BY1101 Introduction to Molecular and Cellular Biology
Tutorial for module BY1101:
Proteins and nucleic acids
Joe Colgan (tcolgan@tcd.ie)
BY1101 Introduction to Molecular and Cellular Biology
Tutorial objectives
• Describe polymeric biological molecules
• Describe structure and functions of proteins
• Describe structure and functions of nucleic
acids
BY1101 Introduction to Molecular and Cellular Biology
Major classes of molecules
• What are the four major classes of molecules of life?
Carbohydrates
Lipids
Proteins
Nucleic acids
BY1101 Introduction to Molecular and Cellular Biology
What is a polymer?
• Long molecule consisting of similar or identical monomers linked
by covalent bonds
• Examples:
• Polymer: Protein
• Monomer: Amino acid
• Polymer: Nucleic acid
• Monomer: Nucleotide
BY1101 Introduction to Molecular and Cellular Biology
Polymeric biological molecules
How are polymers formed?
Dehydration reaction
How are polymers broken down?
Hydrolysis
BY1101 Introduction to Molecular and Cellular Biology
What is a protein?
• Large molecules or polymers consisting of amino acids
• One or more polypeptides each folded and coiled in a 3D
structure
BY1101 Introduction to Molecular and Cellular Biology
What types of proteins are there?
Enzymes
Receptor
Contractile/motor Hormonal
Structural
Transport
Defensive
Storage
BY1101 Introduction to Molecular and Cellular Biology
What is an amino acid?
A monomer that forms peptide bonds with other amino acids to create a polypeptide
An organic molecule consisting of an amino, carboxyl and R-group
R-group
Side chain
R2
R1
Amino
Peptide
backbone
Carboxyl
H3N
CH
H3N
COO
CH
α-Carbon
H
H
H2O
Hydrogen
-> Peptide bonding through dehydration reaction
-> Peptide breakdown through hydrolysis
COO
BY1101 Introduction to Molecular and Cellular Biology
Subgroups of amino acids
How many naturally occurring amino acids are there?
20
4 subgroups
Polar
Hydrophobic
Glycine (G), Alanine (A), Valine (V),
Isoleucine (I), Leucine (L), Phenylalanine (F),
Methionine (M), Proline (P), Tryptophan (W)
Non-Polar
Hydrophilic (Neutral) Serine (S), Threonine (T), Tyrosine (Y),
Cysteine (C), Asparagine (N), Glutamine (Q)
Non-Polar
Hydrophilic (Acidic)
Aspartic acid (D), Glutamic acid (E)
Non-Polar
Hydrophilic (Basic)
Lysine (K), Arginine (R), Histidine (H)
BY1101 Introduction to Molecular and Cellular Biology
BY1101 Introduction to Molecular and Cellular Biology
Protein synthesis
Transcription of mRNA
Migration of mRNA
Translation of protein
BY1101 Introduction to Molecular and Cellular Biology
Protein synthesis
20 amino acids
4 possible nucleotide bases
3 nucleotides = 1 codon
1 codon = 1 amino acid
BY1101 Introduction to Molecular and Cellular Biology
Protein structure
Primary
structure
Primary structure
A linked series of amino acids with a
unique sequence
Function:
Dictates secondary and tertiary structure
due to:
•Chemical nature of the backbone
•R-side chains
BY1101 Introduction to Molecular and Cellular Biology
Protein structure
What are the defining characteristics of the
secondary structure of proteins?
Secondary structure
Coils and folds repeatedly present within a
polypeptide chain
Result from hydrogen bonds forming between
repeating constituents of the polypeptide
backbone
Two main structures:
Alpha helix:
Delicate coil held together by hydrogen bonding
at every fourth amino acid
Beta-pleated sheets:
Form by hydrogen bonds between two parallel
parts of polypeptide backbone
BY1101 Introduction to Molecular and Cellular Biology
Tertiary
structure
What are the defining characteristics of the
tertiary structure of proteins?
Tertiary structure
Shape of a polypeptide resulting from
interactions within the side chains (R Groups) of
various amino acids
BY1101 Introduction to Molecular and Cellular Biology
Quaternary structure
Overall protein structure that results from the
aggregation of multiple polypeptide subunits
BY1101 Introduction to Molecular and Cellular Biology
Protein structure summary
Primary structure: sequence of a chain of amino acids
Secondary structure: when the sequence of amino acids
are linked by hydrogen bonds
• α-helix: bonds every 4 aa
• β-pleated sheet: parallel polypeptides
(note: bonds occur in polypeptide backbone )
Tertiary structure: attractions between  helices and  sheets
• irregular loops and folds that give overall 3D shape
• chaperones help with the folding
(note: interactions occur between side chains eg. hydrophobic)
Quaternary structure: when more than one amino acid chain
is present
BY1101 Introduction to Molecular and Cellular Biology
How does the structure links to function?
e.g. A single amino acid substitution can cause sickle-cell disease as red blood cells will
become less flexible which results in a reduced capacity to carry oxygen.
Symptoms: pain, serious infections, chronic anemia and damage to body organs.
BY1101 Introduction to Molecular and Cellular Biology
Nucleic acids
BY1101 Introduction to Molecular and Cellular Biology
What are nucleic acids?
•Large macromolecules essential for life
What are the two types of nucleic acids?
•Deoxyribonucleic acid (DNA)
•Ribonucleic acid (RNA)
What are the roles of nucleic acids?
• Storage of genetic information
• Transmission of genetic information
•DNA -> RNA -> Protein
BY1101 Introduction to Molecular and Cellular Biology
Components of nucleic acids
Deoxyribonucleic acid (DNA)
Purines
Adenine (A)
Guanine (G)
Pyrimidines
Cytosine (C)
Thymine (T)
Nitrogenous
base
Phosphate group
Sugar molecule
BY1101 Introduction to Molecular and Cellular Biology
Ribonucleic acid (RNA)
DNA vs RNA
1. Single stranded
2. Different sugars
(Deoxyribose vs. ribose)
3. Uracil replaces thymine
BY1101 Introduction to Molecular and Cellular Biology
Structure of nucleic acids
BY1101 Introduction to Molecular and Cellular Biology
Nucleic acids and proteins
•Both polymers
•Both essential for life
•Nucleic acids encode for protein sequence
•Proteins are also involved in cellular processes
•Mutations in nucleic acid sequence can result in changes at the
protein level
BY1101 Introduction to Molecular and Cellular Biology
Past paper questions
Exam 2011
Exam 2008
BY1101 Introduction to Molecular and Cellular Biology
Past paper questions
2010
2. Write an essay entitled ‘Polymeric Biological Molecules’
2008
2. Discuss which you think is the more important for life:
DNA or protein
BY1101 Introduction to Molecular and Cellular Biology
Questions
Further reading:
Campbell Chapter 5