Cell Biology Quiz: Plant and Animal Cells

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Questions and Answers

Which organelle is exclusively found in plant cells?

Plastids (correct)

Centrosomes

Mitochondria

Lysosomes

What is a primary function of the plant cell wall?

Providing structural support (correct)

Facilitating cellular respiration

Storing genetic material

Regulating cell division

Which of the following statements about animal cells is true?

They are typically larger than plant cells.

They produce their own organic matter.

They do not contain a cell wall. (correct)

They have chloroplasts for photosynthesis.

What role do plasmodesmata serve in plant cells?

Connecting cell walls across adjacent cells Signup and view all the answers

Which of the following best describes photoautotrophs?

Organisms that utilize sunlight for energy Signup and view all the answers

Which polymer is primarily present in the plant cell wall?

Cellulose Signup and view all the answers

What is the primary source of energy production for animal cells?

Cell respiration Signup and view all the answers

Which of the following statements about lysosomes in animal cells is correct?

They are responsible for cellular digestion. Signup and view all the answers

What type of bond is formed when two oses join to create a disaccharide?

Glycosidic bond Signup and view all the answers

Which of the following correctly describes a homopolysaccharide?

A long chain of the same type of monosaccharide Signup and view all the answers

Which statement about fatty acids is true?

Fatty acids have a polar hydrophilic head and a nonpolar hydrophobic tail. Signup and view all the answers

What characteristic distinguishes saponifiable lipids from non-saponifiable lipids?

Presence of fatty acids Signup and view all the answers

Which polysaccharide serves structural functions in plant cell walls?

Cellulose Signup and view all the answers

What type of polysaccharide is hyaluronic acid?

Heteropolysaccharide Signup and view all the answers

Which of the following fatty acids is classified as unsaturated?

Oleic acid Signup and view all the answers

Which carbohydrate is formed from two glucose molecules?

Maltose Signup and view all the answers

Which structure is characterized by a sphere of hydrophilic surface and hydrophobic core?

Micelle Signup and view all the answers

What type of bond connects the nitrogenous base to the pentose sugar in nucleotides?

N-glycosidic bond Signup and view all the answers

In comparing the stability of DNA and RNA, which statement is correct?

DNA is more stable than RNA. Signup and view all the answers

What is the diameter of a DNA double helix?

20 Å Signup and view all the answers

Which type of RNA contains ribose and replaces thymine with uracil?

mRNA Signup and view all the answers

Which of the following correctly describes the structural arrangement of nitrogenous bases in DNA?

Bases are complementary and located in the center of the double helix. Signup and view all the answers

Which statement about DNA denaturation is accurate?

DNA can be denatured by heating or alkaline conditions. Signup and view all the answers

What characterizes the major and minor grooves of the DNA double helix?

They provide sites for protein binding and enzymatic activity. Signup and view all the answers

What is the main reason that chromosome number does not correlate with the complexity of a species?

Majority of DNA consists of non-coding sequences. Signup and view all the answers

Which part of a chromosome serves as an attachment point for spindle microtubules during cell division?

Centromere Signup and view all the answers

What is a primary characteristic of euchromatin compared to heterochromatin?

Euchromatin is more transcriptionally active. Signup and view all the answers

During which cell stage do chromosomes reach their highest level of condensation?

Metaphase Signup and view all the answers

What role do telomeres play in chromosomal stability?

They protect chromosome ends from deterioration. Signup and view all the answers

What is the purpose of karyotyping in genetic studies?

To look for chromosomal abnormalities. Signup and view all the answers

Which of the following best describes the composition of chromatin during interphase?

Partially uncondensed and associated with proteins. Signup and view all the answers

In humans, which statement about homologous chromosomes is accurate?

They consist of one maternal and one paternal chromosome. Signup and view all the answers

What component of a bacterial flagellum is responsible for generating rotation?

Basal body Signup and view all the answers

Which of the following statements accurately describes the structure of eukaryotic and bacterial flagella?

Eukaryotic flagella are enveloped by an extension of the plasma membrane. Signup and view all the answers

What is the primary function of pili in bacteria?

Adhesion and conjugation Signup and view all the answers

Which statement about endospores is incorrect?

They are formed by all types of bacteria. Signup and view all the answers

What distinguishes a viroid from a traditional virus?

Viroids only consist of RNA molecules. Signup and view all the answers

Which of the following best describes how viruses operate?

They require host cells to replicate. Signup and view all the answers

In what context do cyanobacteria typically move?

By gliding due to their gelatinous layers. Signup and view all the answers

What is a significant threat posed by certain viruses?

They can lead to the development of cancers. Signup and view all the answers

What is a characteristic feature of the bacterial plasma membrane compared to the eukaryotic plasma membrane?

Has the same lipid bilayer structure Signup and view all the answers

Which of the following correctly describes the composition of a Gram-negative bacterial cell wall?

Thin peptidoglycan layer and an outer membrane containing LPS Signup and view all the answers

What structural role does the bacterial cell wall play for the bacteria?

