BIOL10002 – Biomolecules and Cells

Lecture 2
Assoc Prof Joshua Heazlewood

School of Biosciences
Office: BioSciences 2, Room 305
Email: jheazlewood@unimelb.edu.au
Web: http://heazleome.org/

My research interests include:

• Plant cell walls

• Glycobiology
• Mass Spectrometry

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 1

 Information
Living systems have multiple mechanisms to store, retrieve, and
transmit information

• Information exists in many forms and is relayed within and across

biological molecules, cells, tissues, organisms, populations,
and ecosystems.

Cells
Cells are the fundamental structural and functional unit of life.

• Cells are bounded by a membrane and maintain internal environments

that differ from their external environments.

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 Module 1 – What is Life?
Lecture 1:
• Defining Life

Lectures 2 & 3:
• The building blocks of life

Lecture 4:
• Prokaryotes

Lecture 5 & 6:
• Eukaryotes

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 Lecture 2 - Molecules of Life I – Part 1
What you should know
• Macromolecules are mainly comprised of C, H, O and N – Part 1

• The unique properties of water, and why biological molecules have a

relationship with water – Part 1

• How do nucleic acids assemble from only 4 nucleotides, and how is

DNA and RNA different – Part 2

• How do proteins assemble from only 20 amino acids, and how does
the amino acid sequence determine protein function – Part 3

• How are DNA, RNA and proteins connected – Part 3

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 4
 The Elements of Life

Major elements: H, C, O, N
Smaller amounts: P, S, Ca, Na, Mg, Cl, K
Trace elements: F, Si, V, Cr, Mn, Fe, Ni
Co, Cu, Zn, Se, Mo, I

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 5

 Carbon is the basis of most biomolecules

Ethanol

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 Hydrogen bond or H-bond
An intermolecular bond between an electron rich donor atom, commonly in
biology nitrogen (N) and oxygen (O), and the antibonding orbital of a bond
between hydrogen (H)

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 Water is the medium of life

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 Water is polar (slightly charged)
Polar molecules are Non-polar molecules
Water molecule attracted to water associate with each other

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 Water and ions

Water molecules surround ions and

molecules through ionic
interactions and can maintain them
in solution

Water is the matrix of Life (see Lecture 1)

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 Life = Water + Biomolecules (The Big Five)

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 End of Lecture 2, Part 1

See Activity – Life without phosphorus

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 12

 Lecture 2 - Molecules of Life I – Part 2
What you should know
• Macromolecules are mainly comprised of C, H, O and N – Part 1

• The unique properties of water, and why biological molecules have a

relationship with water – Part 1

• How do nucleic acids assemble from only 4 nucleotides, and how is

DNA and RNA different – Part 2

• How do proteins assemble from only 20 amino acids, and how does
the amino acid sequence determine protein function – Part 3

• How are DNA, RNA and proteins connected – Part 3

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 13
 The Major Biomolecules (macromolecules)

1.Nucleic Acids
Lecture 2
2.Proteins
3.Carbohydrates
Lecture 3
4.Lipids

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 Nucleic Acids

DNA double helix

Rosalind Franklin
(artist impression)
Watson and Crick
The double helix model
Watson and Crick (1953) Nature 171: 737–738. Photo 51

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 DNA Nucleic Acids – the basics RNA

• DNA - DeoxyriboNucleic Acid

• Nucleotides (Only 4)
Adenine - (A)
Cytosine - (C)
Guanine - (G)
Thymine - (T)
RNA - RiboNucleic Acid
• In RNA, Thymine is replaced by the related nucleotide Uracil (U)
• Both form long, linear chains (polynucleotides) that never branch

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 Nucleotides – the building blocks of nucleic acids

2 2
OH H
Ribose Deoxyribose

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 17

 Nucleotides are linked together by phosphodiester
bonds to form nucleic acids
phosphate sugar-phosphate
backbone

base

5’ sugar

3’ dehydration
reaction
3’
5’

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 18

 DNA consists of two strands (double stranded)
5’ end

3’ end Sugar-phosphate
"backbone"
Hydrogen bonds between
nitrogenous bases

Phosphodiester 3’ end
bond

5’ end 3’ end
5’ end

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chromosomes
Genes are found along DNA
Coding regions
Gene 2

Gene 1

Non-coding regions

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 20

 DNA encodes information
Coding strand / sense
5’-ATGAAGTGGGTAACCTTTATTTCCCTTCT-3’
3’-TACTTCACCCATTGGAAATAAAGGGAAGA-5’
Non-coding strand / template / antisense

5’-ATG AAG TGG GTA ACC TTT ATT TCC CTT-3’

We can decode the information in the coding strand into a protein sequence (see later)
Homo sapien albumin (ALB) - ACCESSION NG_009291

