Hydrocarbons

1
Hydrocarbons Macromolecules

• Mrs. Daniels
• Advanced Biology
• Sept. 2005
• (modified Sept. 2008)

2
Hydrocarbons

• What are they?
• Where do we find them?
• What do we use them for?
• Old arguments of organic molecules vitalism vs.
  mechanism

3
Drawing Hydrocarbons

• How many bonds can carbon form?
• This enables it to form long chains (branched or
  unbranched)
• Skeleton structures
• Isomers

4
Isomers

• Structural same formula - different structure
  or arrangement of atoms
• Ex. C2H6O
• H H H H
• H - C - C - OH or H - C - O - C - H
• H H H H

5
Isomers

• Geometric same formula - different spatial
  arrangement around double bond
• Ex. Butene C4H8
• CH3 H CH3 CH3
• C C C C
• H CH3 H H

6
Isomers

• 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

7
Naming Alkanes

• Rules to naming alkanes
• (see handout)

8
Saturation

• 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?
• Yesit is UNSATURATED

9
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

10
Functional Groups

• Polar and hydrophilic
• Hydroxyl
• An OH group
• Alcohols
• Carbonyl
• Double bonded Oxygen
• Ex. Aldehydes ketones

11
Functional Groups

• Carboxyl
• An end carbon is double bonded to an O and is
  single bonded to a hydroxyl group
• Amino
• -weak base
• -NH2
• Sulfhydryl
• SH
• Called thiols
• Phosphate
• PO4 -3

12
(No Transcript)
13
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

14

• 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.

15
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

16

• 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

17
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

18

• 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

19
In aqueous solution, many form rings

• Many monosaccharides can form rings in aqueous
  solns

H O C H- C-OH HO-C- H H-
C-OH H-C-OH H-C-OH H
CH2OH
O
H OH
H OH
H OH
OH H
20

• 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)

21

• 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

22
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)

23

• 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

24

• 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

25

• 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

HO
26
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

27

• There are 20 amino acids
• 10 are essential AAs and must be obtained from
  dietary sources because they cannot be
  synthesized in the body
• Amino acids exist as zwitterions - dipolar ions
• Peptide bondscovalent 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

28

• 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 AAs peptide
• Chains of more than 50 AAs protein

29
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)

30
Proteins 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 globular
  protein cores)

31

• 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

32

• Protein conformation
• Physical and chemical conditions influence
  conformation
• -Denaturation alteration of a proteins 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 thermalagitation.

33

• 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

34
(No Transcript)
35
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

36

• 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

37

• 2. Ribonucleic acid (RNA)
• Functions in actual synthesis of proteins coded
  by DNA
• Site of protein synthesisribosomes 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

38
A DNA strand is a polymer with an
information-rich sequence of nucleotides

• Nucleic acidpolymer of nucleotides linked by
  condensation rxns
• NucleotideBuilding block molecule of a nucleic
  acid
• Made of
• 5 carbon sugar
• Phosphate group
• Nitrogenous base

39

• 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)

40
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

41
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

42

• 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

43

• 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