It determines cell shape and provides protection against osmotic pressure Signup and view all the answers

Which component is specifically absent in the plasma membranes of most bacteria?

Steroids Signup and view all the answers

What is the primary function of the bacterial capsule, also known as glycocalyx?

To promote cell-to-cell adhesion and protect against phagocytosis Signup and view all the answers

What is a mesosome in the context of bacterial cells?

An artifact of sample preparation, not an actual structure Signup and view all the answers

Which of the following is true regarding the Gram-positive bacterial cell wall?

It is enveloped by a capsule Signup and view all the answers

What constitutes the primary structure of a bacterial cell wall?

A 3D network of peptidoglycans Signup and view all the answers

Signup and view all the answers

Study Notes

Cell Structure and Function - Cell Biology

The study of cells and their components, both structurally and functionally, is called cell biology. Cytology focuses only on the structural aspects of cells.

Chapter 1 - Cell Biology Birth

Cell doctrine outlines fundamental principles about cells
Cells are fundamental units of structure and function in living organisms
Cells divide to perpetuate life (mitosis, meiosis, fertilization)
Cells, collectively with their products, form organisms

Cell Biology vs Cytology

Cell biology studies cells and their components structurally and functionally
Cytology studies cells and their components structurally

The Cell Doctrine

Fundamental unit of structure and function
Cells divide
Cells + products = organisms
Basis of life continuity (mitosis, meiosis, fertilization)
Existence of a double-life: one for itself, & one for the organism

Chapter 2 - Molecular Components of Cells

Inorganic and Organic Compounds

Atoms and Molecules in Cells

Carbon (C), Hydrogen (H), Nitrogen (N), and Oxygen (O) are the most abundant atoms in cells, making up 96%.
Sodium (Na), Potassium (K), Chlorine (Cl), Sulfur (S), and Phosphorus (P) account for another 4%.
Remaining elements are trace elements (B, F, Mn, Fe, Co, Cu, Zn, Se, I...)

Molecular Level

Organic molecules ("Biomolecules"): Proteins, Carbohydrates, Lipids, Nucleic acids
Inorganic molecules: Water, Mineral salts

1. Water

Basis of cell life; most abundant
Electrically neutral
Extremely polar: partially negative oxygen and partially positive hydrogen
Forms hydrogen bonds with other molecules, and ionic bonds that solubilize salts.
H₂O is found free or interacting with molecules

2. Mineral Salts

Dissolved and ionized by water (due to water polarity)
Important for membrane permeability, nerve impulse, muscle contraction, and cell division
Metal ions vital for certain protein activities (muscle contraction, O2 transport, intercellular signaling)
Different concentration inside vs outside the cell.

3. Organic Compounds

Molecules: amino acids, monosaccharides, fatty acids, nucleotides
Macromolecules: proteins, polysaccharides, lipids, DNA, RNA
Vitamins: needed at low levels; some are carbs, other are lipids

1. Proteins

Introduction: Most abundant organic molecules; exhibit great diversity in functions due to encoded genes.
Function: All functions for cell & organism life (morphology, gene expression, DNA replication, transportation, communication, immunity, senses, cell cycle, and muscle contraction)
Chemical composition: Composed of amino acids (aa) – identical type for a protein type.
Diverse chemical compositions (number and sequence) lead to diverse 3D structures and diverse functions
The Amino Acids: Composed of C, H, N, O, S, and linked to NH₃, COOH, H, and R side chains. Four group types for different properties: polar uncharged, nonpolar, polar positive, polar negative
Amino acids are soluble in water
Their ionization depends on pH and R
Zwitterions: amino acids with uncharged R and ionized groups at pH = 7
Only L-stereoisomers form polypeptides
Polypeptide Bond Formation: formed by ribosomes; digested by proteases
Reaction between NH₂ of aa (n) & COOH of aa (n-1).
Amide bond (CO-NH).
H₂O is eliminated
Repeating N – Cα – C: backbone of the protein
Polarized: N-terminus (Amino terminus, NH₂) & C-terminus (Carboxy terminus, COOH)
Polypeptide Flexibility: Extended groups not in same plane → confer flexibility, helping folding into 3D conformations.
Structures of Proteins: Primary structure: sequence of amino acids Secondary structure: localized folding patterns (alpha-helices and beta-sheets) Tertiary structure: overall 3D structure of a polypeptide chain Quaternary structure: arrangement of multiple polypeptide chains in proteins with multiple subunits
Primary structure: Linear aa sequence. Determined by DNA nucleotide sequence
Stabilized by: covalent bonds between amino acids.

