Chapter 2

Cells

• Cell Theory:

  • all organism are composed of cells

  • all cells come from pre-existing cells - biogenesis

  • the cell is the smallest living organisational unit

• Eukaryotes: a group of single and multi-celled organisms with a nucleus and mutiple linear strands of DNA in a nucleus

  • membrane bound organelles

  • DNA is packaged into a chromosome in a nucleus

  • replicates through mitosis and meiosis

  • animals, plants, fungi and protista are eukaryotic

• Prokaryotes: a group of single-celled organisms with no nucleus and a circular loop of DNA

  • lack membrane bound organelles and their cytoplasm contains scattered ribosomes

  • contains plasmids: small rings of double-stranded DNA

  • single, circular DNA chromosome

  • replicates through binary fission

  • bacteria and archaea are prokaryotic

• Comparison Table

  	Eukaryotes	Prokaryotes
  Membrane-bound organelles	Present	Absent (except vesicles)
  DNA organisation	More than one linear strand of DNA packaged in a chromosome in a nucleus	One circular chromosome and additional plasmids
  Organism nature	Can be unicellular or multicellular	Unicellular
  Size	Larger (~ 10–100 µm)	Smaller Smaller (~ 0.1–5 µm)
  Method of cell replication	Mitosis and meiosis	Binary fission

Organelles

• Organelles are the subunits of cells.

• Each organelle performs a specific function in the cell.

• This increases cell efficiency as it allows many different metabolic process to occur simultaneously

• All cells have a basic structure:

  • Cell membrane: contains cell contents and controls movement of substances into and out of cell

  • DNA: genetic information controlling cell functions

  • Cytoplasm: fluid content of the cell containing other substances and structures (organelles) which have specific functions

• Organelles

  • Nucleus: Contains the cell's genetic material and controls its activities.

  • Mitochondria: Generate ATP energy for the cell through cellular respiration.

  • Ribosomes: synthesises proteins (translate mRNA into proteins). RER-bound ribosomes synthesise proteins for export from the cell.

  • Endoplasmic Reticulum: Involved in protein and lipid synthesis as well as the detoxification of harmful substances.

  • RER: Rough endoplasmic reticulum modifys and folds protein during protein synthesis. Synthesises and processes proteins (often by adding carbohydrates to proteins produced by the ribosomes to form glycoproteins)

  • SER: Produces, process and moves lipids during lipid synthesis.

  • Cell Membrane: Regulates the movement of substances in and out of the cell.

  • Golgi Apparatus: Responsible for packaging proteins into vesicles prior to transport and modifies proteins as needed.

  • Lysosomes: Contain enzymes to digest waste materials and cellular debris.

  • Vacuoles: Storage organelles for nutrients, water, and waste products.

  • Cytoskeleton: Provides structure and shape to the cell, and enables movement of the cell and internal parts.

  • Centrioles: Involved in cell division and the formation of the spindle fibers.

  • Chloroplasts (in plant cells): Responsible for photosynthesis, the process of converting sunlight, water, and carbon dioxide into food.

  • Cell Wall (in plant cells): Provides and maintains the shape of these cells and serves as a protective barrier.

Molecular composition

• Organic compounds

  • are derived from or produced by living organisms and contain carbon.

  • Four main types of organic molecules are carbohydrates, proteins, nucleic acids and lipids(biomacromolecules)

  • Biomacromolecules are chain like molecules called polymers

  • Polymers are formed by joining together many smaller units(monomers) to form a chain

  • Large biomolecules are called biomacromolecules. Biomacromolecules can be made up of thousands of atoms and include proteins and nucleic acids.

  • Large biomolecules are called biomacromolecules. Biomacromolecules can be made up of thousands of atoms and include proteins and nucleic acids.

• Inorganic compounds

  are derived from nonliving components, and generally do not contain carbon (Oxygen, Carbon dioxide, Nitrogen and Minerals)

Organic Molecules

• Organic molecules can be converted into different forms within organisms.

• Smaller units can link together to form larger molecules.

  • Glucose units can combine to form carbohydrates like starch, glycogen, and cellulose.

• Chemical groups can attach to molecules to create new compounds.

  • Glycoproteins: proteins with attached sugars.

  • Phospholipids: lipids with attached phosphate.

• Organisms adapt to food availability:

  • Excess carbohydrates are converted into fats for storage.

  • Stored fats can be broken down into carbohydrates when food is scarce.

  • Proteins can be converted into smaller molecules for energy.