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 Genes are expressed

A process in which information in

DNA is converted into a functional
gene product (protein)

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 RNA is single stranded, but bases can also bond
3’ end

5’ end Folded RNA molecule

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 23

 Types of ribonucleic acid (RNA)

messenger ribonucleic acid (mRNA)

ribosomal ribonucleic acid (rRNA)

transfer ribonucleic acid (tRNA)

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 24

 Messenger RNA transmits the encoded information
Coding strand / sense
5’-ATGAAGTGGGTAACCTTTATTTCCCTTCT-3’
3’-TACTTCACCCATTGGAAATAAAGGGAAGA-5’
Non-coding strand / template / antisense

5’-ATG AAG TGG GTA ACC TTT ATT TCC CTT-3’

mRNA is produced from DNA via a process call transcription
5’-AUG AAG UGG GUA ACC UUU AUU UCC CUU-3’
Homo sapien albumin (ALB) - ACCESSION NG_009291

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 25

 End of Lecture 2, Part 2

See Activity – PCR malfunction

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 26

 Lecture 2 - Molecules of Life I – Part 3
What you should know
• Macromolecules are mainly comprised of C, H, O and N – Part 1

• The unique properties of water, and why biological molecules have a

relationship with water – Part 1

• How do nucleic acids assemble from only 4 nucleotides, and how is

DNA and RNA different – Part 2

• How do proteins assemble from only 20 amino acids, and how does
the amino acid sequence determine protein function – Part 3

• How are DNA, RNA and proteins connected – Part 3

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 27
 The Major Biomolecules (macromolecules)

1.Nucleic Acids
Lecture 2
2.Proteins
3.Carbohydrates
Lecture 3
4.Lipids

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 28

 Proteins

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 29

 Proteins are the most functionally diverse of all
biological molecules RUBISCO
structural insulin Muscles e.g. myosin CO2 glucose

hair contractile
keratin
hormones enzymes
gluten

antibodies

defence Proteoglycans
e.g. cartilage

mucilage transport storage

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 30

 Amino acids – the building blocks of proteins

All amino acids have a

basic amino group and
an acidic carboxyl group
(hence the name amino
acid) and a variety of
different side-chain
groups (R).

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 Peptide bond formation

N-terminus C-terminus

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 Polypeptides can be hundreds or thousands of
amino acids long

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 The 20 amino acids (R-group is shaded)

R-groups non-polar (are hydrophobic)

R-groups polar, uncharged (are hydrophilic)

R-groups charged (are hydrophilic)

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 34

 Decoding mRNA into protein (translation)
We can decode the information from the coding strand into a protein

5’-AUG AAG UGG GUA ACC UUU AUU UCC CUU-3’

codon

N- Met Lys Trp Val Thr Phe Iso Ser Leu -C

M K W V T F I S L
Homo sapien albumin (ALB) - ACCESSION NG_009291

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 35

 A protein can be described at four levels
(a) PRIMARY STRUCTURE - the amino acid sequence
(b) SECONDARY STRUCTURE - the conformation changes in primary structures due to the formation of electrostatic
and hydrogen bonds between nearby amino acids
(c) TERTIARY STRUCTURE - the ultimate configuration that a polypeptide chain takes in reaching the configuration of
minimal free energy.
(d) QUATERNARY STRUCTURE - association of the polypeptide chains in proteins which have more than one
polypeptide.

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 36

 Sidechains drive proteins folding

“the hydrophobic effect”

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 37

 Proteins are the cellular workhorses
uridine
dihydroorotate
monophosphate uridylate kinase
dehydrogenase and nucleoside
synthase
diphosphate kinase
UTP
+ PRPP (for RNA)

PRPP = phosphoribosyl pyrophosphate

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 38

 Can we see proteins?

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 DNA, RNA and proteins are connected

The “central dogma” of molecular biology

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 End of Lecture 2, Part 3

See Activity – Giant proteins

See Quiz – 5 Questions

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 41

 Summary
• C, H, O and N are fundamental elements of biomolecules

• Carbon can form four bonds making it a pivotal part of biomolecules

• DNA is comprised of 4 nucleotides (A, C, G and T) and is a double

stranded biomolecule of two complementary strands

• RNA is comprised of 4 nucleotides (A, C, G and U) and is single

stranded and mRNA is the intermediate between DNA and protein

• Proteins are comprised of 20 amino acids and are encoded by genes

found in DNA

• Proteins have a variety of roles in biology including enabling a range

of biochemical reactions that maintain life
BIOL10002 - Biomolecules and Cells Module 1: What is Life? 42
 Upcoming Lectures
The building blocks of Life….continued

Lecture 3
• Carbohydrates (sugar)
• Lipids (oils and fats)
• Membrane transport (moving through bilayers)

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 43