BIOL1XX7 - Lectures - Textbook Refs With Intact Links

Summary of LOs/Text
refs/Glossary
• Includes live links to references
From
Molecules to
Ecosystems
Biol1xx7 - 2021
Lecture 2A -The Chemistry of Life:
Life
Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

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A note about my textbook references
There isn’t a recommended textbook for this course, any good Biochemistry text book will
cover most of the topics in this Module; Lehninger – “Principles of Biochemistry” or Stryer
(Actually Berg Tymoczko & Stryer – “Biochemistry” are both good basic texts that will be
helpful to have on hand if you are thinking of studying Biochemistry in the next few years. I
still often refer to Lehninger when I want to check details or refresh topics.
Use the lecture slides as a guide to what you should focus on and what depth to go into.
I’ll include references links – for two on-line text books -
https://openstax.org/books/biology-2e (start here – it will usually have the appropriate
level of information for this course) and https://www.ncbi.nlm.nih.gov/books/NBK21154/
(this is an older edition of Stryer but the fundamental concepts are still valid; it often goes
into more depth than you need for this course, but the explanations are a bit different
so it may suit some of you better, or you might want a bit deeper understanding). Note that
sometimes there is just a small part of the link that is useful to the particular mini-lecture.
You can find a lot of information on Wikipedia or other internet sites. Wikipedia seems
pretty accurate for this type of thing, but be aware that both it and random internet
searches go straight to complex details/exceptions and controversies that can be
misleading when you are still learning, whereas a good textbook sticks to the
fundamentals and well established facts or theories.
Learning Outcomes 2A
1. Appreciate the common origins and makeup of
the molecules of life.
2. Explore the properties of living organisms.
3. Appreciate that life is made up of a small
number of elements of which carbon is
particularly important
4. Define the terms polar/hydrophilic and non-
polar/hydrophobic
Textbook
Biology 2e Stryer
1.2-Themes-and-concepts-o Not very useful for this
f-biology minilecture as the
– Properties of Life information is widely
– Levels of Organization of distributed in different
Living Things
sections
– The Diversity of Life
2.3 Carbon (introduction)
Glossary
• Charged – fully charged positive or negative (has gained or lost an
electron)
• Covalent bond – holds molecules together
• Dipole –has a partially positive and partially negative end
• Eukaryote – organism has cells with a defined nucleus (can be
single celled or multicellular)
• Homeostasis – Maintenance of a relatively constant internal
environment
• Hydrophilic – water liking/soluble in water
• Hydrophobic/non-polar – water hating/insoluble in water
• Polar – partly or fully charged/with a dipole
• Prokaryote – single celled organism without a nucleus
From
Molecules to
Ecosystems
Biol1xx7 - 2021
Lecture 2B - The Chemistry of Life:
Molecules

WARNING
the Act.
Text references
Stryer – if you want more

Biology 2e - Start here details/a different perspective
2.2 Water 1.3.2 The properties of wate
3.2 Carbohydrates r…
3.3 Lipids 11.1 Monosaccharides
3.4 Amino acids (in the 11.2 .1-3 Complex carbohyd
rates
middle of the proteins entry)
12. Introduction
3.5 Nucleic Acids
12.2 Fatty acids
3.1 Amino acids
1.1.1 Bases
Start here 5.1 Nucleic Acids
Learning Outcomes 2B
1. Describe the building blocks of life: water,
carbohydrates (sugars), lipids, amino acids and
nucleic acids.
2. Describe some chemical properties of amino
acids (solubility hydrophobic/hydrophilic,
polarity, charge), given their chemical
structures.
Glossary
• Base pairing – complementary hydrogen bonding potentials means
C/G, A/T, A/U form pairs
• Capillary action – ability of liquid to flow in narrow spaces, even
against gravity
• Hydrogen bond – attraction between partially electronegative and
electropositive atoms in the form O-H…O, N-H…N, N-H…O, O-H…N.
• Nucleotide – base + sugar + phosphate
• Nucleobase – base (A, T, U, C, G)
• Purine – double ring, flat aromatic base (A, G)
• Pyrimidine – single ring flat aromatic base (C, T, U)
From
Molecules to
Ecosystems
Biol1XX7 - 2021
Lecture 3A – Biopolymers: The basic structure of DNA and