• Carbohydrates

  • Carbohydrates are abundant organic molecules with diverse functions:

    • Energy source: Glucose provides chemical energy for organisms.

    • Energy reserve: Starch (plants) and glycogen (animals) store energy.

    • Structural components: Cellulose forms plant cell walls.

    • Genetic material: Part of DNA and RNA.

    • Cellular components: Glycoproteins and glycolipids in plasma membranes.

  • Carbohydrate composition and classification:

    • Composed of carbon, hydrogen, and oxygen.

    • Classified into three main groups:

      • Monosaccharides: Simple sugars like glucose, fructose, and galactose.

      • Disaccharides: Two monosaccharides linked together.

      • Polysaccharides: Many monosaccharides linked together.

  • Polysaccharides: Large molecules formed by linking many sugars together.

    • Cellulose: The most abundant organic molecule on Earth, forms plant cell walls.

    • Starch: Used for energy storage in plants, has a long chain structure.

      • Starch is the polysaccharide used for energy storage in plants.

    • Glycogen: Used for energy storage in animals, has a branching structure.

      • polysaccharide glycogen is used for energy storage.

    • All three polysaccharides are composed of glucose subunits but differ in structure and function.

• Lipids

  • Lipids: hydrophobic molecules with diverse functions

    • Insoluble in water, forming barriers between watery environments.

    • Roles in organisms:

      • Membrane components: Phospholipids form the basis of plasma and organelle membranes.

      • Energy storage: Fats and oils store energy efficiently.

      • Hormones: Steroids like cholesterol, cortisone, and testosterone.

  • Lipid structure and classification:

    • Lipids are relatively small molecules and vary widely in structure. There are two general forms of lipids

    • Simple lipids: Composed of carbon, hydrogen, and oxygen.

      • Fats: Formed from fatty acids and glycerol.

      • Steroids: Include cholesterol, cortisone, and testosterone.

    • Compound lipids: Contain fatty acids, glycerol, and other elements.

      • Phospholipids: Have hydrophilic (phosphate) and hydrophobic (lipid) ends, essential for membrane structure and function.

• Nucleic Acid

  Nucleic acids: Genetic material of all organisms

  • They determine features of organisims

  • Biomacromolecules composed of long chain of monomers(Nucelotide).

  • Nucelotide consists of phosphate, sugar and nitrogrenous base

  • Types of nucleic acids:

    • Deoxyribonucleic acid (DNA):

      • Stores genetic information.

      • Instructions required to assemble proteins from amino acid monomers

      • Composed of four bases: adenine (A), thymine (T), guanine (G), and cytosine (C).

    • Ribonucleic acid (RNA):

      • Involved in protein synthesis.

      • Composed of four bases: adenine (A), uracil (U), guanine (G), and cytosine (C).

• Proteins

  • Proteins: Diverse biomacromolecules

    • Over 50% of cellular dry weight.

    • Thousands of different types with various functions.

    • Protein functions:

      • Enzymes: Catalyze reactions (e.g., amylase).

      • Hormones: Regulate processes (e.g., insulin).

      • Carrier molecules: Transport substances (e.g., hemoglobin).

      • Structural components: Form tissues (e.g., collagen).

      • Immune system: Antibodies and antigens.

  • Protein structure:

    • Composed of carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, and other elements.

    • Biomacromolecules formed from chains of amino acid monomers.

    • Amino acids linked by peptide bonds to form polypeptides.

      • Amino acids are linked by a particular kind of chemical bond, called a peptide bond, and form polypeptides or polypeptide chains.

      • Polypeptide means many peptide bonds

    • 20 different amino acids, 9 of which are essential for humans.

      • Cannot be produced by humans

      • Obtained through consumption of organisims

    • Proteins are fully functional polypeptides.

      • Protein are formed by one or more polypeptides in a biologically functioning way.

      • proteins are fully functioning molecule while polypeptide is the non-functioning version.

    • Protein shape, determined by amino acid sequence, influences function.

Inorganic Molecules

• Inorganic molecules are typically molecules that do not contain carbon-hydrogen bonds.

• Some exceptions exist, such as carbon dioxide (CO2) and carbonates.

• They are abundant in nature and found in various states (solid, liquid, gas).

• Play a crucial role in natural processes and are essential for life.

• Examples include water (H2O), carbon dioxide (CO2), sodium chloride (NaCl), ammonia (NH3), and sulfuric acid (H2SO4).