5. Polypeptides

Linear unbranched chain of amino acids joined by covalent bonds (“peptide bonds”)
Formeed by ribosomes; digested by proteases
Formed by nucleophilic attack between NH₂ of aa(n) and COOH of aa(n-1)
Amide bond (CO–NH)
Backbone: Repeating N-Cα-C
Polarized: N-terminus (NH₂) and C-terminus (COOH)

6. Polypeptide Flexibility

Extended groups (R, H, =O) are not in the same plane; they rotate in different directions.
Helps folding to adopt 3D conformations

7. Structures of Proteins

Primary Structure: The sequence of amino acids in the protein
Secondary Structure: Hydrogen bonding creates alpha-helices and beta-sheets
Tertiary Structure: Overall protein folding. Stabilized by hydrogen bonds, ionic bonds, and hydrophobic interactions, disulfide bridges.
Quaternary Structure: Multiple polypeptide chains forming a functional protein. Stabilized by weak bonds, sometimes by covalent bonds.

a. Primary Structure

Linear amino acid sequence
Determined by the nucleotide sequence in DNA
Fundamental to its other structures; its alternation impairs protein functions
Copies of the same protein have identical primary structures

b. Secondary Structure

Folding of amino acid portions into alpha-helices or beta-sheets
Stabilized by hydrogen bonds
Denaturation can occur with heating or chemicals
Specific sequence leads to specific folding patterns

c. Tertiary Structure

Helical & non-helical regions are folded back in precise positions
Hydrophobic amino acids in the core and charged amino acids exposed on the surface
Stabilized by: hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges.

d. Quaternary Structure

Some proteins require multiple subunits (identical or different)
Assembly forms active domains.
Stabilized by weak bonds, sometimes covalent bonds
Protein activation/deactivation: by changing its 3D conformation
- by phosphorylation/ dephosphorylation
- by allosteric transition (ligand binding/dissociation)

8. Classification of Proteins

By composition: Holoproteins (only amino acids); Heteroproteins (amino acids + other molecules: ex: lipoproteins, glycoproteins; nucleoproteins, hemoproteins).
By structure: Fibrous (insoluble in water, e.g. keratin, collagen); Globular (soluble in water, e.g., globulin, albumin, histones).
By function: structural, defense, regulatory, transporter, catalytic, contractile ...

II. Carbohydrates

Functions: Energetic (glycogen in animals); Structural (cellulose in plant cell walls); Cell identity (blood groups)
Monosaccharides (Definition): “Simple oses”; mostly D-stereoisomers; CnH₂nOn (3≤n≤6) – less diverse than proteins.

1. Monosaccharides Definition

Aka “simple oses”
Mostly D-stereoisomers
CnH₂nOn (3 ≤ n ≤ 6)
Less diverse than proteins as only a few types form polymers; different types do not combine much

1. Classification of Monosaccharides

By functional group: Aldoses; Keto
By n: Trioses; Tetroses; Pentoses: ribose; Hexoses: glucose, galactose, mannose, fructose.

2. Cyclic Oses

n>4 → straight chain or cycle. Cycle is more stable. Pryanoses (6C) & furanoses (5C).
From intramolecular reaction between OH & aldehyde/ketone group.
α & β isomers differ by orientation of OH replacing the aldehyde/ketone group. α: downward, β: upward
Usually cyclic oses are switchable between α & β until polymerized.

4. Modification

Osamines: addition of amine group (-NH₂); eg: glucose → glucosamine. galactose → galactosamine
N-acetyl osamines: addition of acetyl group (–COCH₃) to the amine group ; eg: NAG: N-acetyl galactosamine
Uronic acids: acidification of CH₂OH into COOH; eg: NANA: N-Acetyl Neuraminic Acid(from mannose).

5. Dimers and Polymers

Disaccharide: 2 oses joined by covalent bond "glycosidic bond"
- Saccharose = glucose + fructose
- Lactose = glucose + galactose
- Maltose = 2 glucose
Oligosaccharide: Short polymer of monosaccharaides
- Can be branched/unbranched
- Can be linked to proteins/lipids for maturation.
Polysaccharide (Glycan): Long chain of monosacharides, branched or unbrached.
- Functions: structural (cellulose in plant cell walls, and peptidoglycans in bacterial cell walls), or energetic (glycogen in muscles and starch in plants). Homopolysaccharides: polymers of the same molecule
- eg Starch & glycogen: branched chains of a-D-glucose; Cellulose: an unbranched chain of β-D-glucose; Chitin: a polymer of N-acetylglucosamine (insects shells).
Heteropolysaccharides: polymers of 2 different simple/modified oses
- eg: GAG, Hyaluronic acid, Chondroitin Sulfate, Keratan sulfate.

