Biology Chapter: Cell Structure and Function

Living Organisms

• Characteristics of living organisms include cellular organization, ordered complexity, sensitivity to the environment, growth, development, reproduction, energy utilization, and homeostasis.

Taxonomy

• Taxonomy is a system used to name and classify organisms.
• The highest level of biological classification is the domain.

Prokaryotes

• Prokaryotes are organisms with small, single-celled cells lacking a nucleus.
• Examples include bacteria and archaea.
  • Prokaryotic cells are the simplest organisms.
  • They lack a membrane-bound nucleus.
  • DNA is present in the nucleoid.
  • A cell wall is outside the plasma membrane.
  • Ribosomes are present.
  • They lack common organelles.
  • Bacterial cell walls are composed of peptidoglycan.
  • Archaea cell walls lack peptidoglycan.

Eukaryotes

• Eukaryotes are organisms with larger, complex cells that have nuclei.
  • They contain a membrane-bound nucleus.
  • Their cells are more complex than prokaryotic cells.

Cell Theory

• All organisms are composed of cells.
• Cells are the smallest living units.
• Cells arise only from pre-existing cells.

Basic Structural Similarities

• Genetic material
• Cytoplasm
• Ribosomes
• Plasma membrane are found in all living organisms

Cytoskeleton

• Molecules related to actin and tublin are found in prokaryotes and influence cell wall shape, strength, and shape.
• Keeps organelles in fixed location

Nucleus

• Nucleus is the repository of genetic information.
• Nucleolus is the region where ribosomes/RNA synthesis takes place.
• The nucleus envelope is composed of two phospholipid bilayers.
• Nuclear pores control the movement of materials in and out of the nucleus.

Ribosomes

• Ribosomes are the cell's protein synthesis machinery.
• Found in all three domains (bacteria, archaea, and eukaryotes).
• A complex of ribosomal RNA (rRNA) and protein.

Endomembrane System

• A series of membranes throughout the cytoplasm in eukaryotic cells.
• Divides the cell into compartments for different functions.
• This system is a fundamental distinction between eukaryotes & prokaryotes.
• Proteins are transported through the endomembrane system.

Endoplasmic Reticulum (ER)

• Rough ER: site of protein synthesis, ribosomes attached
• Smooth ER: lipid synthesis (phospholipids, store calcium), detoxification
• The longest internal membrane system

Golgi Apparatus

• Flattened stacks of interconnected membranes (Golgi bodies).
• Function in packaging & distribution of molecules.
• Has a cis (receiving) face near the ER and a trans (shipping) face.

Lysosomes

• Membrane-bounded digestive vesicles.
• Arise from the Golgi apparatus.
• Contain enzymes that break down macromolecules (garbage disposal).
• Break down old organelles.
• Activated by fusing with a vesicle produced by phagocytosis.

Microbodies

• Variety of vesicles in eukaryotes that contain enzymes.

Peroxisomes

• Microbodies containing enzymes for oxidizing fatty acids.
• Produce hydrogen peroxide as a byproduct.

Vacuoles

• Membrane-bound structures, typically found in plants, fungi, and protists.
• Central vacuole: involved in cell growth (plants)
• Contractile vacuole: in some protists for maintaining water balance
• Storage vacuole: in plants for storage

Mitochondria

• Found in all types of eukaryotic cells.
• Has two membranes (smooth outer and inner folded membrane).
• Has its own DNA.
• Has matrix and intermembrane compartments.
• Embedded proteins carry out oxidative metabolism.

Chloroplast

• Present in plants and some other eukaryotic cells.
• Surrounded by two membranes.
• Contains chlorophyll (green pigment).
• Has thylakoids (membrane sacs) and grana (stacked thylakoids).
• Has its own DNA.

Microfilaments (Actin)

• Two protein chains loosely twined together.
• Involved in contraction, crawling, and pinching movements.

Microtubules

• Largest cytoskeletal elements.
• Dimers of α- and β-tubulin subunits.
• Facilitate movement of cell and materials.

Intermediate Filaments

• Very stable, not usually broken down.
• Medium size.

Endosymbiosis Theory

• Prokaryote engulfed by another cell = eukaryote.

Eukaryotic Cell Walls

• Different composition depending on the organism.
• Plants and protists: cellulose. Fungi: chitin.
• Animals lack cell walls but have glycoproteins and collagen

Cell Connections

• Three main types:
  1. Adhesive junctions
  2. Tight junctions
  3. Communicating junctions

Cell-to-Cell Interactions

• Cells make contact, read signals, and respond.

Glycoproteins/Glycolipids

• cell-surface markers

Plasmodesmata

• Specialized openings in plant cell walls.
• Connect the cytoplasm of adjoining cells, similar to gap junctions in animal cells.

Viruses

• Nucleic acid core surrounded by a protein coat (capsid).
• No cytoplasm (not a cell).
• Nucleic acid: DNA or RNA, single or double-stranded, linear or circular, segmented or not.
• Host range: types of organisms infected.
• Tissue tropism: viruses may only infect certain tissues in a host.

