Transcript Lecture 3

Chapter 2
Chemical Principles
part B
Structure and Function
• The chain of carbon atoms in an organic molecule is the carbon skeleton
• Saturated hydrocarbons: Carbon-carbon single bond
– Ethane – C2H6
– Hexane –
C6H14
-
Cyclohexane
• Unsaturated hydrocarbons: Carbon-carbon double bond,
– Ethylene – C2H4
Benzene – C6H6
Structure and Function
• Replacing one of the H atoms in propane molecule with a functional group:
– Propane – C3H8
– With OH- will become an alcohol (Propanol)
Propanol - C3H7OH - Isopropanol
Functional group – hydroxyl group
• Replacing two more H atoms from the same C with Oxygen –will become an
acid - Propanoic acid - CH3CH2COOH – C2H5COOH
Radical
Functional group – carboxyl group - COOH
Organic compounds in life organisms
Macromolecule
Carbohydrates
Functional group
R-OH (alcohol)
Lipids
R-COOH (acid)
R-OH (alcohol)
R-COOC (ester)
Proteins
R-NH2 (amino)
R-COOH (acid)
R-SH (sulfhydryl)
Nucleic acids
R-CH3 (methyl)
R-PO4 (phosphate)
Organic Compounds
• The small molecules are called monomers.
M
Glucose C6H12O6
• Monomers join by dehydration synthesis or condensation reactions
into large molecules -polymers .
M
Cellulose
M
n
(C6H10O5)n
n
• Macromolecules are polymers consisting of many
small repeating molecules-monomers.
M
M
M
M
M
M
M
M
M
Organic Compounds
1. Monomers join by dehydration synthesis or condensation
reactions.
1
Enzyme 1
R-OH
+
HO-R
R-O-R
+ H2O
Enzyme 2
2
2. Macromolecules degrade to monomers by hydrolysis or
decomposition reactions
Figure 2.8
Organic compounds in life organisms
Macromolecule
Carbohydrates
Functional group
R-OH (alcohol)
Monomer
Monosaccharides
Lipids
R-COOH (acid)
R-OH (alcohol)
R-COOC (ester)
Glycerol
Fatty acids
Proteins
R-NH2 (amino)
R-COOH (acid)
R-SH (sulfhydryl)
Amino acids
Nucleic acids
R-CH3 (methyl)
R-PO4 (phosphate)
Nucleotides
1. Carbohydrates
• Consist of C, H, and O with the formula (CH2O)n
Glucose – C6H12O6
• Monomers - Monosaccharides are simple sugars with 3 to 7
carbon atoms.
– glucose, fructose, galactose, ribose, deoxyribose
• Disaccharides are formed when two monosaccharides are
joined in a dehydration synthesis.
– Sucrose (glucose-fructose), lactose (glucose-galactose)
• Disaccharides can be broken down by hydrolysis.
Figure 2.8
• Oligosaccharides consist of 2 to 20 monosaccharides.
• Polysaccharides consist of tens or hundreds of
monosaccharides joined through dehydration synthesis.
– Starch, glycogen, dextran, and cellulose are polymers of
glucose that are covalently bonded differently.
– Chitin is a polymer of two sugars repeating many times.
Function of Carbohydrates
• Cell structures
– Nucleic acids - ribose, deoxyribose
– Cell wall – peptidoglycan, cellulose, chitin
– Bacterial capsule
• Cell energy
– Energy sources
– Short term energy storage
2. Lipids
• Lipids are a broad group of naturally-occurring molecules which
includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins
A, D, E and K), phospholipids, and others.
• Consist of C, H, and O.
A. Simple lipids - called fats – contain an alcohol glycerol and a
group of compounds as fatty acids
• Fatty acids - long chains of carbon
and hydrogen atoms, with a carboxylic
acid group at one end
• Saturated
C C
• Unsaturated fats have one or more double
bonds between carbons in the fatty acids.
C
C
– Are nonpolar and insoluble in water
• A molecule of fat is formed when a molecule of glycerol combines
with one to three fatty acid molecules by dehydration synthesis
– Monoglycerides, diglycerides, triglycerides
– Saturated and Unsaturated fatty acids
Figure 2.9c
B. Complex lipids
– Contain C, H, and O + P, N, or S.
– Membranes are made of phospholipids
C. Steroids
• Steroid skeleton consist of four carbon rings
• Steroids vary by the functional groups attached to these
rings
• Sterol - modified steroid with an –OH group attached to the
ring A.
• Are part of membranes.
Figure 2.11
Function of Lipids
•
•
•
•
Plasma membranes
Cell organelles
Some cell walls
Long term energy storage
3. Proteins
• Consist of one or more polypeptide molecules typically folded into
a globular or fibrous form, facilitating a biological function.
• Protein macromolecules monomers - amino acids
– Only 20 amino acids
Amino acids
Table 2.4.1
Peptide Bonds
• A peptide bond is a covalent bond that is formed between two
amino acids when the carboxyl group of one molecule reacts with
the amino group of the another molecule.
