Molecules of Life

1
Molecules of Life

• Chapter 3

2
Molecules of Life

• The molecules of life are made by living cells
• They are organic compounds
• Molecules consisting of carbon and at least one
  hydrogen atom
• Usually have one or more functional groups
• Certain atoms or clusters of atoms covalently
  bonded to carbon
• Organic compounds are not all molecules of life
• Methane and other hydrocarbons
• Molecules of life can also be synthesized in a
  laboratory

3
Molecules of Life

• Why carbon?
• Carbons bonding behavior
• Forms four covalent bonds with other atoms
  (including itself)

4
Molecules of Life

• Why carbon?
• Carbon forms backbones
• Multiple carbon atoms bond to each other to form
  chains or rings
• These become the backbone of organic compounds

5
Molecules of Life

• Why carbon?
• Carbon forms backbones
• Other atoms and functional groups can be attached
  to the backbones
• The most common atoms are oxygen and hydrogen
• Can also include nitrogen, phosphorous, or sulfur
  atoms

6
Molecules of Life

• Models for drawing organic compounds
• (also see appendix V)
• a. b. ball and stick model of a chain and a
  ring form of the same molecule
• Black carbon
• Red oxygen
• White hydrogen
• Flat structural formula
• Corner carbon
• Line covalent bond
• Simple icon
• Corner or end of line carbon
• Line covalent bond

Fig. 3-2, p. 36
7
Molecules of Life

• Why carbon?
• Carbon forms backbones
• Functional groups
• Certain atoms or clusters of atoms covalently
  bonded to carbon
• The number, kind, and arrangement give rise to
  specific properties
• Polarity, acidity, hydrophobicity, etc

8
In alcohols (e.g., sugars, amino acids) water
soluble
hydroxyl
methyl
In fatty acid chains insoluble in water
carbonyl
In sugars, amino acids, nucleotides
water soluble. An aldehyde if at end of a
carbon backbone a ketone if attached to an
interior carbon of backbone
(ketone)
(aldehyde)
carboxyl
In amino acids, fatty acids, carbohydrates water
soluble. Highly polar acts as an acid (releases
H)
(ionized)
(non-ionized)
Fig. 3-3, p. 36
9
amino
In amino acids and certain nucleotide bases
water soluble, acts as a weak base (accepts H)
(ionized)
(non-ionized)
phosphate
In nucleotides (e.g., ATP), also in DNA, RNA,
many proteins, phospholipids water soluble,
acidic
icon
Fig. 3-3, p. 36
10
Molecules of Life

• Why carbon?
• Carbon forms backbones
• Functional groups
• Minor differences in functional groups can make a
  lot of difference in the function of the entire
  molecule
• Estrogen and testosterone differ only in the
  position of two functional groups

11
Fig. 3-4, p. 37
12
Molecules of Life

• Cells construct, rearrange, and split organic
  compounds
• These metabolic activities help the cell stay
  alive, grow, and reproduce
• Require enzymes to make the reactions proceed
  faster than they would on their own

13
Molecules of Life

• Cells construct, rearrange, and split organic
  compounds
• Reactions include
• Condensation
• Two molecules covalently bond into a larger one
• Cells maintain pools of small organic molecules
  (monomers)
• Used as necessary to build larger molecules
  (polymers)
• Cleavage/hydrolysis
• A molecule splits into two smaller ones

14
Fig. 3-5, p. 37
15
Molecules of Life

• Cells construct, rearrange, and split organic
  compounds
• Reactions include
• Functional group transfer
• One molecule transfers a functional group to
  another molecule
• Phosphate group is transferred from one molecule
  to another to form ATP (energy currency of the
  cell)
• Very important for photosynthesis and cellular
  respiration

16
Molecules of Life

• Cells construct, rearrange, and split organic
  compounds
• Reactions include
• Electron transfer
• One or more electrons taken from one molecule are
  donated to another molecule
• Very important for photosynthesis and cellular
  respiration
• They both use an electron transfer chain
• Rearrangement
• Juggling of internal bonds converts one type of
  organic compound to another
• Used for several metabolic pathways like
  glycolysis, Krebs cycle, and Calvin-Benson cycle
  (chapter 6 and 7 and appendix VI)

