a concentration gradient) stops when equilibrium is reached
- Simple diffusion
- Facilitated diffusion - uses channel and carrier proteins
Osmosis → movement of water from a region of higher concentration to lower
- Osmolarity - total concentration of penetrating and non-penetrating solutes
- Tonicity - total concentration of non-freely penetrating solutes

Active → substances moving in or out of the cell against the concentration gradient - require energy

Active transport
- Na+/K+ pump → transmembrane protein pump (animal cells) - transports sodium and potassium ions across cell in ratio of 3:2 → creates electrochemical potential
H+ pump in mitochondria
Bulk transport → endocytosis and exocytosis
- Endocytosis → large molecules and substances are brought into the cell
- Exocytosis → transporting molecules from within a cell to the outside space

Enzymes in Metabolic Processes

Metabolism - chemical reactions carried out to maintain the living state of cells in organisms

Anabolic pathways → synthesize molecules and require energy (photosynthesis)
Catabolic pathways → break down molecules and produce energy (cell respiration) → thermodynamics and life

1st law: light energy converted to chemical energy by cells in leaves (photosynthesis) → chemical energy stored as glucose (forms complex carbs) → cellular respiration allows organisms to access energy from carbs, lipids, and other macromolecules through the production of ATP.

2nd law: as energy is transferred or transformed, more and more is wasted -→ 'wasted' energy goes towards entropy

Activation energy → energy required for a reaction to occur and determines its rate → enzymes - biological catalysts produced by cells - responsible for 'high rate' and specificity of one or more intracellular or extracellular biochemical reactions
- Mode of action
  - Lock and key model - substrate same shape as active site
  - Induced fit model - active site morphs to match substrate
- Feedback inhibition → the product of a pathway controls the rate of its own synthesis by inhibiting an enzyme catalyzing an early step
- Feed-forward activation → metabolite early in pathway activates enzyme further down the pathway
- Factors affecting enzyme activity
  - Substrate concentration
  - Enzyme concentration
  - Temperature
  - PH
  - Presence of inhibitors
Irreversible inhibition - an irreversible inhibitor inactivates an enzyme by binding to its active site
- Permanently deactivates enzyme
- Does not resemble substrates
- Allosteric enzymes - a group of regulatory enzymes whose catalytic activities are controlled by noncovalent binding to activators or inhibitors
  - Multi-subunit and possess an active and regulatory site
  - Regulated by binding to its regulatory site
  - Kinetics is a sigmoid growth curve.
  - Molecules involved in allosteric regulation can either increase (stimulate) or decrease (inhibit) enzyme activity
Adenosine triphosphate (ATP)
- All living things need energy to stay alive
  - Animals → oxidation of food
  - Plants → trap sunlight using chlorophyll
  - Must be transformed first

Cellular Respiration → converts food into energy (ATP)

Cellular respiration releases energy by breaking down glucose
Photosynthesis stores energy by synthesizing glucose → C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O + energy

1. Glycolysis → pathway for glucose catabolism

Glucose converted to pyruvate in 10 steps
1 glucose → 2 pyruvate
+ 2 ATP (uses 2 ATP but produces 4 ATP)
2NAD^+ \rightarrow 2NADH

Intermediate Stage - Fate of Pyruvate

Anaerobic Respiration - Fermentation

In plants and yeast, pyruvate is converted into ethanol and carbon dioxide
- 2 pyruvate → 2 ethanol + 2CO_2
- 2NADH oxidized to NAD^+
In animals, pyruvate is converted into lactic acid (lactate)
- 2 pyruvate → 2 lactate
- 2NADH oxidized to NAD^+
Cori cycle → metabolic pathway producing lactate by anaerobic glycolysis in muscles → transported to the liver and converted to glucose → returns to muscles → metabolized back to lactate
- Prevents lactic acidosis

Aerobic Respiration

Pyruvate decarboxylation → oxidation of pyruvate to acetyl-CoA
- Connects glycolysis and the Krebs cycle
- Controls the amount of acetyl-CoA fed into the citric acid cycle

Stage 2: TCA/Krebs Cycle/Citric Acid Cycle

Key metabolic pathway that connects carbohydrate, fat, and protein metabolism
Reactions in cycle are carried out by 8 enzymes that oxidize acetyl-CoA into carbon dioxide and water
NADH and FADH_2 generated by the citric acid cycle → used by the oxidative phosphorylation pathway to generate
For each turn of the cycle:
- 2 carbons enter from acetyl-CoA and 2 molecules of carbon dioxide are released (oxidation)
- 3 \times NAD^+ \rightarrow NADH
- 1 \times FAD \rightarrow FADH
- 1 \times GDP \rightarrow GTP
- 1 glucose molecule allows the cycle to run twice
- Only 2 ATP generated 'directly'

