Cell Biology Basics

Mammalian Cell Organelles

• Identify the main organelles in a mammalian cell and list their functions
• The main organelles are:
  • Plasma membrane
  • Nucleus
  • Endoplasmic Reticulum (ER)
  • Ribosomes
  • Vesicle
  • Golgi Apparatus/Body/Complex
  • Lysosome
  • Peroxisome
  • Mitochondria
  • Cytoskeleton

Plasma Membrane

• Controls what enters and exits the cell
• Composed of a phospholipid bilayer

Nucleus

• Controls everything in the cell
• Contains DNA/chromosomes
• Enclosed by a porous double membrane called the nuclear membrane
• Functions
  • RNA synthesis
  • RNA processing and ribosome assembly (nucleolus)
  • DNA synthesis and repair

Endoplasmic Reticulum (ER)

• Thin folded membranes that are connected together and contains ribosomes
• Functions
  • Exports of proteins
  • Membrane synthesis
  • Lipid and steroid synthesis
  • Detoxification reactions
  • Protein Synthesis

Ribosomes

• Links together amino acids to make proteins (enzymes)
• Tiny organelles that consist of proteins and RNA
• Found on Rough ER

Vesicle

• Membrane-bound containers that carry substances throughout the cell
• Microtubules, the rod-like components of the cytoskeleton, aid in the transport of vesicles
• The cytoskeleton aids in vesicle formation at the ER and Golgi apparatus and facilitates their movement to various parts of the cell

Golgi Apparatus/Body/Complex

• Checks, modifies and packages proteins
• Closely layered stacks of membrane-enclosed discs

Lysosome

• Breaks down food, waste and damaged cell parts within the cell
• Contains enzymes; membrane bound

Peroxisome

• Contains enzymes, is membrane bound and functions in:
  • Fatty acids and purine breakdown
  • Detoxification of hydrogen peroxide
  • Synthesis of cholesterol, bile acids and myelin

Mitochondria

• Supplies energy (ATP) to the cell, the site of cellular respiration and known as the 'powerhouse' of the cell
• Bean shaped with 2 membranes, their own DNA and ribosomes

Cytoskeleton

• Supports & shapes the cell
• A network of protein filaments (microtubules, microfilaments)

Prokaryotic vs. Eukaryotic Cells

• List the principal differences between a prokaryotic and an eukaryotic cell
• Prokaryotes are the simplest type of cell.
• Prokaryotes are unicellular organisms found in all environments.
• Prokaryotes are smaller in size when compared to Eukaryotes.
• Prokaryotes do not have a nuclear membrane
  • Their circular shaped genetic material dispersed throughout cytoplasm
• Prokaryotes do not have membrane-bound organelles
• Ribosomes are the only organelles

Macromolecular Structure and Interaction

• Discuss the bonds important for macromolecular structure and interaction
• Macromolecules are formed when monomers are linked together to form longer chains called polymers
• Monomers are linked together by a process called dehydration synthesis (condensation reaction)
  • Covalent bond formed between the two monomers, while a water molecule is also formed from the OH groups
• Types of Macromolecules:
  • Lipids
    • Diverse groups of molecules in nonpolymorphic form
  • Carbohydrates
    • Sugars
  • Nucleic Acids
    • Nucleotides
  • Proteins
    • Amino Acids

Proteins

• Consist of one or more polymers called polypeptides made by linking amino acids together with peptide linkages
• Peptide linkages are formed through condensation reactions

Carbohydrates

• Always composed of carbon, hydrogen and oxygen molecules
• Monosaccharides typically have five or six carbon atoms
• Monosaccharides like ribose and deoxyribose of RNA and DNA, can serve very important functions in cells

Nucleic Acid

• Two types of nucleic acids
  • DNA
  • RNA
• DNA and RNA are polymers composed of subunits called nucleotides and a nitrogenous base
• Five nitrogenous bases found in nucleotides:
  • Purines include:
    • Adenine (A)
    • Guanine (G)
  • The pyrimidines
    • Cytosine (C)
    • Thymine (T) (DNA only)

Lipids

• A very diverse group of molecules that all share the property of being hydrophobic
• Fatty acids, which make up fats and oils, can be saturated or unsaturated
  • Depending on the absence or presence of double bonds between carbon atoms
• Lipids are joined together by ester linkages
• Triglyceride is composed of 3 fatty acids and 1 glycerol molecule
• Fatty acids attach to Glycerol by covalent ester bonds
• A long hydrocarbon chain makes the triglyceride molecule nonpolar and hydrophobic