Viral Replication

• Viruses hijack host cellular machinery for replication, transcription and translation
• End result assembly and release of virus.

Virus Structure

• Viral structure types:
  1. Helical: spiral
  2. Icosahedral: almost spherical

Viral Genomes

• Can vary greatly in both type of nucleic acid (DNA or RNA) and number of strands (single or double).
• Most RNA viruses are single-stranded.

Retroviruses

• Have a single-stranded RNA genome reverse-transcribed into double-stranded DNA.
• Employ reverse transcriptase.

Virus Classification

• Methods include taxonomy, disease caused, or host infected.
• Baltimore system sorts viruses based on genome structure & expression.

Viral Diseases in Humans

• Categorized as persistent (chronic or latent), or acute
• Influenzavirus as an example.

Influenza

• Examples: 1918-1919 pandemic
• Subtypes differ in protein spikes (hemagglutinin & neuraminidase).
• Antigenic drift & shift can cause pandemics.

Prions

• Infectious proteins.

Viroids

• Tiny naked molecules of circular RNA; use host proteins to replicate.

Cell Membranes

• Form a barrier; regulate passage; receive stimuli; composed of a phospholipid bilayer; with proteins embedded.

Fluid Mosaic Model

• Proteins float in a fluid bilayer.

Membrane Components

• Phospholipid bilayer
• Transmembrane proteins
• Interior protein network
• Cell-surface markers

Types of Lipids

• Phospholipids
  • Amphipathic, spontaneously form bilayers.
• Sphingolipids
• Cholesterol

Protein Functions

• Transport
• Enzymes
• Cell-surface receptors
• Cell-surface identity markers
• Cell-cell adhesion
• Attachment to cytoskeleton
• Affect membrane structure

Anchoring Molecules

• Link membrane proteins to the membrane surface: modified lipids (non-polar regions insert into the bilayer, chemical bonds link to proteins).

Transmembrane Proteins

• Spanning the lipid bilayer: non-polar regions embedded, polar regions protrude.

Transmembrane Domains

• Hydrophobic amino acids arranged in helices.
• Single transmembrane domain anchors proteins.

Membrane Pores

• Non-polar regions create pores in transmembrane proteins for water and small polar molecules to pass

Membrane Transport

• Active transport (requires energy, substances move against concentration gradient.
• Passive transport (no energy needed, substances move down concentration gradient).

Active Transport Mechanisms

1. Uniporters (one molecule at a time).
2. Symporters (two molecules in the same direction).
3. Antiporters (two molecules in opposite directions).
4. Coupled transport

Vesicular Transport (Endocytosis & Exocytosis)

• Endocytosis: movement INTO cell (requires energy, phagocytosis, pinocytosis, receptor-mediated).
• Exocytosis: movement OUT of cell (requires energy)

ATP

• Energy currency of cells

Cellular Respiration

• Series of chemical reactions releasing energy from sugar, producing ATP.

Sodium-Potassium Pump

• Direct use of ATP, antiporter action.

Facilitated Diffusion

• Uses proteins (channels or carriers) to aid movement across membrane.

Channel Proteins

• Hydrophobic interior; "open or close". (aqueous channels) - polar molecules

Carrier Proteins

• Bind molecules for assisted passage
• Movement through diffusion Requires a concentration difference.

Osmosis

• Net diffusion of water across membrane towards higher solute concentration.

Osmolarity

• Hypertonic (higher solute concentration). Hypotonic (lower solute concentration). Isotonic (equal concentrations).

Factors Affecting Diffusion

• Concentration, molecular size, temperature

Scientific Method

• Hypothesis: possible explanation tested.
• Experiment: designed test to validate hypothesis.
• Control group: baseline for comparison.
• Experimental groups: different from control group.

Homologous & Analogous Structures

• Homologous: same origin, different structure/function.
• Analogous: different origin, similar function.

Genes, Genomes, and Atomic Components

• Gene: discrete info unit. Genome: entire DNA instructions.
• Ions: unbalanced charged particles. Isotopes: atoms with same element differing neutrons.
• Half-life: decay time. Valance electrons: outermost energy level electrons.

Chemical Bonds and Compounds

• Molecules: groups of atoms; compounds: more than one type of element.
• Ionic bonds: electron donation; covalent bonds: electron sharing.
• pH: potential of hydrogen, acids increase H+, bases decrease H+.

Macromolecules

• Carbohydrates (1:2:1 ratio C, H, O).
• Monosaccharides: simple sugars. Disaccharides: two simple sugars linked. Polysaccharides: long chains.
• Nucleic acids: nucleotides (sugar, phosphate, base). DNA (amino acid codes), RNA (similar to DNA but with ribose).
• Proteins: amino acids linked by peptide bonds.

Protein Structure

- Primary structure: amino acid sequence
- Secondary structure: peptide backbone interactions
- Tertiary structure: final folded shape
- Quaternary structure: multiple polypeptide chain arrangement

Chaperones

• Proteins that assist in protein folding.
• Denaturation: protein loses structure and function.

