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Hydrocarbons & Macromolecules. Mrs. Daniels Advanced Biology Sept. 2005 (modified Sept. 2008). Hydrocarbons. What are they? Where do we find them? What do we use them for? Old arguments of organic molecules: vitalism vs. mechanism. Drawing Hydrocarbons. How many bonds can carbon form?

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hydrocarbons macromolecules

Hydrocarbons & Macromolecules

Mrs. Daniels

Advanced Biology

Sept. 2005

(modified Sept. 2008)

  • What are they?
  • Where do we find them?
  • What do we use them for?
  • Old arguments of organic molecules: vitalism vs. mechanism
drawing hydrocarbons
Drawing Hydrocarbons
  • How many bonds can carbon form?
  • This enables it to form long chains (branched or unbranched)
  • Skeleton structures
  • Isomers
  • Structural: same formula - different structure or arrangement of atoms
  • Ex. C2H6O


| | | |

H - C - C - OH or H - C - O - C - H

| | | |


  • Geometric: same formula - different spatial arrangement around double bond
  • Ex. Butene C4H8


C = C C = C


  • Optical (also called enantiomers): same formula - mirror images of the same covalent bonds
  • Ex. Lactic acid

2 2

1 C 3 3 C 1

4 4

naming alkanes
Naming Alkanes
  • Rules to naming alkanes
  • (see handout)
  • If a hydrocarbon has the greatest number of “openings” filled with hydrogen, then it is said to be SATURATED
  • This means it is full and can hold no more
  • If a hydrocarbon has a double bond, does it have the potential to hold more hydrogen than it has now?
  • Yes…it is UNSATURATED
attachments to hydrocarbons
  • There are many places along the hydrocarbon chain where functional groups can be attached
  • These areas are the regions of the organic molecule which are often chemically reactive
  • Depending on their # and arrangement, they determine the unique chemical properties of the molecule in which they occur
functional groups
Functional Groups
  • Polar and hydrophilic:
  • Hydroxyl
    • An OH group
    • Alcohols
  • Carbonyl
    • Double bonded Oxygen
    • Ex. Aldehydes & ketones
functional groups1
Functional Groups
  • Carboxyl
    • An end carbon is double bonded to an O and is single bonded to a hydroxyl group
  • Amino

-weak base


  • Sulfhydryl
    • SH
    • Called thiols
  • Phosphate
    • PO4-3
most macromolecules are polymers

Most macromolecules are polymers

Monomer- subunit/building block molecule of a polymer.

Polymer -

-poly means “many” and mer means “part”

-large molecule consisting of many identical or similar parts or subunits connected together

Polymerization Reaction: the process of

creating a polymer from its constituent parts

-A chemical rxn that links two or more small molecules to form larger molecules with repeating structural units

Condensation reaction(Dehydration reaction) = most

polymerization rxns for organisms are condensation rxns.

  • Monomers covalently linked, producing a net removal of water for each covalent linkage.
  • One monomer loses a H+ and the other loses an OH-.
  • This process requires NRG and the presence of biological enzymes and catalysts.
  • Hydrolysis = rxn that breaks the covalent bonds between monomers by the addition of water molecules.
  • H bonds to one monomer and OH bonds to another monomer thus connecting the two.
a limitless variety of polymers can be built from a small set of monomers
A limitless variety of polymers can be built from a small set of monomers
  • Macromolecules are: large organic polymers
  • 4 Main Categories of Macromolecules:
  • Carbohydrates
  • Lipids
  • Proteins
  • Nucleic acids
Unity and diversity of all life is tied to the specific arrangement and resultant emergent properties of these universal monomers.
  • There is unity in life as there are only about 40-50 common monomers used to construct all macromolecules
  • There is diversity in life as new properties emerge when these universal monomers are arranged in different ways
organisms use carbohydrates for fuel and building material
Organisms use carbohydrates for fuel and building material
  • Carbohydrates = organic molecules made from sugars and their polymers.
  • Carbohydrates are classified according to the number of simple sugars
Monosaccharides = simple sugars
  • CH2O ratio
  • major nutrients for cells - Glucose is most common(produced by photosynthesis)
  • Chemical bond energy is harvested during cellular respiration
  • carbon skeletons are the raw materials for other organic molecules
  • incorporated into di and polysaccharides.
  • EX = triose (3 C), pentose (5 C), hexose (6 C)
  • Sugars end with “ose”
    • Aldose- sugar with a carbonyl group at a terminal carbon (aldehyde)
    • Ex. Glucose (Galactose is its enantiomer)
    • Ketose- sugar with carbonyl group within the carbon skeleton (ketone)
    • Ex. Fructose
in aqueous solution many form rings
In aqueous solution, many form rings
  • Many monosaccharides can form rings in aqueous solns



