III. Lipids

All are non-polar
- Insoluble in water, soluble in non-polar solvents
Functions: Structural (phospholipids: component of cell membranes), Energetic (triglycerides: stored in plant seeds and animal adipose tissue), Communication (steroid hormones, eicosanoids, phosphatidylinositol) 2 types: • Saponifiable: have fatty acids [f.a] can undergo saponification reaction • Non-saponifiable: no f.a, cannot undergo saponification reaction

1. Saponifiable Lipids

a. Fatty Acids:
Amphipathic: one polar hydrophilic head (COOH) and non-polar hydrophobic tails (hydrocarbon chain).
Formula: CH₃ – (CH₂)n – COOH (2≤n≤20) n is even
Less diverse than carbs.
Differ by length of chain & unsaturation degree (nb of C=C)

b. Triglycerides / Triacylglycerols / neutral fats

Neutral fats → no polar groups
Glycerol + 3 f.a joined by ester bonds
Function: stored energy reserve
Hydrolysis by lipases or by alkaline medium + heating

c. Phospholipids

Function: structural (found in cell membranes)
- Amphiphilic: One large polar head (phosphate) + 2 hydrophobic tails - Glycerol-derived: Glycerophosphatides (Phosphate + glycerol + 2 f.a.)
- Sphingosine-derived: Sphingophospholipids (Phosphate + sphingosine + 1 f.a) Found in myelin sheath
Ceramide = sphingosine + f.a
Certain molecules can be added to increased head polarity.

d. Glycolipids

Function: cell identity (blood group, immunity, cell-cell recognition). Found on the outer cell membrane
Glycerol-derived: (plants & bacteria); (sugar + glycerol + 2 f.a)
Sphingosine-derived: (animals); (sugar + sphingosine + 1 f.a)
Cerebrosides: simple ose monosaccharide; eg: galactocerebroside in brain’s myelin sheath
Gangliosides: oligosaccharide

e. Cerides

Esters of f.a + "fatty alcohol" (long hydrocarbon chain ending with OH). In bee wax, leaf cuticle, cork

2. Non-saponifiable Lipids

a. Terpenes: polymers of propene with cyclization at one end.
Vit. A, E, K, and carotenoids
Steroids: cyclic molecules with diverse functional groups • • Functions: communication (steroid hormones: estrogen, progesterone, testosterone, corticosterone, adrenal hormones...), vitamins (Vit.D for growth & bone development(synth in skin)), as structural components (cholesterol).

3. Hydrophobic Interactions

Lipids are amphipathic and water insoluble, hence they mix to form heterogeneous mixtures. Monolayers. Bilayers: polar hydrophilic surfaces, hydrophobic center stopping the diffusion of large hydrophilic molecules Micelles: sphere of hydrophilic surface and hydrophobic core. Liposomes: long bilayer folded back on hydrophilic surfaces and lumen.

IV. Nucleic Acids

Composition: Nucleic Acid = Unbranched chain of nucleotides (DNA/RNA); Nucleotide = Nucleoside + Phosphate; Nucleosides = Nitrogenous base + Pentose; Nitrogenous bases: Purines (A, G) – Pyrimidines (C, U, T)
Nucleosides: Adenosine, Guanosine, Thymidine, Uridine, Cytidine. Nucleotides: AMP, ADP, ATP, GMP, GDP, GTP, CMP, CDP, CTP, TMP, TDP, TTP, UMP, UDP, UTP
Preceded by d (deoxy) for DNA
NTP is used during building nucleotides → 2 P are used for energy
Bonds: Nitrogenous Base & Pentose → N-glycosidic bond (1’); Pentose & Phosphate → phosphoester bond (5’); Adjacent nucleotides → phosphodiester bond (5’ & 3’); Facing nitrogenous bases → hydrogen bond.

IV. Nucleic Acids

Pentose: DNA → Deoxyribose; RNA → Ribose
Nitrogenous base: DNA → Thymine; RNA → Uracil
Secondary structure: DNA → Double-stranded; RNA → Single-stranded
Location: DNA → Nucleus, mitochondria; chloroplast; RNA → Nucleus, mitochondria, chloroplasts + cytoplasm
Stability: DNA → More stable; RNA → Less stable

2. DNA Structure

2 polynucleotide chains in a double helix
Backbone = phosphate and sugar
Nitrogenous bases in the middle of the helix
Complimentary Purine-Pyrimidine: A &T,C&G
Antiparallel (One strand is rotated 180° wrt the other)
Grooves (major and minor): functional groups bind to proteins involved in condensation, replication and transcription

3. DNA Replication

Aim: Transmission & Preservation of Genetic info
Replication complex: set of enzymes: helicase, primase, topoisomerase (gyrase), DNA polymerase, ligase
Requires a lot of energy (from precursors: dNTPs)
Semi-conservative: each new doublestrand molecule contains 1 old template strand and 1 newly synthesized strand

3. Nuclease activity

Some polymerases have the ability to degrade DNA
Exonuclease activity: ability to degrade DNA from extremities.

