by1101 introduction to molecular and cellular biology tutorial for module by1101: proteins and...

BY1101 Introduction to Molecular and Cellular Biology

Tutorial for module BY1101:

Proteins and nucleic acids

Joe Colgan ([email protected])

mailto:[email protected]

Tutorial objectives

• Describe polymeric biological molecules• Describe structure and functions of proteins• Describe structure and functions of nucleic

acids


Major classes of molecules• What are the four major classes of molecules of life?


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


Polymeric biological moleculesBY1101 Introduction to Molecular and Cellular Biology

How are polymers formed? How are polymers broken down?

Dehydration reaction Hydrolysis


What is a protein? • Large molecules or polymers consisting of amino acids• One or more polypeptides each folded and coiled in a 3D

structure


What types of proteins are there?Enzymes Receptor

Contractile/motor Hormonal

Structural Transport

Defensive Storage


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


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)


Protein synthesis

Transcription of mRNA Migration of mRNA Translation of protein


20 amino acids

4 possible nucleotide bases

3 nucleotides = 1 codon

1 codon = 1 amino acid

Protein synthesis


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


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?


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?


Quaternary structureOverall protein structure that results from the aggregation of multiple polypeptide subunits


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?


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.


Nucleic acids


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


Components of nucleic acidsDeoxyribonucleic acid (DNA)

Nitrogenous base

Sugar molecule

Phosphate group

PurinesAdenine (A)Guanine (G)

PyrimidinesCytosine (C)Thymine (T)


Ribonucleic acid (RNA) DNA vs RNA

1. Single stranded2. Different sugars

(Deoxyribose vs. ribose)3. Uracil replaces thymine


Structure of nucleic acids


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


Exam 2008

Exam 2011

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

Past paper questions


Questions

Further reading: Campbell Chapter 5

by1101 introduction to molecular and cellular biology tutorial for module by1101: proteins and...

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