17
Molecules of Life

• There are four major groups of organic molecules
  made and used by cells
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

18
Questions

• What atom is essential for the molecules of life?
• How many bonds can it make?
• Carbon can bond to carbon to create what part of
  the molecules of life?
• What are the other atoms most commonly used in
  organic molecules?
• What reaction builds large organic molecules?
• What reaction breaks down large organic
  molecules?
• What reaction is essential for forming ATP?

19
Carbohydrates

• The carbohydrates are the most abundant
  biological molecule
• Consist of carbon, hydrogen, and oxygen in a
  121 ratio
• Used for instant energy, energy storage, and
  structural materials
• The monomer is monosaccharides
• There are three main types of carbohydrates

20
Carbohydrates

• Monosaccharides
• Consist of a 5 or 6 carbon backbone
• Tends to form a ring when dissolved in water
• Also called simple sugars or reducing sugars
• Laboratory test
• Monosaccharides can be detected because they
  reduce Benedicts solution (blue ? orange)
• Thus the name reducing sugar
• Examples
• Glucose C6H12O6 (Energy source, monomer,
  precursor)
• Fructose (found in fruit)
• Ribose and deoxyribose (important for DNA and RNA)

21
Fig. 3-6, p. 38
22
Carbohydrates

• Short-chain carbohydrates
• Consist of a short chain of covalently bonded
  sugar monomers
• Also called disaccharides (two monomers) and
  oligosaccharides (2 monomers)
• No specific laboratory test
• Examples
• Sucrose glucose fructose
• Table sugar from sugar cane or sugar beets
• Lactose glucose galactose
• Sugar found in milk
• Lactose intolerance no enzymes to break lactose
  down

23
Fig. 3-6, p. 38
24
Carbohydrates

• Complex carbohydrates
• Consist of very long chains of sugar monomers
• Usually glucose
• 100s to 1000s of monomers
• Also called polysaccharides
• Laboratory test
• Iodine interacts with the coils of long polymers
  (yellow ? blue/black)
• Examples
• On the next slides

25
Carbohydrates

• Complex carbohydrates
• Examples
• Starch
• Bonding patterns of the glucose monomers produce
  coils and possibly branching
• Starches are used to store energy
• Animal starch is called glycogen
• Stored in liver and muscle cells
• Plant starches include amylose and amylopectin
• Stored temporarily in leaves following
  photosynthesis
• Stored for long-term use in other plant parts
  (potato)

26
Fig. 3-8, p. 39
27
Starch
28
c Glycogen. In animals, this polysaccharide is a
storage form for excess glucose. It is especially
abundant in the liver and muscles of highly
active animals, including fishes and people.
Fig. 3-8, p. 39
29
Carbohydrates

• Complex Carbohydrates
• Examples
• Cellulose
• Glucose chains stretch side by side and
  hydrogen-bond to one another
• Stabilized in a bundled pattern creating fibers
  used for structural support of plant cell walls,
  stems, wood, etc.
• We lack enzymes to digest cellulose
• Dietary fiber

30
Hydrogen bonds
Cellulose
31
Fig. 3-8, p. 39
32
Carbohydrates

• Complex Carbohydrates
• Examples
• Chitin
• Similar to cellulose except that it is modified
  with a nitrogen-containing group on each monomer
• Found in exoskeletons and fungi cell walls

33
Fig. 3-9, p. 39
34
Questions

• What is the simplest type of carbohydrate?
• What is the most common, simple sugar?
• What functional group is used for simple sugars?
• How is a disaccharide made (including the name of
  the chemical reaction)?
• What is the name of table sugar?
• What is the most common monomer for
  polysaccharides?
• Name three types of polysaccharides and indicate
  what they are used for.