3. DNA replication

Helix unwinding: helicase separates the 2 strands at specific points (origin)
Eukaryotes have many replication origins per chromosome
Replicon: long segment of DNA starting from origin; primase (RNA polymerase) adds a primer (RNA sequence) to provide 3’OH end for DNA polymerase to start
DNA polymerase binds and starts synthesizing new strand using dNTPs
Adding them in a complementary manner (A↔T, C↔G)
Template is read 3’-5’, new strand is synthesized 5’-3’
Topoisomerase (gyrase): releases the tension → relaxes supercoiled DNA
DNA polymerase I removes primers (5’-3’ exonuclease)
Ligases join Okazaki fragments

4. RNA Structure

Single polynucleotide chain
Some intramolecular pairing
snRNA: Bound to proteins to form snRNP
mRNA: Most abundant; encoded by many genes. single-stranded and paired in some regions
rRNA: Most abundant
tRNA: Least diverse

4. RNA Structure

Single polynucleotide chain
Some intramolecular pairing
snRNA: Bound to proteins to form snRNP
mRNA: encodes a protein; translated into protein/mRNA maturation by splicing.
rRNA: highly abundant and structured; forms ribosomes.
tRNA: brings amino acids in a specific order, has 3′ & 5′ ends.

Replication vs Transcription

Replication: Both DNA segments are templates. The whole strand is replicated. Uses helicase, ligase.. + DNA Polymerase.
Transcription: Only 1 strand is a template. Only genes are transcribed. Uses helicase, ligase.. + RNA Polymerase.

I. Definition of Eukaryotes & Prokaryotes

Eukaryotes:
Nuclear membrane (DNA & ribosomes separated)
Compartmentalized (organelles)
Unicellular or multicellular
Size: tens to hundreds of µm Animals, plants, fungi, protists, protozoa
Prokaryotes
No nuclear membrane
Non-compartmentalized (no organelles)
Eubacteria, archaebacteria, mycoplasma (PPLO) unicellular
Size: 1-2 μm
Viruses: Not living things; cannot reproduce on their own; sizes in nm. visible by electron microscopy

II. Eukaryotic Cells

Organelles:
Only in animals: Centrosomes, Lysosomes, Cilia, Flagella, Microvilli
Only in plants: Plastids, Vacuoles, Cell walls, Plasmodesmata
Common ones: Nucleus, Cytosol (hyaloplasm), ribosomes, cytoskeleton, Endoplasmic Reticulum, Golgi, mitochondria, plasma membrane, peroxisome

1. Animal cells

Heterotrophs: feed on organic matter
Smaller than plant cells

2. Plant cells

Photoautotrophs: produce their own organic matter by photosynthesis
Bigger than animal cells

Cell Wall

Thick surrounds the plasma membrane
Made of cellulose, hemicellulose, pectin, and glycoproteins

Plasmodesmata

Cytoplasmic bridges between neighboring cells that interrupt the cell wall
Exchange of molecules between cells

Plastids

Family of organelles
Functions: Photosynthesis; storage of organic compounds
Example: Chloroplast – Photosynthesis in green plants
CO₂ + H₂O → Glucose + O₂
light
other plastids: Amyloplast, elaioplast, proteoplast

Vacuoles

In mature plant cells: Large; occupies major part of the cell
In young dividing cells: Small; fuse together
Single membrane: tonoplast
Role: expand cell volume, store water, cell products, metabolic intermediates

II. Prokaryotes

Structurally: appear simple; Biochemically: diverse and complex biochemical reactions.
Not all bacteria are harmful. Some are beneficial (e.g. lactic bacteria). Some are harmful (e.g. tetanus toxin)
Oxygen requirement: Aerobic: require oxygen; strict anaerobes: cannot survive in presence of oxygen; facultative anaerobes survive in presence or absence of oxygen
Trophic mode: Heterotrophs (feed on organic nutrients); Photoautotrophs (make photosynthesis); Chemoautotrophs (make chemosynthesis)
Colonies: unicellular; can live in clusters; no differentiation; all cells are identical
Growth: asexual (by fissparity or binary fission)
Size & shape diversity: Spherical; elongated, spiral-shaped
Classifications: Eubacteria (true bacteria): Live in mild conditions similar to eukaryotes Archaebacteria (ancient bacteria) extremophile: Live in extreme conditions (pH, temperature, salinity). Chemoautotrophs(thermophile; halophile; methanogens) Mycoplasma (PPLO): Small bacteria; spherical or filamentous; intracellular parasites; causes diseases (respiration & urogenital); no cell wall and capsule

II. Prokaryotic Cells

Cellular Structures
- Nucleoid
- Plasmid
- Cytoplasmic structures
- Plasma membrane
- Cell wall
- Capsule
- Flagella
- Pili & fimbriae
- Endospore

a. Nucleoid

Dense region in cytoplasm; NOT separated by a membrane
Contains circular DNA (chromosome), condensed by proteins
It separates the 2 DNA copies during cell division. No nucleolus;