Chemical Bonds

• Forces that hold atoms and molecules together
• Intramolecular bonds:
  • Covalent Bond
    • Sharing of electrons between two nonmetallic atoms
      • Can either be shared evenly between the atoms, or not
      • Uneven sharing creates ionic character
  • Ionic Bond
    • A bond formed between two atoms
    • There is a complete transfer of an electron resulting in the formation of two ions
    • One is positive and one is negative charged
• Intermolecular bonds:
  • Hydrogen bond
    • A weak electrostatic interaction between a hydrogen atom bound to an electronegative atom (N, O) and another electronegative atom
  • Van der Waals Forces:
    • A weak interaction between any two atoms in close proximity.
  • Hydrophobic Interactions
    • Force that brings two non-polar molecules together when they exist in a polar environment

Hydrophobic vs Hydrophilic Molecules

• Explain the differences between hydrophobic and hydrophilic molecules in water
• Properties of water are important biologically:
  • Water is a polar molecule
  • Water is highly cohesive (hydrogen bonds between water molecules)
  • Water is the principal fluid medium of the cell. Many cellular chemicals dissolve in the water
  • Helps in regulation of temperature since it is able to absorb large amounts of heat
  • Helps in regulation of intracellular pH since it is amphoteric solvent
  • Used for transport, delivers nutrients and removes waste from cells
• Water is a dipolar molecule
  • The oxygen atom carries a partial negative charge
  • The hydrogen atoms carry partial positive charges
• Molecules must contain charged or polar groups that can associate with the partial positive and negative charges of water to be soluble in water
• The solubility of organic molecules in water depends on:
  • Proportion of polar to nonpolar groups attached to the carbon-hydrogen skeleton
  • Their relative positions in the molecule
• Substances terms hydrophilic, can dissolve readily in water .
  • Attract water molecules through electrical charge effects
  • Water molecules surround each ion or polar molecule and carry it into solution
• Polar groups or molecules are called hydrophilic (water loving)
• Nonpolar groups or molecules are hydrophobic (water fearing)
• Water molecules interacting with a polar or ionic compound form a hydration shell around the compound, which includes hydrogen bonds or ionic interactions
• Compounds that have large nonpolar regions are relatively water-insoluble
  • Tend to cluster together in an aqueous environment and form weak associations through van der Waals interactions and hydrophobic interactions

Hydrophobic Molecules

• Substances that contain a preponderance of nonpolar bonds and are insoluble in water are termed hydrophobic
• Water molecules are not attracted to hydrophobic molecules
  • Have little tendency to surround them and bring them into solution

pH, pK and Buffers

• Explain the concept of pH, pK and buffers
• pH:
• A convenient way to express the concentration of H+ in solution
  • pH = -log [H+]
• The "p" denotes "negative logarithm of".
• A low pH
  • Represents a high concentration of H+ and acidic solution
• A high pH
  • Represents a low concentration of H+ (and a high concentration of OH-) and a basic solution
• Strong acids and bases completely dissociate in solution
• Weak acids and bases
  • Compounds that are not completely dissociated when dissolved in water
• Acids are defined as molecules that can donate protons
  • When this molecule is placed in water it dissociates to release a H+ and the ethanoate (acetate) anion, CH3COO-
• In an acidic solution, [H+] > 10-7 and pH < 7
• A basic solution is when [OH-] > [H+].
• In a basic solution, [OH-] > 10-7, pOH < 7, and pH >7
• When the pH = 7, the solution is neutral
• Physiological pH range is 6.5 to 8.0
• The tendency of an acid to lose a proton defines the dissociation constant, Ka.
  • Ka = [H+] [A-]/[HA]
• Ka values are usually converted to pKa values
  • pKa = -log Ka
• The stronger the tendency of an acid to dissociate the lower the pKa value
• Virtually all biological processes are pH dependent
• The pH of a solution affects the charge on biological molecules
  • Biological molecules are kept in optimal ionic state in order to function correctly
  • Organisms use buffers to keep pH relatively constant
• Buffers
  • Mixtures of a weak acid and its conjugate base
  • Resists changes in pH when a small amount of acid or alkali is added to them
• Concentration of ethanoate ion and ethanoic acid are similar
• Buffers are only effective in a pH range of pKa +/- 1.