Disaccharides = two monosaccharides joined by glycosidic linkage
    • Glycosidic linkage =covalent bond formed by condensation rxn between two sugar monomers.
    • Ex = maltose, lactose, sucrose
  • Maltose: glucose and glucose (sugar important in brewing beer)
  • Lactose: glucose and galactose (sugar present in milk)
  • Sucrose: glucose and fructose (table sugar; most prevalent disaccharide)
Polysaccharides = macromolecules made of 100s to 1000s of monosaccharides. Enzyme mediated condensation rxns - NRG storage and structural support
    • Storage Polysaccharides- cells hydrolyze these into sugars as needed
      • Starch- storage polysaccharide of plants- stored in plastids(granules)
      • Glycogen- glucose polymer - storage polysaccharide in animals
        • Large glucose polymer - highly branched- stored in muscle & the liver
    • Structural Polysaccharides
      • Cellulose- linear unbranched polymer- major component of plant cell walls
      • Chitin- structural polysaccharide- polymer of an amino sugar
lipids are mostly hydrophobic molecules with diverse functions
Lipids are mostly hydrophobic molecules with diverse functions
  • Lipids-
    • diverse group of organic compounds
    • insoluble in water
  • 1. Fats, Triacylglycerol, or Triglycerides
  • hydrophobic due to many C-H bonds
  • variation arises from fatty acid composition, number, & arrangement
  • Glycerol = 3 carbon alcohol
  • Fatty acids (carboxylic acids)= carboxylic acid group at one end =“head” and an attached hydrocarbon chain as a “tail”
      • Saturated- no dbl bonds (solid at room temp.; animal fats)
      • Unsaturated-one or more dbl bonds present (liquid; plants & fish)
Triacylglycerol -A fat made of 3 fatty acids bonded to one glycerol by ester linkages (triglyceride)
  • Major fxn of fat is energy storage
  • Humans and other mammals stock their long-term food reserves in adipose cells (expandable as needed)
  • A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch
Phospholipids = Glycerol + 2 F.A. + phosphate
  • a chemical group can be attached to the phosphate
  • Micelle: the phospholipids will form around a nonpolar particle with their hydrophobic (hydrocarbon) tails towards the particle and the hydrophilic (phosphate) head facing the water
  • This is how particles can be washed away
  • Cell Membrane: a phospholipid bilayer makes up the majority of the cell membrane
  • Two layers of phospolipids arrange themselves so that the hydrocarbon tails are facing each other and the phosphate heads form a hydrophilic sheet on both sides of the membrane
Steroids =
    • Lipids made of 4 fused carbon rings with various functional groups attached
  • Cholesterol- (C27)
  • Common component of animal cell membranes
  • Precursor to many other steroids
  • Too much cholesterol can lead to atherosclerosis (see p. 835) –

