by1101 introduction to molecular and cellular biology tutorial for module by1101: proteins and...
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BY1101 Introduction to Molecular and Cellular Biology
Tutorial for module BY1101:
Proteins and nucleic acids
Joe Colgan (tcolgan@tcd.ie)
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?
BY1101 Introduction to Molecular and Cellular Biology
Carbohydrates
Proteins Nucleic acids
Lipids
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 moleculesBY1101 Introduction to Molecular and Cellular Biology
How are polymers formed? How are polymers broken down?
Dehydration reaction 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 polypeptideAn organic molecule consisting of an amino, carboxyl and R-group
H3N COOCH
R1
H2OH
H3N COOCH
R2
H
Amino Carboxyl
R-group
Hydrogen
α-Carbon
Side chain
Peptide backbone
-> Peptide bonding through dehydration reaction-> Peptide breakdown through hydrolysis
BY1101 Introduction to Molecular and Cellular Biology
Subgroups of amino acidsHow 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
20 amino acids
4 possible nucleotide bases
3 nucleotides = 1 codon
1 codon = 1 amino acid
Protein synthesis
BY1101 Introduction to Molecular and Cellular Biology
Protein structurePrimary
structure
Primary structureA 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
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
Secondary structureCoils and folds repeatedly present within a polypeptide chain
Result from hydrogen bonds forming between repeating constituents of the polypeptide backbone
What are the defining characteristics of the secondary structure of proteins?
BY1101 Introduction to Molecular and Cellular Biology
Tertiary structure
Tertiary structureShape of a polypeptide resulting from interactions within the side chains (R Groups) of various amino acids
What are the defining characteristics of the tertiary structure of proteins?
BY1101 Introduction to Molecular and Cellular Biology
Quaternary structureOverall protein structure that results from the aggregation of multiple polypeptide subunits
BY1101 Introduction to Molecular and Cellular Biology
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
Protein structure summary
How does the structure links to function?
BY1101 Introduction to Molecular and Cellular Biology
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 acidsDeoxyribonucleic acid (DNA)
Nitrogenous base
Sugar molecule
Phosphate group
PurinesAdenine (A)Guanine (G)
PyrimidinesCytosine (C)Thymine (T)
BY1101 Introduction to Molecular and Cellular Biology
Ribonucleic acid (RNA) DNA vs RNA
1. Single stranded2. 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
Exam 2008
Exam 2011
Past paper questions
BY1101 Introduction to Molecular and Cellular Biology
2010
2. Write an essay entitled ‘Polymeric Biological Molecules’
2008
2. Discuss which you think is the more important for life: DNA or protein
Past paper questions
BY1101 Introduction to Molecular and Cellular Biology
Questions
Further reading: Campbell Chapter 5
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