b. Cytoplasmic Structures

Bacterial cytoplasm = single compartment
Can perform many processes without organelles
Example 1: mitochondria in eukaryotes: has enzymes for cell respiration and production of ATP. Bacteria have such enzymes in the cell membrane and cytoplasm.
Example 2: chloroplast in eukaryotes: perform photosynthesis.
Photosynthetic bacteria have photosynthetic lamellae: infoldings of plasma membrane. Can become independent structures (chromatophores). But not comparable to eukaryotic ER.
Example 3: Cyanobacteria: have gas vacuoles that control buoyancy, and carboxysomes: enzymes that fix CO2 for photosynthesis.
Example 4: Chlorobium: have chlorophyll-containing vesicles
Ribosomes: different from eukaryotic ribosomes, free in cytoplasm or attached to plasma membrane; no attachment to lamellae
Granules / inclusions: storage of organic & inorganic compounds (sulfur, phosphates, carbohydrates)

c. Bacterial Envelope

Bacterial envelope = plasma membrane + cell wall (except mycoplasma) + capsule (if present)
1* Plasma membrane: Lipid bilayer similar to eukaryotes, but without steroids; selective permeability; many metabolic reactions (transporters, ATP synthase, respiratory chain)
2* Cell wall: determines cell shape; protects against changes in osmotic pressure (bacteria cell wall = peptidoglycans=3D network heteropolysaccharides (glucose + N-acetylglucosamine)) joined by peptide bridges -
Gram (+): thick wall; + teichoic acids.
Gram(-): thin wall; peptidoglycans; 2nd lipid bilayer (outer membrane) + maybe capsule
Cyanobacteria: thin wall; peptidoglycans.
3* Capsule (glycocalyx): outer structure of cell envelope in many bacteria (not all); made of polysaccharides; functions: adhesion, cell-cell and cell-support; protects bacteria against phagocytosis; increases pathogenicity of bacteria
d. Flagella: Thread-like appendages; 1 or more per cell; At 1 pole, or distributed over the entire cell. Function: cell locomotion. 3 parts: basal body, hook, filament.
e. Pili & Fimbriae: - Pili = hair, Rigid appendages on cell surface, Shorter and finer than flagella, Functions: Bacteria-bacteria adhesion & conjugation, bacteria-host adhesion, receptors for viruses.
f. Endospores: Formed by several bacteria (not all) - Formed in stress & nutritional depletion. Highly resistant to dessication, heat & chemical stress, Resists harsh conditions for decades. When medium becomes favorable again: germinates the original bacterium.

III. Viruses

Multimolecular complexes; not cells, not living things
Cannot divide by themselves; need metabolic enzymes and pathways; need host cells to multiply
Infect animals, plants and bacteria
Cause many diseases (e.g., AIDS, smallpox, chickenpox, rabies, poliomyelitis, mumps, measles, hepatitis, mononucleosis, influenza, common cold)
Some can cause cancers
Composition: Nucleic acids (DNA/RNA, linear/circular, ss/ds), Capsid (made of protein subunits: capsomeres), Few proteins (polymerases, integrase), some have envelopes (lipid bilayer) e.g. HIV, influenza, smallpox, some have tails linked to heads
Viroid = only RNA molecule. Very simple virus with no proteins.

Virus-Host Relationship

Viruses deviate/alter the cell metabolism (transcription, translation, replication) for their own benefit
Viruses are specific to certain species, organ, tissue, cell, and even sub-cell type since they require specific receptors on their cells
viruses change after leaving the host(e.g H1N1: infects humans and pigs; H5N1: infects humans and birds). H: hemagglutinin, N: neuraminidase (antigens on envelope)

1. Structure & Classification of Viruses

Size: 20 – 200 nm
Nucleic acids: DNA (e.g., adenoviruses) or RNA (e.g., HIV, influenza)
Envelope: present or absent
Capsid: helical (TMV), polyhedral (adenovirus), complex (bacteriophage), or no symmetry
Host cell: infecting prokaryotes (bacteriophages/phages)/eukaryotes
Determinant of viral shape: rod, globular, polyhedral, helical, or complex

2. Proliferation of Viruses

Viral capsid / membrane proteins recognize host cell receptor
Virus adheres to host surface
Virus injects its nucleic acid + proteins (polymerases...) into the host cytoplasm
Enveloped virus: fuses its lipid bilayer with cell membrane
nucleocapsid enters the cytoplasm → capsid dissociates → nucleic acid released
Non-enveloped virus: only nucleic acid is injected through a channel
Host cell dies
Thousands of new viruses are produced

RNA Viruses

Retroviruses: RNA → DNA (provirus)
No reverse transcriptase (RNA replication by "RNA-dependent RNA Polymerase" “replicase”)
Lytic or Lysogenic cycle
Lytic: Cell genes are repressed and viral genes are expressed to produce more viruses. The host cell lyses at the end.
Lysogenic: Viral DNA is inserted into host cell DNA; no immediate expression of viral genes, but viral genes are replicated and passed on to the daughter cells.