– Peptide bonds between amino acids are formed by dehydration synthesis.
• A single linear chain of amino acids bonded together by peptide
bonds is called polypeptide
• For chains under 40 residues the term peptide is frequently used
Figure 2.14
instead of protein.
Proteins structure - Primary structure
Met - Cys - Val - Ala - Tyr - Arg
Peptide bonds
• The primary structure of a protein is the amino acid sequence of
the peptide chains.
– It is reported starting from the amino-terminal (NH2) end to the carboxylterminal (COOH)
Proteins structure - Primary structure
R
R
R
R
R
R
Figure 2.15 Protein structure.
Peptide bonds
Hydrogen bond
(a) Primary structure:
polypeptide strand
(b) Secondary structure:
helix and pleated sheets
(with three polypeptide
strands)
Helix
Pleated sheet
Insert Fig 2.15a
2.15
Hydrophobic interaction
Disulfide
bridge
(c) Tertiary structure:
folded helix and
pleated sheet
Functionally active
(d) Quaternary structure:
two or more polypeptides
in their folded states
Functionally active
Polypeptide
strand
Hydrogen
bond
Disulfide bridge
(between cysteine
molecules)
Ionic bond
Details of bonds associated
with tertiary structure
• Conjugated proteins consist of polypeptide chain bound to
other organic molecules:
• Glycoproteins
• Nucleoproteins
• Lipoproteins
Function of Proteins
• Are essential in cell structure and function.
– Enzymes are proteins that speed chemical reactions.
– Transporter proteins move chemicals across membranes.
– Structural or mechanical functions, that maintain cell shape
( actin, cell wall).
– Cell signaling - complex system of communication that
coordinates cell actions.
– Flagella are made of proteins.
– Some bacterial toxins are proteins.
– Immune responses – antibodies, cytokines are proteins.
4. Nucleic Acids
• Macromolecules - DNA and RNA
• Monomers are nucleotides.
• Nucleotides consist of a:
• Sugar pentose (with 5 carbons)
• ribose
• deoxyribose
• Nitrogen-containing base (purine or pyrimidine)
• Phosphate group
Purines – Adenine and Guanine
Pyrimidines – Cytosine, Thymine and Uracil
DNA
• Monomers are deoxyribonucleotides
– sugar-deoxyribose
– Purines - Adenine and Guanine; Pyrimidines - Cytosine and Thymine
• Primary structure – nucleotide sequence
• The primary structure of DNA or RNA molecule is reported from
the 5' end to the 3' end
PO4
– 5’ end – PO4 (phosphate group)
– 3’ end – OH (hydroxyl group)
OH
• The sugar-phosphate backbone of one
strand is upside down, or antiparallel,
relative to the backbone of the other strand.
OH
PO4
Figure 2.16
DNA – secondary structure – double helix
• Two molecules form
the double helix
Phosphate
Sugar
Adenine (A)
-
Adenine nucleotide
Hydrogen bonds
Individual DNA nucleotides are composed of a
deoxyribose sugar molecule covalently bonded
to a phosphate group at the 5’ carbon, and to a
nitrogen-containing base at the 3’ carbon. The
two nucleotides shown here are held together
by hydrogen bonds.
Insert Fig 2.16
Sugar-phosphate backbone
•
•
Sugars
Phosphates
A hydrogen bonds with T (2 hydrogen bonds)
C hydrogen bonds with G (3 hydrogen bonds)
Thymine (T)
Sugar
Phosphate
Thymine nucleotide
RNA
• Monomers are ribonucleotides
– sugar ribose
• Primary structure – nucleotide sequence
• Single-stranded
• Can form secondary structure
– A hydrogen bonds with U (2 hydrogen bonds)
– C hydrogen bonds with G (3 hydrogen bonds)
tRNA
siRNA
Figure 2.17
Function of Nucleic acids
• DNA contains all the information - coding which is used to
control functions, behavior and development of an organism.
– Long term storage device to store the genetic instructions.
– The code from which all proteins in the cell are synthesized
– Code for the way proteins turn genes on or off.
• RNA carries out the instructions encoded in DNA
– Protein synthesis
– In some organisms it is also responsible for carrying the
genetic code.
– Some RNA are involved in the regulation of the gene
expression
ATP – Adenosine triphosphate
• Is made by dehydration synthesis.
• Is broken by hydrolysis to liberate useful energy for the cell.
ATP
ADP
Function of ATP
• ATP is the main energy source for the majority of cellular
functions.
• Important player in cell respiration.
• Synthesis of macromolecules in the cell - DNA and RNA,
proteins, lipids and carbohydrates.
• Supply energy for the transport of macromolecules across
cell membranes.
• ATP is critically involved in maintaining the locomotion
of the cell .
Learning objectives
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•
•
•
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Identify the structure and function of carbohydrates.
Identify the structure and function of lipids.
Identify the structure and function of proteins.
Identify the structure and function of nucleic acids
Describe the role of ATP in cellular activities.