• Inorganic molecules exhibit a wide range of properties and functions.

• Oxygen and Carbon dioxide in celullar processes

  • Oxygen: Essential for cellular respiration, providing energy from food molecules.

    • Constant supply necessary to maintain Cell Activity

    • Organisms obtain oxygen from air or water.

    • Aquatic organisms require efficient ventilation systems (e.g., fish gills) to extract oxygen from water.

  • Carbon Dioxide: Used by plants, bacteria, and protists in photosynthesis to produce sugars.

    • Released into the atmosphere through organic matter decay and cellular respiration.

    • Cycles through the environment, linking photosynthesis and respiration.

    • Critical for survival of all organisims

• Nitrogen

  • Nitrogen: is a key component of proteins.

    • The atmosphere is 78% nitrogen gas, but most organisms can't use it directly.

    • Nitrogen-fixing bacteria convert atmospheric nitrogen into usable compounds.

      • Process known as Nitrogen Fixation

    • These bacteria are often symbiotic with plants like legumes, casuarinas, and acacias.

      • Plants absorb nitrogen compounds from the soil to make amino acids.

    • Heterotrophs get amino acids by consuming plants and other organisms.

      • Nitrogen-rich waste (manure from Heterotroph) can be used as a plant fertiliser.

• Minerals

  • Mineral salts are inorganic compounds from weathered rocks.

    • Plant roots absorb water-soluble mineral salts as ions.

    • Making them avaliable to be eaten by animals

  • Consumed by animals, including humans, obtain minerals from plants.

    • Humans need over 20 minerals, including phosphorus, potassium, calcium, magnesium, iron, sodium, iodine, sulfur, and trace minerals.

  • Mineral ions are essential for various cellular functions:

    • Cytosol composition

    • Structural components (e.g., bones)

    • Enzyme and vitamin molecules

    • Incorporation into organic compounds

  • Specific mineral roles:

    • Phosphorus: phospholipids, ATP

    • Magnesium: chlorophyll

    • Iron: hemoglobin

    • Calcium, potassium, sodium: cardiac muscle function

    • Calcium, phosphorus: bone and teeth structure

Protein structure and function

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Proteins are essential for nearly all functions in living organisms. They perform various roles such as speeding up chemical reactions, aiding in cell recognition and communication, movement, storage, and providing structural support. Humans have tens of thousands of different proteins, each with a unique sequence of amino acids that gives them a specific shape to carry out their particular function.

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• A protein is an organic compound consisting of one or more long chains of amino acids connected by peptide bonds.

  • Proteins are also known as Polypeptides

• Proteins are present in every living organism and are essential to their structure and function.

• are a diverse group of molecules that are found in all living organisms

• perform many different functions

• contain Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N) and sometimes Sulphur (S)

Proteome Nature

• Proteome is the complete set of proteins expressed by a genome at a specific time.

  • The complete array of proteins produced by a single organism is called a proteome

• Proteome varies based on cell type, developmental stage, and environmental conditions.

  • Cells may contain an entire genome but express only specific genes to produce necessary proteins at a given time.

    • This ensures a cell produces only the proteins required for the specific functions it carries out.

    • because it is a waste of energy and resources to produce all proteins possible.

    • Different cell types produce different proteins to fulfill their specific functions.

• Human proteome shares similarities with other organisms due to common evolutionary origins.

Proteomics

• Proteomics is the large-scale study of proteins' structure, function, and interactions of proteins.

• Proteomics is essential as it is proteins that actually carry out most cellular activities, not the genes that encode them.

• By studying protein expression and interaction, we can better understand cellular and organismal function.

• Comparing proteomes of different conditions (e.g., diseased vs. healthy cells) helps identify disease-related proteins.

• Proteomics research can lead to protein biomarkers for early disease detection.

• Proteomics is crucial for developing drugs that target disease-related proteins.

Protein Synthesis

Amino Acid structure

• Amino acids are building blocks of proteins

  • They are Monomers that bond together to form Polymers(polypeptide chain)

  ---

• All amino acids have the same basic structure:

  • A carboxyl group(COOH)

  • an amino group(NH2)

  • A variable R-group

    • ( e.g. charged or uncharged, polar or non-polar, hydrophobic or hydrophilic)

    • Non polar

    • Acidic

    • Basic

    • Polar

• Each type of amino acid has its own specific R-group

  • R-group determines identity of amino acid

• There are 20 naturally occuring amino acids

  • Human body produces 11 of these

  • The remaining 9 are obtained through external sources(food).