35
Lipids

• Lipids are fatty, oily, or waxy organic compounds
  that are insoluble in water, but can dissolve in
  other nonpolar substances
• Consist primarily of carbon and hydrogen
• There are various types of lipids with different
  ratios of atoms
• Used for energy storage, cell membranes, cell to
  cell signals, insulation, cushion for internal
  organs, etc
• There is not one specific monomer, but many
  lipids use fatty acids
• Long carbon chains (4-36 carbons) with a carboxyl
  group at one end (more on these later)
• There are four types of lipids that we will cover

36
Lipids

• Fats and oils
• Usually have 3 fatty acids that dangle like tails
  from a small 3-carbon molecule called glycerol
• Also called triglycerides
• Laboratory test
• Insoluble in water, Sudan IV dye, and the brown
  paper test
• Examples
• Essential fatty acids (our bodies dont make
  them)
• Omega-3 and omega-6

37
Fig. 3-11, p. 40
38
Lipids

• Fats and oils
• Fatty acids
• Long carbon chains (4-36 carbons long)
• 1 Carboxyl group
• Many hydrogen atoms

39
Lipids

• Fats and oils
• Fatty acids
• Remember carbon can make up to four covalent
  bonds
• In a fatty acid each carbon (except the 1st and
  last carbon atoms) uses 2 bonds to make the chain
  of carbons
• The other two bonds can be saturated each with a
  hydrogen atom or can be unsaturated with only one
  hydrogen atom and carbon forming a double bond
  (shares two pairs of electrons)

40
Double bonds
Saturated fatty acid
Unsaturated fatty acids
41
Lipids

• Fats and oils
• Fatty acids
• Saturated fatty acids
• Have no double bonds, all of the carbons are
  saturated with hydrogen
• Solid at room temperature
• The tails are fairly straight without kinks, so
  they can pack in tightly
• Triglycerides with saturated fatty acids are
  typically referred to as fats
• bad fatty acids

42
Lipids

• Fats and oils
• Fatty acids
• Unsaturated fatty acids
• Have one or more double bonds, so some carbons
  are not saturated with hydrogen
• Liquid at room temperature
• The double bonds create kinks which prevent them
  from packing tightly
• Triglycerides with unsaturated fatty acids are
  typically referred to as oils
• good fatty acids
• But they just dont taste as good or work as well
  in cooking

43
Lipids

• Fats and oils
• Fatty acids
• Unsaturated fatty acids
• Because they are the good fatty acids food
  companies tried to use them
• They had to come up with a way to get them to be
  solid at room temperature and to moisten and
  improve baked goods

44
Lipids

• Fats and oils
• Fatty acids
• Unsaturated fatty acids
• The food companies hydrogenated the unsaturated
  fats
• This process breaks some of the double bonds and
  forces hydrogen atoms onto the carbons
• Forms trans fatty acids
• Some trans fatty acids occur naturally in some
  foods

45
Lipids

• Fats and oils
• Fatty acids
• Unsaturated fatty acids
• Trans fatty acids
• Solid at room temperature and work well in baked
  goods
• The hydrogen atoms attach on opposite sides
  keeping double bonds straight
• It seemed like a good solution.
• However, a diet high in trans fatty acids
  increases risk of heart attack

46
Lipids

• Fats and oils
• Fatty acids
• Unsaturated fatty acids
• Cis fatty acids
• The hydrogen atoms attach on the same side
  keeping the kinks
• Cis fatty acids dont seem to carry the same
  health risk

47
Fig. 3-12, p. 41
48
Lipids

• Phospholipids
• Composed of two fatty acids and one phosphate
  group attached to glycerol
• Very similar to triglycerides (one fatty acid is
  replaced by the phosphate group)
• The fatty acids are hydrophobic (tails of the
  molecule)
• The phosphate group is hydrophilic (head of the
  molecule)

49
Fig. 3-13, p. 41
50
Lipids

• Phospholipids
• Phospholipids are abundant in cell membranes
• Membranes are composed of two layers of
  phospholipids
• The heads of one layer are exposed to the cells
  water based fluid interior
• The heads of the other layer are exposed the
  water based fluid surroundings of the cell
• Sandwiched between the two are all of the
  hydrophobic tails
• Nicely protected from any water based fluids