Glyoxylate Cycle - Anabolic Pathway Occurring in Plants, Bacteria, Protists, and Fungi

In plants → occurs in special peroxisomes called glyoxysomes
In the absence of available carbs (needed for growth) → the glycoxylate cycle permits the synthesis of glucose from lipids via acetate generated in fatty acid ß-oxidation
Bypasses steps in the citric acid cycle where carbon is lost

Stage 3: Oxidative Phosphorylation → Electron Transport Chain

Electrons flow down the energy gradient from NADH to O2 → 4 protein complexes catalyze redox reaction
- Complex I = NADH-Q reductase complex
- Complex III = cytochrome C reductase complex
- Cyt C = cytochrome C
- Complex IV = cytochrome C oxidase complex
Electrons flow down energy gradient from FADH_2 to O2 → 4 protein complexes catalyse redox reaction
- Complex II = succinate dehydrogenase
- Complex III = cytochrome C reductase complex
- Cyt C = cytochrome C
- Complex IV = cytochrome C oxidase complex
32 ATP generated

Other Biomolecules: Fatty Acids

ß-oxidation
- Requires 2 ATP
- Produces 1 NADH, 1 FAD, 1 acetyl-CoA

Other Biomolecules: Proteins

Protein catabolism
- Amino acids → products of stage 1 of PC - used to synthesise proteins and other substances that need nitrogen
  - Can degrade into pyruvate or oxaloacetate - called glucogenic → form glucose through the glucogenis pathway
  - Can degrade into acetyl-CoA or acetoacetic acid - called ketogenic → cannot form glucose but instead ketone bodies

Photosynthesis

Key Concepts

Photosynthesis converts light energy into the chemical energy of food
Light sections convert solar energy to chemical energy of ATP and NADPH
The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO_2 to sugar
Alternative mechanisms of carbon fixation have evolved in hot, arid climates
Life depends on photosynthesis

Terms

Autotrophs

Self-sufficient organisms that synthesize organic materials they require from inorganic sources (e.g., CO_2, nitrates)
Primary producers of the biosphere
Almost all plants are the photoautotrophs

Photoautotrophs

Use energy from the sun to make organic molecules from water and carbon dioxide
Photosynthesis occurs in plants, algae, some eukaryotes and prokaryotes
Feed themselves and most of the living world

Heterotrophs

Organisms energy is derived from the intake and digestion of organic substances produced by other organisms
Consumers of the biosphere
Almost all heterotrophs depend on photoautotrophs for food and oxygen

Chloroplasts → Site of Photosynthesis

Stroma - dense fluid within chloroplast surrounding thylakoid membrane and containing ribosomes and DNA - involved in the synthesis of organic molecules from carbon dioxide and water
Thylakoid - flattened membranous sac inside the chloroplast - often exists in stacks (grana) that are interconnected - the membrane contains molecular "machinery" used to convert light energy into chemical energy

Photosynthesis

Two processes:
1. Light is absorbed
2. Light reactions split water, release oxygen → produce ATP and NADPH
3. Calvin cycle uses ATP and NADPH to produce sugars

Light Reactions → Convert Solar Energy to Chemical Energy

Visible light absorbed by chloroplast
Chlorophylls are light absorbers - change state with light → when a pigment absorbs light it goes from the ground state to an excited, unstable state
Pigments absorb light
Absorbance spectrum → which pigments absorb which wavelengths best
Action spectrum → which wavelength is best for photosynthesis
Photosystems - composed of reaction centre surrounding light-harvesting complexes - two types of photosystems in the thylakoid membrane (PS1 and PSII).
Light-harvesting complexes - consist of pigment molecules bound to proteins - funnel energy to reaction centre
Reaction-centre chlorophyll molecule (special pair) - absorbs energy, one of its electrons gets bumped to a primary electron acceptor
Linear electron flow generates ATP and NADPH

Carbon Reactions

The Calvin cycle uses ATP and NADPH to fix CO_2 and produce sugars
1. Fixation
2. Reduction
3. Regeneration
H2O + CO2 + light \rightarrow O_2 + sugar

Alternate Mechanisms of Carbon Fixation

Stomata
- Allow for gas exchange → CO2 enters and O2 exits
- Water escapes when stomata open → stomata close to save water when hot, dry
C4 plants spatially separate carboxylases
- Carbon fixation and the Calvin cycle happen in different types of cells
CAM plants temporally separate carboxylases
- Carbon fixation and the Calvin cycle happen in the same cells at different times