Lysogenic Cycle

Viral DNA is inserted into cell chromosome by “integrase”, silent active DNA
As cell divides, cellular DNA & viral DNA is replicated, transmitted to daughter cell → silent reproduction of virus
Can transform cells and cause cancer

Lytic Cycle

Cell metabolism is deviated; viral genes are preferably transcribed over cell gene.
RNA is produced; translated to proteins by host cell equipment.
Viral nucleic acids are produced by replication/transcription.
Assembly of viral particles; release of viral particles.
Enveloped: released by budding; nucleocapsid interacts with host cell membrane. Takes a fragment to become an envelope.
No lipid envelope: released by causing cell lysis; their enzymes

IV. Prions

Unusual pathogens = only proteins (no nucleic acids)
Abnormal conformation
Can transform its abnormal conformation to other normal proteins.
Protease resistant Causes toxicity
accumulate in cells.
Disease in animals and humans due to prions → Death of nerve cells (neurodegeneration).
Disease examples: Scrapie, BSE, Creutzfeldt-Jacob disease.

1. Plasma membrane and other cell membranes

Cell membranes = "Biomembranes"
Plasma membrane/cell membrane/cytoplasmic membrane.
Cytomembranes: membranes of nucleus, ER, Golgi, mitochondria, vacuole, plastids….
Visible by electron microscopy (not bright light) microscopy; Less developed in prokaryotes than eukaryotes.

Functions

Physical:- Cell membrane separates the cytoplasm from the surrounding medium → cell integrity
- Organelle membranes separate organelles from cytosol → cell integrity
Biochemical: Signal transduction, phosphorylation & cell respiration
Communication: with neighboring cells.
Selective & controlled permeability: Regulates passage of solutes in & out

Permeability

Hydrophobic molecules
Most can easily pass the membrane
Hydrophilic molecules
Require channels/transporters (membrane proteins)
Large molecules
By vesicles (exocytosis, endocytosis, phagocytosis)

Composition

Phospholipids: glycerol/sphingosine-derived
Glycolipids: antigens (eg: gangliosides) on outer leaflet
Steroids: eg cholesterol
Proteins: most membrane functions
Carbohydrates: linked to proteins/lipids → glycocalyx
protection against proteolytic enzymes, adhesion, recognition.

1. The Lipid Bilayer

A study on hydrophobic interactions:
Polar heads directed outward & inward
Non-polar tails directed to one another
Bilayer stabilized by hydrophobic interactions
Staining by osmnium tetroxide (polar):
2 outer dark lamina → osmophilic → polar
1 central clear lamina → osmophobic → nonpolar
Thickness: Variable according to f.a & proteins
- Osmophilic lamina 20→25 A
- Osmophobic lamina 25→35 A
- Total 65→85 A

II. The Fluid Mosaic Model

Bimolecular-lipid layer
E = exoplasmic(outer); P = protoplasmic(inner)
Composed of phospholipids+neutral fats & steroids+proteins in a mosaic manner.
Mosaic = irregular distribution of proteins in the bilayer

Membrane Proteins

Types - Peripheral/extrinsic: at inner & outer surfaces
attached by weak bonds (not covalent) to lipids or other proteins - Peripheral/extrinsic: at inner & outer surfaces → attached by covalent bonds. - Integral/intrinsic: penetrate the membrane. - Partially (1 layer): “monotopic” - Entirely (both layers): “polytopic” - Single-pass polytopic (bitopic) - Multipass: crosses the membrane once/many times - All have segments of ~ 20 hydrophobic aa (a helix) to interact with hydrophobic tails. Many spans → many hydrophobic segments.

III. Functional Domains

Polarisation = membrane composition and function are not uniform through the entire cell surface.
Distinct poles; distinct proteins & lipids; distinct properties & functions
Epithelial cell
- apical
transporters & channels for nutrient absorption from lumen
- basal
adhesion to basement membrane; transport of nutrient to blood vessels
- lateral
adhesion to neighbouring cell
Hepatocyte: parenchymal liver cells
- pole facing endothelial cells exchange substaces with blood
- pole facing neighbouring hepatocytes exchange substances; make junctions (desmosomes)
- pole in contact with bile canaliculi discharge of bile pigments & salts into gallbladder

5. Microdomains: "Lipid Rafts"

Subdomains in plasma membrane
Role: signal transduction, contains specific phospholipids and proteins (kinase-like signaling proteins)
Caveoli: lipid rafts at an invagination of the plasma membrane. Contain caveolin(protein); role: endocytosis.

III. Specialization of Plasma Membrane

Specialized junctional regions
Function: adhesion, intercellular transport, communication, wound healing
Formed: embryonic life & remain stable
Involve: SAM & CAM membrane proteins, cytoskeleton components, proteins that function in adhesion → function in signalling

1. Tight Junctions

Narrowed/plugged intercellular space → barrier to flow of materials
Location: belt between the apical & lateral pole; belt that surrounds the cell
Cell membranes of neighboring cells fuse together (like 2 halves of a zipper)
Protein family involved: occludins
Cytoskeletal component: actin filaments → determines cell shape
Tissues: epithelia (eg: intestine enterocyte), seminiferous tubules (sertoli cells), endothelial cells (blood-brain) → control: disassociated by immune cells

2. Intermediate Junctions / Belt Desmosomes / Zonula Adherens

Function: adhesion of cells. Leaves intercellular space
Location: just below tight junction belt; encircles the cell
Protein: cadherins.
Cytoskeletal component: actin filaments.
Linked to cadherins by catenin → dense thick zone (network of protein filaments).
Tissues: many, especially epithelia

3. Spot Desmosomes / Macula Adherens

Punctual junctions = strongest junction
Location: everywhere between neighbouring cells
Function: connect intermediate filaments (keratin) by a 3D network
Support and resistance to pressure
Protein: cadherins.
Cytoskeleton component: intermediate filaments interact with cadherins at a discoid dense region & anchorage proteins.
Tissues: All (skin epithelium, uterus, cardiac muscle).