Common Buffer Systems

• The Bicarbonate Buffer System
  • The major source of metabolic acid in the body is the gas CO2
  • Produced mainly from fuel oxidation in the tricarboxylic acid (TCA) cycle
  • CO2 dissolves in water and reacts to produce carbonic acid, H2CO3
  • Reaction that is accelerated by carbonic anhydrase
  • Carbonic acid is a weak acid that partially dissociates into H and bicarbonate anion, HCO3
• Bicarbonate and Hemoglobin in Red Blood Cells
  • Cooperation in buffering blood and transporting CO2 to the lungs
  • The bicarbonate buffer system and hemoglobin in red blood cells cooperate.
  • CO2 goes from tissue metabolism in the TCA cycle diffuses into the interstitial fluid and the blood plasma and then into red blood cells -Red blood cells contain high amounts of the carbonic anhydrase enzyme, and CO2 is converted to carbonic acid (H2CO3) within these cells.
• Intracellular pH
  • Phosphate anions and proteins are the major buffers involved in maintaining a constant pH of ICFs
  • Phosphate anions generate H and conjugate base HPO4 with a pKa of 7.2 - a major intracellular buffer in the red blood cell and in other types of cells
  • Organic phosphate anions such as glucose 6-phosphate and ATP also act as buffers
  • ICF contains proteins (histidine and other amino acids) that accept protons akin to hemoglobin
  • Nonvolatile acid produced from body metabolism cannot be excreted as expired CO2 as the nonvolatile acid hydrogen ion is excreted in the urine
• Urinary Hydrogen, Ammonium, and Phosphate lons
  • As undissociated acid that generally buffers the urinary pH between 5.5 and 7.0
  • A pH of 5.0 the minimum urinary pH includes phosphates and ammonium ions, uric acid, dicarboxylic acids, and TCA (citric acid; see Table 4.2)
  • Urinary excretion of H2PO4 helps to remove acid to maintain metabolic homeostasis by excreting the phosphate in the urine that we ingest with food

Amino Acid Structure

• Recognise and illustrate the general structure of an amino acid
• Amino acids
  • Used for the formation of proteins
  • 20 different amino acids commonly found in proteins
  • All have:
    • A carboxyl group (-COO-)
    • An amino group (-NH3+)
    • Covalently bound to a central carbon atom
      • (the a carbon)
    • A side chain or R group also bonded to the a carbon that differs between amino acids
  • All of the amino acids, except for glycine contain an a carbon bound to 4 different groups since the a carbon that binds to the 4 different groups is a chiral centre - Causes the amino acids to exhibit stereoisomerism to have the same formula with a different arrangement - This condition where two more isomers that have the same arrangement is known as isomerism

Classification of Amino Acids

• Most commonly classified by:
  • The chemical nature of their R group
  • Tendency to interact with water at pH 7.0 i.e. their polarity
• Can be described by:
  • Having a benzene ring are described as aromatic
  • Lacking benzene rings, known as aliphatic.
• Classification
  • Nonpolar, aliphatic R groups
  • Aromatic R groups
  • Polar, uncharged R groups
  • Positively charged R groups
  • Negatively charged R groups
• The side chains of some amino acids are charged at pH 7.0
  • Classified according to whether they are positively or negatively charged.

Amino Acids and pH

• Explain how the charges on amino acids are affected by pH.
• Amino acids w/carboxyl groups/ some R groups form internal ions
  • Able to ionize (gain/lose a proton)
• Ionisable R-group is a dipolar, or zwitterion in water at pH 7.0
  • Fully protonated/ deprotonated
• In zwitterions, amino acids uncharged and charged groups cancel

Isoelectric Point

• Amino acids where positive and negative charges at isoelectric
• The pH occurs in isoelctric pH
• The point in least soluble
• At is the pH at the amino acid an overall (net) zero charge.
• Isoelectric points of common vary: 2.8-10.8.
• Glycine is isoelectric at pH 6.0 exist lowest levels.

Peptide Bond Formation

• How peptide bond is formed/ list
• Peptide bonds proteins that connect
• Linear AA bond peptide in C-terminus acid of two AA with OH of acid with other the chain.
• Key features of a peptide bond:
  • All atoms in the same plane
  • No rotation-double due charachter
  • Carbonyl oxygen and amide are in the trans plane