Lipids

• Triglycerides: glycerol + 3 fatty acids.
• Phospholipids: glycerol + 2 fatty acids + phosphate.
• Micelles & Phospholipid bilayers
• Waxes: fatty acids + alcohols.
• Steroids: important lipid molecules (cholesterol, sex hormones).

Energy and Thermodynamics

• Energy: capacity to do work.
• Kinetic energy: energy of motion; potential energy: stored energy.
• Heat: convenient energy measure.
• Energy flow: passage of energy through ecosystem (photosynthesis, potential energy, breaking bonds); oxidation (atom/molecule loses electron); reduction (gains electron); Electron transport chain.
• 1st & 2nd laws of thermodynamics; free energy (G = H - TS), enthalpy (H), entropy (S), exergonic, endergonic reactions; activation energy (raising energy of reacting molecules & lowering activation energy).

Catalysts and Enzymes

• Catalysts: lower activation energy of chemical reactions.
• Enzymes: most are proteins; speed up reactions by binding substrates in active sites.

Cellular Respiration

• 4 stages of aerobic respiration: glycolysis, pyruvate oxidation, citric acid cycle, electron transport chain & chemiosmosis
• Glycolysis: splitting of glucose, produces 2 ATP, 2 NADPH.
• Pyruvate oxidation: produces Acetyl-CoA, 2 CO2, 2 NADH
• Krebs Cycle: Oxidizes acetyl group, 6 CO2, 4 ATP, 10 NADH, 2 FADH2
• ETC/Chemiosmosis: electron carriers generate a proton gradient which in turn used by ATP synthase to make ATP (32 or 30 ATP).

Oxidation Without O2

• Anaerobic respiration (inorganic molecules as final electron acceptor)
• Fermentation (organic molecules as final electron acceptor).

Photosynthesis

• Overview: captures energy from the sun (6CO2 + 12H2O + Light = C6H12O6 + 6H2O + 6O2).
• Stages: light-dependent reactions (capture energy, make ATP & NADPH), light-independent reactions (Calvin Cycle: carbon fixation, reduction, RuBP regeneration).
• Pigments (Chlorophyll, carotenoids).
• Photosystems: antenna complex & reaction center.

Calvin Cycle

• 3 phases: carbon fixation, reduction, regeneration.
• Output: G3P (3-carbon sugar formed); used to make glucose, sucrose and starch; cycle runs in reverse during glucose formation.

Photorespiration

• Rubisco: enzyme with carboxylation and photorespiration activities; issues with maximizing CO2 uptake in C3 and environmental conditions.

C4 and CAM Photosynthesis

• Adaptations for carbon fixation in hot, dry environments
  • C4 plants: spatial separation of CO2 fixation pathways in different cell types.
  • CAM plants: temporal separation of CO2 fixation, with carbon fixation in different conditions.

DNA Replication

• Replication requires a template, enzymes, and building blocks of nucleotides.
• Stages: initiation, elongation, termination.
• DNA polymerases: main enzyme for building new strands; proofreading functions.
• Replication fork: point of opening.
• Leading strand. Lagging strand. Okazaki fragments

Eukaryotic DNA Replication

• Multiple origins.
• Complexity of replication enzymes.

Telomeres and Telomerase

• Protective structures at chromosome ends.
• Enzyme that maintains telomere length.
• Telomerase activity during development

DNA Repair Mechanisms

• Mismatch repair
• Photorepair (thymine dimers)
• Excision repair

Bacterial Cell Division

• Binary fission

Prokaryotic & Eukaryotic Chromosomes

• Chromatin: DNA & protein complex.
• Eukaryotes: multiple linear chromosomes.
• Prokaryotes: single circular chromosome.

Eukaryotic Cell Cycle

• G1 (gap 1). S (synthesis). G2 (gap 2). M (mitosis). C (cytokinesis).
• checkpoints: regulate progression.

Mitosis

• Stages: prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis.
  • Spindle apparatus. Centromeres. Kinetochores.

Meiosis

• Stages: 2 rounds of nuclear division (I, II),
• Synapsis Recombination (crossing over)
• Independent assortment
• Prophase I, Metaphase I, Anaphase I, Telophase I, Prophase II, Metaphase II, Anaphase II, Telophase II.
• Final result: 4 haploid cells (gametes).

Meiosis vs Mitosis

• Differences in chromosomal behavior and outcomes.

Errors in Meiosis

• Non-disjunction: failure of chromosome separation,
• Aneuploidy: abnormal chromosome number.

Sex Chromosomes

• X and Y chromosomes.

Sexual Reproduction

• Meiosis and fertilization.
• Variation increased.

Cell Cycle Control

• Checkpoints ensure accuracy.
• MPF (cyclin-dependent kinase), Cyclins, CDKs.

Cancer

• Uncontrolled cell growth due to mutations in tumor suppressor genes and proto-oncogenes.

Asexual Reproduction

• Clonal reproduction; in organisms like bacteria