• The joining of amino acids involve the release of water

  • Condensation reaction

  • Results in formation of peptide bond between adjacent amino acids

• When complex proteins are broken down into simple amino acids, it requires the addition of water

  • Hydrolysis reaction

Functional Diversity of Proteins

• Proteins have diverse functions and unique 3D structures.

• Each protein type has a specific function.

• Proteins are essential for cell and organism regulation, function, and maintenance.

• Almost all life functions rely on proteins.

polypeptide chain:

• Amino acids are linked by peptide bonds.

• A chain of amino acids connected by peptide bonds is called a polypeptide chain.

• The polypeptide chain's backbone consists of repeating carboxyl and amine groups.

• R groups form the side chains of the polypeptide chain.

• The primary structure of a protein is a polypeptide chain.

• Further folding and modification of the primary structure lead to a fully functional protein.

Enzymes

• Enzymes are a crucial group of proteins.

• Enzymes act as biological catalysts, accelerating biochemical reactions.

• Enzymes are large, globular structures.

• They can either speed up anabolic (building) or catabolic (breaking down) reactions.

• An example of an enzyme is lipase, which breaks down lipids during digestion.

• Enzymes are essential for life, as many cellular reactions would be too slow without them.

Protein structure

• Proteins are large biomolecules composed of thousands of amino acids.

• They can be synthesized as single or multiple polypeptide chains.

• These chains fold into specific shapes crucial for protein function.

• Most proteins are often required to bind to other molecules.

• A single amino acid change can alter protein shape and function.

• Protein structure has four levels of organization:

  • Primary structure

  • Secondary structure

  • Tertiary structure

  • Quaternary structure

• Primary structure

  • The primary structure of a protein is the linear sequence of amino acids in the polypeptide chain.

  • It is unique to each protein.

  • The length of a polypeptide chain can vary widely, from as few as 50 amino acids to over 1000.

  • Linear sequences shorter than 50 amino acids are known as peptides.

  • The primary structure provides information on how proteins will fold.

  • By comparing the primary structures of functional and non-functional proteins, scientists can identify the specific changes that render a protein non-functional.

  • Comparing the primary structures of different proteins can reveal evolutionary relationships and functional similarities.

• Secondary structure

  • The secondary structure of a protein involves the folding or coiling of the polypeptide chain.

  • This folding is driven by the formation of hydrogen bonds between the amine and carboxyl groups of amino acids.

  • There are three main types of secondary structures:

    • Alpha helix: The polypeptide chain coils into a helical shape due to hydrogen bonds between non-adjacent amino acids.

    • Beta-pleated sheet: Adjacent polypeptide chains fold back on each other, forming a sheet-like structure stabilized by hydrogen bonds.

    • Random coil: Although the structure appears random, it is consistent across all molecules of the same protein.

• Tertiary structure

  • Polypeptides fold into 3D shapes (globular or fibrous).

  • Involves alpha helices, beta-pleated sheets, and other folded areas.

  • Stabilized by bonds (disulfide, hydrogen) between R groups.

  • Critical for protein function.

  • Smaller polypeptides fold spontaneously due to their chemical environment.

  • Larger, complex proteins require specialized proteins (chaperones) to help them fold correctly and refold if denatured.

  • Can be the final structure for some proteins, or a precursor to quaternary structure.

• Quaternary structure

  • Formed by 2+ polypeptide chains or prosthetic groups (inorganic helpers).

    • by 2 or more teritiary structures

  • Chains can be identical or different.

  • Necessary for some proteins to function.

  • Proteins with prosthetic groups are called conjugated proteins (e.g., hemoglobin).

Protein Secretory Pathway

Secretory proteins are proteins produced by a cell for export. They follow the protein secretory pathway, which involves synthesis and modification before being released from the cell via exocytosis.

Ribosome and Endoplasmic reticulum

• Proteins for intracellular use are synthesized by free ribosomes in the cytosol.

• Secretory proteins are synthesized by ribosomes on the rough endoplasmic reticulum (RER).

• The polypeptide chain is inserted into the RER lumen as it's synthesized.

• Secretory proteins are modified in the RER, such as glycosylation.

• Modified proteins are packaged into transport vesicles.

• The RER also produces transmembrane proteins, which are inserted into its membrane.

Golgi apparatus

• The Golgi apparatus processes and packages proteins for export.

• Transport vesicles from the ER fuse with the cis face of the Golgi.