51
Fig. 3-13, p. 41
52
Lipids

• Waxes
• Firm and water repellent
• Composed of tightly packed fatty acids bonded to
  long-chain alcohols or carbon rings
• Examples
• Plant cuticle
• Beeswax
• Feathers

53
(No Transcript)
54
Lipids

• Sterols
• Consist of a rigid backbone of four carbon rings
  and no fatty acids
• The number and type of functional groups
  determines their properties and function
• Examples
• Cholesterol
• Bile salts
• Vitamin D
• Steroid hormones

55
Questions match the following

• Triglycerides Four carbon rings
• Saturated fatty acids Hydrogenated fats
• Unsaturated fatty acids 3 fatty acids glycerol
• Trans fatty acids Component of cell membranes
• Phospholipids bad fatty acids
• Waxes Fatty acids with double bonds
• Sterols Found in plant cuticles

56
Protein

• Proteins are the most diverse of the large
  organic biological molecules
• Proteins are long chains of amino acids
  consisting of carbon, hydrogen, oxygen, nitrogen,
  and some times sulfur
• Used for a wide variety of functions
• Enzymes, antibodies, structure, communication,
  muscle, etc
• The monomer is amino acids
• There are two main types of protein
• Globular
• Fibrous
• Laboratory test
• Biurets

57
Protein

• Amino acids
• Small organic compound
• Has a central carbon bonded to
• An amino group
• A carboxyl group (the acid)
• A hydrogen atom
• One of 20 possible R groups
• Each group confers different properties to the
  amino acid
• Polar/nonpolar, charged/uncharged,
  acidic/basic/neutral

58
Fig. 3-15, p. 42
59
Fig. 3-15, p. 42
60
tyrosine (tyr)
lysine (lys)
glutamate (glu)
glycine (gly)
UNCHARGED, POLAR AMINO ACID
POSITIVELY CHARGED, POLAR AMINO ACID
NEGATIVELY CHARGED, POLAR AMINO ACID
valine (val)
phenylalanine (phe)
methionine (met)
proline (pro)
Fig. 3.12, p. 42
61
Protein

• Amino acids
• Are linked together by a specialized type of
  condensation reaction called a peptide bond
• The carbon of one amino acids carboxyl group is
  linked to the nitrogen of another amino acids
  amino group
• This creates a backbone of -N-C-C-N-C-C-etc
• The sequence of amino acids is determined by
  instructions in the DNA (genes)
• The sequence determines what type of protein is
  synthesized

62
Fig. 3-16, p. 42
63
Protein

• Terminology
• Amino acid
• Monomer of proteins
• Peptide bond
• Covalent bond joining amino acids
• Peptide
• A chain of 2 or more amino acids
• Polypeptide
• A chain of many amino acids
• Protein
• Finished and modified polypeptide

64
Protein

• Protein structure
• Protein structure is related to protein function
• Just like tools have to be the right shape for a
  job
• Screw driver screw Hammer nail
• If the protein isnt shaped correctly, then it
  will not function correctly

65
Protein

• Protein structure
• Primary structure
• The unique sequence of amino acids for each
  protein

66
Protein

• Protein structure
• Secondary structure
• As a polypeptide is synthesized regions or
  stretches of the amino acid chain will twist,
  bend, loop, or fold
• Hydrogen bonds can hold the twists etc in place
  to make
• Helixes
• Coils like a spiral staircase
• Sheets or loops
• Flat sheet-like regions

67
Fig. 3-17, p. 43
68
Protein

• Protein structure
• Tertiary structure
• Final three dimensional folding of the
  polypeptide
• Held together by hydrogen bonds, disulfide bonds,
  and other weak interactions
• Becomes a working molecule

69
Protein

• Protein structure
• Quaternary structure
• Two or more polypeptide chains are bound or
  associate together
• Not all proteins have a fourth level of
  organization

