Thursday Notes

Lecture

Biochemistry

CHNOPS anyone?

C – Carbon: Found in all organic molecules

H – Hydrogen: Part of water

N – Nitrogen: Found in proteins (amino acids)

O – Oxygen: Part of water

P – Phosphorus: Nucleic acid

S – Sulfur: Proteins.

Molecule: More than one atom bonded together.

Types of Bonds Found in Living Things…

Hydrogen Bond – attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen has a polar bonding to another electronegative atom to create the bond. (weaker bond)

All the information I have found shows Hydrogen bonds can only happen between H and F, O or N.

Ionic Bond – a type of chemical bond formed through an electrostatic attraction between two oppositely charged ions. Ionic bonds are formed between a cation, which is usually a metal, and an anion, which is usually a nonmetal. Cation “gives” away an electron to the anion. (stronger bond)

Covalent Bond – sharing of electrons between two atoms. (strong bond)

Chemical Reactions (RXN = Reaction)

Decomposition RXN –

  • Breakdown  – A chemical reaction in which bonds are broken
  • Catabolic RXN – The sum total of decomposition reactions exhibited by an organism.

AB → A + B.

Synthesis RXN – A chemical reaction in which new bonds are formed. Building larger molecules from smaller molecules.

ex.       A + B → AB

Exchange RXN –

  • An individual reaction than involves both synthesis and decomposition. 
  • Implied in this definition is the idea that a collision between two molecules occurs which results in some degree of exchange of atoms and bonds, for example as occurs in hydrolysis.

ex.       AB + CD ↔ AD + CB

Hydrolysis means ‘water’ &  ‘break’

Water is Essential for Life!

Life as we know it depends on water.

  • Water is the most abundant molecule found in living things (by weight)
  • All living organisms are 70% + water
  • The chemical structure of water gives it life sustaining properties.
  • The H atoms of an individual water molecule are bound to the oxygen atom by polar covalent bonds.

Polar means one atom has a larger electronegativity pull than another atom. The electronegativity pull of an atom is based on its size, therefor the bigger the atom the more pull it will have on another atoms electrons. This makes the bigger atom negatively charged because it has more of the electron than the small atom making the small atom positively charged.

Life Sustaining Properties of Water

  1. Frozen water is less dense than liquid water. (Floats) As water cools below 4°C, the hydrogen bonds adjust to hold the negatively charged oxygen atoms apart (becoming rigid). This produces a crystal lattice, which is commonly known as ‘ice’. This allows life to go on beneath the surfaces of frozen bodies of water. 
  2. Water is a good solvent for polar molecules or ionic molecules.
  3. Water has adhesion & cohesion properties. Adhesion – Sticks to others: Important for moving water (ex. plants & roots)     Cohesion – sticks to itself: surface tension is the result of the tendency of water molecules to attract one another (called cohesion).
  4. Bodies of water have high surface tension.
  5. Water has relatively high specific heat compared to other liquids.

Specific heat – amount of energy it takes to change 1 gram of water by 1°C.

Acids & Bases

Acids – Substances that release hydrogen when added to water.

Bases – Substances that release hydroxide (OH¯) when added to water.

Each time you move up or down the pH scale it is an exponential power.

ex. going from 5pH to 8pH would be an increase of 1000.

7pH – is the middle of the scale.

Buffers

Substances that resist pH changes.

4 Major Categories of Macromolecules Found in Living Things:

Carbohydrates – Hydrates of Carbon

  • Monosaccharides (monomers) – Contain C, H, O in a 1C:2H:1O ratio.  Ex. fructose, glucose, galactose
  • Disaccharide – 2 monosaccharides or monomers linked together form a covalent bond called a GLYCOSIDIC BOND :a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. ex. sucrose, lactose, maltose                      sucrose = glucose + fructose; lactose = glucose + galactose; maltose = glucose + glucose
  • Polysaccharides (polymers) – 3+ molecules of repeated monomer units joined together by glycosidic bonds. ex. cellulose, chiten (fungi cell walls), amylose (starch), glycogen (animal muscle)

Lab

Colony Morphology Terms

Form: Overall shape of entire colony : Punctiform; Circular; Irregular; Filamentous; Rhizoid

Margin: Edges: Entire; Undulate; Lobate; Serrate; Filamentous; Curled

Elevation: Flat; Raised; Convex; Pulvinate; Umbonate

Surface Texture: Shiny, smooth, glistening (wet appearance), dull/rough, wrinkled, dry or powdery.

Optical Character: opaque, translucent, opalescent or iridescent.

  • Translucent – Allowing light but not detailed images to pass through.
  • Opaque – Not allowing light to pass through
  • Opalescent – Exhibiting a milky iridescence like that of an opal.
  • Iridescent – Displaying a play of lustrous colors like those of the rainbow

Cell Morphology Terminology

Cocci – Spherical Shapes

Pairs – Diplococci

Chains – Streptococci

Four Cells – Tetrad

Clusters – Staphyloccocus (grape like)

Cubicle packet – Sarcinae

Single Cells – Singles

Bacilli – Rod-like/Cylindrical Shapes

Pairs – Diplobacilli

Chains – Streptobaccili

Side-by-side – Palisading

V-shape – Snapping

Short Rods – Coccobacilli

Spirilla – Spiral Shape

One-half spiral turn – Vibrio

Also loose spirals & tight spirals.

Direct vs. Indirect Staining

(Repeat of the notes she already gave us)

Introduction:

  • Microbiologist observe both living and dead microorganisms with microscopes
  • Dead organisms can be stained to make cell features more visible. (However, there shapes distort slightly when dead)
  • Stains are salts, w/ one ion being colored (chromophore – the part of a molecule responsible for its color.)
  • Direct stains: color the cell & leave the background colorless
  • Indirect stains: color the background, leaving the cell colorless.

Types of Stains:

  1. Basic Stains: Color is associated w/ the cation. Cations are attracted to cell membranes. (ex. methylene blue, crystal violet, safranin)
  2. Acidic Stains: Color is associated with the anion or the neutral particles. Anions and neutral particles are not attracted to cell membranes. (ex. Nigrosin, Congo Red) 

Direct Staining:

  1. Using aseptic technique put two “loop fulls” of water 
  2. Obtain a visible “blob” of cells & smear onto slide with water.
  3. Use sterile loop to mix until the smear is a consistency of skim milk.
  4. Air dry
  5. Heat fix. (3 swipes over flame – to kill the microorganisms)
  6. Liberally apply Methylene Blue to slide & allow to set for 60 sec.
  7. Rinse off & air dry

Indirect Staining:

  1. Using aseptic technique put two “loop fulls” of water 
  2. Obtain a visible “blob” of cells & smear onto slide with water.
  3. Use sterile loop to mix until the smear is a consistency of skim milk.
  4. Add 2 loop fulls of Nigrosin while still wet & smear in.
  5. Air dry
  6. GENTLY Heat fix. (1 swipe over flame – to kill the microorganisms)

Hope everyone’s projects are coming out good! I will put up the review questions on week 1 again for our Monday quiz.

 

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