• Proteins move through cisternae, undergoing modifications like carbohydrate modifications.

• Mature proteins are packaged into secretory vesicles at the trans face.

• Secretory vesicles can fuse with the plasma membrane for exocytosis or be stored in the Golgi.

• Pancreatic cells store digestive enzymes in Golgi vesicles until needed.

Excocytosis

• Steps in Exocytosis

  • vesicular transport: a vesicle containing secretory products is transported to the plasma membrane

  • fusion: the membrane of the vesicle and cell fuse

    • possible because plasma membrane is fluid and can fuse with the phospholipid bilayers of a vesicle

      • when fused adds a phospholipid to the bilayer

        • makes the plasma membrane surface area slightly bigger

  • release - the secretory products are released from the vesicle and out of the cell

  • summary

    1. Vesicle containing secretory products is transported to plasma membrane

    2. Membrane of vesicle fuses with plasma membrane

    3. Secretory products are released from cell into extracellular environment

  • diagram

• Secretory vesicle and plasma membrane proteins facilitate membrane fusion.

• The fluid nature of the plasma membrane allows for fusion.

• Vesicle contents are released outside the cell (exocytosis).

• The vesicle membrane becomes part of the plasma membrane.

• The plasma membrane is constantly recycled through endocytosis and exocytosis.

• The RER and Golgi apparatus play key roles in protein secretion.

Roles of rough endoplasmic reticulum and Golgi apparatus in the protein secretory pathway:

Protein Classification

Proteins can be classed as one of two types depending on their shapes:

• Fibrous proteins are typically elongated and insoluble. Many have structural roles and have little or no tertiary folding ( e.g. collagen found in connective tissue and keratin found in hair and nails).

• Globular proteins are compactly folded and coiled into spherical tertiary and quaternary structures. Globular proteins are generally soluble. They have a core with hydrophobic properties and an outer hydrophilic region. Most enzymes and hormones are globular proteins.

FACTORS THAT AFFECT THE FUNCTION OF A PROTEIN

The environment surrounding proteins plays an important role in maintaining the structure and function of the protein. Usually the loss of function of the protein is due to denaturation of the protein.

• Temperature: Extreme temperatures can disrupt hydrogen bonds and other weak interactions, leading to denaturation.(hydrogen bonds break at temperatures above 40C)

• pH: Changes in pH can alter the ionization state of amino acid side chains, affecting their interactions and disrupting the protein's structure.(most proteins have an optimal pH range at which they function – pH levels outside of the range will cause the protein to denature)

• Ion or molecule concentration: Ions or molecules that bind to proteins can influence their conformation and function. For example, cofactors are essential for the activity of some enzymes.

Denaturation and Renaturation of proteins

• Denaturation is the process where the structure is disrupted

  • Protein is denatured when the hydrogen bonds, disulfide bridges, hydrophobic interactions and dispersion forces that creates the tertiary structure of the protein are broken and shape of protein is altered.

  • Misshapen(denatured) proteins become biologically inactive.

  • If protein is fully denatured, the reaction is permenant and proteins remains non-functional.

  • If protein is partially denatured, it is possible to be folded again(renature) when appropiate conditons are met.

The Effect of temperature on protein function

• High temperatures can denature proteins by breaking bonds.

• Hydrogen bonds are particularly susceptible to breaking at temperatures above 40°C.

• Low temperatures can also hinder protein function by reducing bond flexibility.

• Optimal temperature for protein function varies between organisms and their environments.

• Human proteins function best at 37°C.

• Extremophile proteins are adapted to function at significantly higher or lower temperatures.

The Effect of pH on protein function

• Proteins have optimal pH ranges for their function.

• Optimal pH varies widely between proteins, even within the same organism.

• Human examples:

  • Salivary amylase: pH 7

  • Pepsin: pH 2

  • Trypsin: pH 8

• Extreme pH can denature proteins by disrupting R-group interactions and breaking bonds.

• Denaturation can lead to loss of protein function, including decreased enzyme activity.

The Effect of cofactors on protein function

• Some proteins require non-protein chemical compounds known as cofactors for their biological function.

• Cofactors are non-protein chemical compounds essential for protein function.

• Cofactors include salts, metal ions (e.g., iron, magnesium, calcium), and organic molecules (e.g., vitamins).

• Cofactors influence protein folding and function.

• Magnesium is a vital cofactor for chlorophyll function in plants.

• Magnesium deficiency leads to chlorosis, resulting in yellowing of leaves.