4. Hemidesmosomes

Half-desmosomes
Location: basal pole of epithelia
Function: attachment of epithelia to basement membrane (laminins)
adhesion between epithelia and connective tissue.
Proteins: integrins
Cytoskeletal component: intermediate filaments attach to plectin plaques

5. Synaptic Junctions

Function: signal transduction
Location: contact point between axon and cell
Protein involved: cadherin
Functions: transmission of action potential from presynaptic to postsynaptic
Change in presynaptic membrane permeability → neurotransmitters release → bind to receptors in postsynaptic membrane → Change in postsynaptic membrane permeability → postsynaptic message (action potential)

6. Gap Junctions

Pipeline-like structures; Location: between neighbouring cells; extend from cytosol of 1 cell to that of the other, narrow space (tightened).
Proteins: connexins
- Function: transportation → exchange of molecules between neighbouring cells.
- Tissues: all except skeletal muscle and nerve cells. Structures: channels in clusters; 1 channel = 1 connexon = 6 connexin subunits; hydrophilic sides at channel centre (2nm diameter) → passage of any hydrophilic molecule size <2 nm (a.a, monosacharides..)
Control
- Channel can open and close by rotating connexins (1 direction opens&the opposite closes).
Cytosolic conditions
Opens: when pH ↘ & [Ca²⁺] ↗
Closes: when pH ↗ & [Ca²⁺] ↘

7. Cell Wall & Plasmodesmata

Location: Surrounds plasma membrane
Composition: Primary cell wall (cellulose + matrix : hemicellulose + pectin + some glycoproteins); Secondary cell wall = primary + lignin (mature cells)
Quantities vary by: cell type – species – maturation
Synthesis
Cellulose: synthesized by enzymes of plasma membrane.
Matrix: synthesized by Golgi
Function: Cell adhesion by pectin; Exchange of molecules by plasmodesmata (cytoplasmic, continuous bridges between cells); Desmotubule: structure at the centre; narrows the opening (annulus); only molecules < 1 KDa pass; dilate if needed for larger molecules.

7. Plant cell wall specializations for tissues

Lignification: adding lignin (phenol derivatives) → hardness
Mineralization: adding minerals (calcium carbonate, silicon…) → hardness
Cutinization :adding cutin (complex cerides: hydrophobic) on leaves → shiny cover → watertight → protection
Suberification: adding cork (complex cerides: hydrophobic) on epidermis cells →watertight
Gelification: in ripe fruits : middle lamella solubilized → cells round up and lose adhesion → dissociate and float in a gel of pectin.

8. Microvilli

Finger-like extensions of the plasma membrane; Stable → permanent
Location: apical surface of epithelial cells.
Function: absorption/secretion
In enterocytes: abundant → form brush border → increase surface for absorption
In leukocytes:low abundance
Composition :
Actin filaments (support & motility).
Villin & fimbrin: connecting actin filaments
Myosin 1: connects actin filaments to the membrane
Glycocalyx: viscous coat of carbs (makes movement more efficient)

9. Stereocilia

Long extensions (irregular size & shape); flexuous; confluent together
Location: apical pole of some cells
Composition: actin filaments
Function : secretion & reabsorption
Tissues: some sensory epithelia – male epididymis epithelium

10. Basal infolds

Deep intracellular invaginations at the basal pole
Tissues: Large & abundant in tissues exchanging hydrominerals, eg: proximal tubule of nephron in kidneys
- Function: confines privileged cytoplasmic compartments for exchange
- Rich in elongated mitochondria → energy for exchange

Chapter 5 - Ribosomes & Protein Synthesis

Brief view of the cytosol
- Cytosol = hyaloplasm (viscous aqueous solution) → space between and organelles in the cytoplasm
  - pH approximately 7
  - Contains organic and inorganic molecules
  - Contains cytosolic components
- Site of metabolic reactions → Anabolic (synthesis) reaction e.g. translation = protein synthesis by ribosomes
  - Catabolic (degradation) reaction e.g protein degradation by proteasomes
Ribosome structure, composition, and assembly
- ribosome = ribonucleoprotein complex (ribosomal RNA and ribosomal proteins)
  - (No carbs or lipids) ; Made of 2 oval subunits; Assemble only during translation → Function : translation of mRNA into protein
    - regions:

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