plaques build up in lining

of arteries and constrict

the blood flow


amino acids connected polypeptide
Amino acids connected= polypeptide
  • Amino Acid = building block molecule of a protein
  • most consisting of an asymmetric carbon
  • Since the AA can exist in three ionic states (weak acid, weak base, and neutral) the pH of the solution determines the dominant ionic state
  • Every AA includes the following around a central  carbon:
  • Hydrogen atom
  • Carboxyl group
  • Amino group
  • Variable R group
There are 20 amino acids
  • 10 are essential AA’s and must be obtained from dietary sources because they cannot be synthesized in the body
  • Amino acids exist as zwitterions - dipolar ions
  • Peptide bonds=covalent bond formed by a condensation rxn that links the carboxyl group of one amino acid to the amino group of another. N-C-C-N-C-C repeating sequence
Polypeptide chains- range in length from a few monomers to more than a thousand with unique linear sequences of AA
    • N-terminus and C-terminus
    • Polypeptide chain = polymers of AAs that are arranged in a linear sequence and linked by peptide bonds
  • Chains of 50 or less AA’s = peptide
  • Chains of more than 50 AA’s = protein
proteins are molecular tools
Proteins are molecular tools
  • Proteins = macromolecule consisting of one or more polypeptide chains folded and coiled into specific conformations
  • Important functions include:
    • Structural support
    • storage (of amino acids)
    • transport (hemoglobin)
    • signaling(chemical messengers)
    • cellular response to chemical stimuli(receptor proteins)
    • movement(contractile proteins)
    • Defense(antibodies)
    • and catalysis of biochemical rxns(enzymes)
protein s fxn depends upon specific conformation
Protein’s fxn depends upon specific conformation
  • Four Levels of Protein Structure
  • Primary- determined by genes- sequenced in lab
  • Secondary-regular, repeated coiling & folding of a polypeptide backbone
    • Alpha helix- helical coil stabilized by H bonding by every 4th peptide bond(found in fibrous proteins)
    • Beta pleated- sheet of antiparallel chains folded into accordion pleats- held together by intrachain or interchain H bonds between adjacent polypeptides(some fibrous and many globularprotein cores)
Tertiary- irregular contortions of a protein due to bonding between side chains(R groups) superimposed upon the primary and secondary structure- bonding is weak interactions and covalent linkage
    • Hydrophobic interaction= clustering of hydrophobic molecules as a result of their mutual exclusion from water
    • Disulfide bridges(covalent linkage)=formed between two cysteine monomers brought together by folding of the protein(strong bond).
  • Quaternary-protein with two or more polypeptide chains
Protein conformation
  • **Physical and chemical conditions influence conformation**
  • -Denaturation = alteration of a protein’s native conformation and emergent biological activity
  • -Proteins can be denatured by:
    • Organic solvents- turns the hydrophobic chains normally inside the core of the protein towards the outside- hydrophilic chains turn away from the solvent towards the interior of the protein.
    • Chemical agents that disrupt the H bonds, pH, ionic bonds, and disulfide bridges.
    • Excessive heat- disrupts the weak interactions with increased thermal“agitation”.
Protein folding- most proteins pass thru several intermediate stages to reach their final conformation
  • Chaperone proteins= newly discovered “brace” to a folding protein- this bracing plays an important role as a protein conforms to its “final” 3D shape
nucleic acids store and transmit hereditary information
Nucleic acids store and transmit hereditary information
  • Remember that Protein conformation is determined by primary structure. -Primary structure, in turn is determined by genes-Gene = hereditary units of DNA
Two types of nucleic acids
  • 1. Deoxyribonucleic acid (DNA)
  • Coded information that programs all cell activity
  • Contains directions for its own replication
  • Copied and passed from one generation of cells to the next
  • In Eukaryotes- found primarily in the nucleus (but is also found in mitochondria of cells)
  • Make up genes-contain instructions for making mRNA, which in turn is responsible for protein synthesis
2. Ribonucleic acid (RNA)
  • Functions in actual synthesis of proteins coded by DNA
  • Site of protein synthesis=ribosomes in the cytoplasm of the cell
  • 3 main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA)
  • mRNA carries the encoded genetic message from nucleus to cytoplasm
  • Two processes : Transcription and translation (we will examine more closely when we know more about the cell) involve rRNA and tRNA
a dna strand is a polymer with an information rich sequence of nucleotides
A DNA strand is a polymer with an information-rich sequence of nucleotides
  • Nucleic acid=polymer of nucleotides linked by condensation rxns
  • Nucleotide=Building block molecule of a nucleic acid
  • Made of :
      • 5 carbon sugar
      • Phosphate group
      • Nitrogenous base
Pyrimidine-6 membered ring made up of carbon and nitrogen atoms
          • Cytosine(C)
          • Thymine(T)-found only in DNA
          • Uracil(U)-found only in RNA
  • Purine-5 membered ring fused to a 6 membered ring
          • Adenine(A)
          • Guanine(G)
nucleotides have several fxns
Nucleotides have several fxns:
  • Many are monomers for nucleic acids
  • Many transfer chemical energy from one molecule to another (ex. ATP)
  • Many are electron acceptors in enzyme controlled redox rxns of cell
inheritance is based on precise replication of dna
Inheritance is based on precise replication of DNA
  • Double helix-Proposed by Watson and Crick(1953)
  • Rosalind Franklin
  • Two nucleotide chains wound in a double helix
  • Sugar-phosphate backbones are outside the helix
  • Nitrogenous bases paired in the interior of the helix(H bonds)
  • Adenine to Thymine, Cytosine to Guanine pairing rule
Two strands are complimentary thus they serve as templates to make new strands- it is this mechanism of precise copying that makes inheritance possible
  • Most DNA molecules - 1000s to 1000000s of base pairs long
Species that have many characteristics in common, are found to have many of the same DNA sequences which cause the production of similar amino acids and proteins
  • Other structures and their functions (which ultimately are based on the DNA code) in many cases are very similar as well