70
Proteins

• Protein structure
• If the protein does not have the correct shape,
  then it will not be able to function properly
• Several factors can influence shape
• Denaturation
• Heat, pH change, salts, and detergents can all
  disrupt bonds holding proteins in their proper
  shape

71
Proteins

• Protein structure
• Several factors can influence shape
• Mistakes in the sequence of amino acids (genetic
  mutations)
• If the wrong amino acid is placed in a protein
  sequence, it can change the chemical interactions
• Example
• Hemoglobin and sickle-cell anemia

72
Proteins

• Hemoglobin and sickle-cell anemia
• A globular protein which carries oxygen through
  the blood
• Hemoglobins ability to bind oxygen depends on
  its structure
• Primary structure amino acid sequence
  (glutamate is the 6th amino acid)
• Secondary structure multiple helixes
• Tertiary structure folds up as globin to form a
  pocket that cradles heme
• Heme is a functional group with an iron atom at
  its center
• Quaternary structure Four globulin molecules
  (two alpha and two beta) held together by
  hydrogen bonds

73
alpha globin
heme
Fig. 3-18, p. 44
74
alpha globin
alpha globin
beta globin
beta globin
Fig. 3-18, p. 44
75
Proteins

• Hemoglobin and sickle-cell anemia
• Sickle-cell anemia is a genetic disease where the
  hemoglobin is mis-shapen because of a mutation
  resulting in a different amino acid at the 6th
  position
• Glutamate is replaced with valine

76
Protein

• Hemoglobin and sickle-cell anemia
• Because of the mutation (glutamate ? valine), the
  shape and thus the function of hemoglobin changes
• When available oxygen is low, the protein forms
  large clumps
• The red blood cells distort into sickled shape
• The sickle cells clog blood vessels and disrupt
  blood circulation
• A proteins structure dictates its function!

77
VALINE
HISTIDINE
LEUCINE
GLUTAMATE
VALINE
THREONINE
PROLINE
sickle cell
normal cell
Fig. 3-19, p. 45
78
Questions

• What is the monomer for protein?
• What atom is found in protein that is not usually
  found in carbohydrates or lipids?
• What type of bond links amino acids?
• What is the primary structure of a protein?
• Coils and sheets are part of a proteins ___
  structure.
• When proteins unfold or lose their shape due to a
  pH change they are ______________.

79
Nucleotides

• Nucleotides are small organic compounds
• Nucleotides consist of
• one sugar (deoxyribose or ribose)
• at least one phosphate group
• one nitrogen-containing base
• Used as
• Energy carriers (ATP), enzyme helpers, and
  messengers
• Building blocks (monomers) for DNA and RNA

80
Nucleotides

• ATP
• Has three phosphate groups
• Used as the energy currency of the cell
• Transfers its 3rd phosphate group to prime other
  molecules for action
• Coenzymes (some are nucleotides)
• NAD and FAD
• Move electrons and hydrogens

81
Nucleotides

• Nucleic acids DNA and RNA
• Chains of four types of nucleotides
• Adenine, guanine, thymine (or uracil), and
  cytosine
• DNA encodes the genetic instructions
• Double stranded
• Located in the nucleus
• Makes up chromosomes
• RNA carries out genetic instructions
• Single stranded
• Made in the nucleus, but functions in the
  cytoplasm

82
Fig. 3-21, p. 46
83
Fig. 3-21, p. 46
84
covalent bonding in carbon backbone
hydrogen bonding between bases
Fig. 3-22, p. 47
85
Questions

• What are the three parts of an nucleotide?
• Which nucleotide is the energy currency of the
  cell?
• Nucleic acids are long chains of __________.
• What are the four nucleic acids in DNA?
• T or F DNA is single stranded
• T or F RNA stays in the nucleus

86
Summary

• Organic molecules
• Carbon
• Carbohydrates
• Monosaccharides, disaccarides, polysaccharides
• Lipids
• Fatty acids
• Proteins
• Amino acids, structure
• Nucleotides
• ATP, DNA, RNA

87
Good fat
Fig. 3-11, p. 40
88
Bad fat?