RNA and proteins
COMMONWEALTH OF AUSTRALIA
WARNING
Prof Jacqui Matthews

the Act.
Text References
Biology-2e detail
3.1 Synthesis of Biological 3.2 Protein Primary Structur
Molecules e
3.4 Proteins 5.1 Nucleic Acids
3.5 Nucleic acids
Start here
1. Identify the conventions of direction/ends of protein and
nucleic acids.
2. Describe the repeating units (backbones and sidechains
or bases) in proteins and nucleic acids
3. Identify the main chemical components of nucleic acids
and proteins/peptides.
4. Describe how the physical and chemical properties of
proteins and nucleic acids can be exploited in
experimental situations.
Glossary
• Aromatic rings – have alternating single and double bonds; flat and
have absorbance in the UV
• Biopolymer - a polymeric substance occurring in living organisms
• N-glycosidic bond – covalent bond between sugar and base in
RNA/DNA
• Peptide Bond – covalent bond between amino acids in peptides
and proteins which is planar and rigid.
• Phosphodiester bond – covalent bond between nucleotides in
RNA/DNA
• Residue – generic name for a subunit in a polymer (more often
used for proteins – also as “amino acid residue”)
From
Molecules to
Ecosystems
Biol1XX7 – 2021
Lecture 3B – Biopolymers:
DNA vs RNA
WARNING
Prof Jacqui Matthews

the Act.
Textbook References
Biology 2e information
14.1 Historical basis of mod 5.1.1 RNA and DNA differ…
ern understanding 5.2.1/2/3/5 The Double Helix
14.2 DNA structure (and …
sequencing)
3.5 Nucleic acids - DNA
Double-Helix Structure
Start Here
1. Appreciate that DNA is the source of genetic information
2. Describe the base pairing between nucleobases and
appreciate that C/G base pairing is stronger than A/T(U)
base pairing in nucleic acids
3. Describe the double-helical structure of DNA
4. Distinguish DNA from RNA, in terms of structure and
stability
Glossary
• B-DNA – standard double helix • Base-pairing –hydrogen bonding
structure of DNA between bases
• Electrophoresis – separation of • Major Groove – wide groove in B-
molecules by electric current in DNA
permeable matrix • Minor Groove – narrow groove in B-
• Electrostatic repulsion - repulsing DNA
between charged atoms of the same • ssDNA – single stranded DNA
charge • Tm/Melting point – when 50% of the
• Deamination – loss of amine molecule is unfolded/separated
• dsDNA – double stranded DNA
18
From
Molecules to
Ecosystems
Biol1xx7 -2021
Lecture 4A – The Central Dogma of Molecular Biology
WARNING
Prof Jacqui Matthews • This material has been reproduced and communicated to you by or
the Act.
Text book References
Stryer –if you want more
Biology 2e details
15.1 The genetic code 1.1.2/3/4 DNA/RNA/Protein
flow of information
5.4.1 Several kinds of RNA
Start Here
1. Outline the central dogma of molecular biology and
describe the information flow between DNA, RNA and
Proteins
2. Define the genome, transcriptome and proteome and
how they differ from cell to cell.
3. Appreciate the difference in size and construction
between bacterial and eukaryotic genomes
Glossary
• Central Dogma of Molecular Biology - flow of genetic information
within a biological system (DNA>RNA>Protein)
• Chromosome – DNA molecule with part or all of the genome,
usually combined with proteins
• Epigenetics – DNA modifications that do not change the DNA
sequence can affect gene activity
• Genome – the complete genetic composition of a cell or species
• Proteome - the complete set of proteins expressed by an organism,
cell or tissue type.
• Transcriptome – the set of all RNA molecules in one cell or a
population of cells.
From
Molecules to
Ecosystems
Biol1xx7 -2021
Lecture 4B – The Central Dogma of Molecular Biology:

The Genetic Code
WARNING
the Act.
Textbook References
Stryer – for more details
15.1 The genetic code 5.5 Genetic code
14.2 DNA Packaging in cel
ls
Start Here
1. Define the universal genetic code (triplet/non-
overlapping/common)
2. Understand the concept of reading frames for
translating a nucleic acid sequence into a protein
sequence
3. Understand how to read a genetic code table and
translate nucleic acid sequence into protein sequence
using such a table.
Glossary
• (Triplet) Codon – Set of three bases that encodes an amino acid or stop
codon
• Genetic Code – how cells translate nucleotide sequence into protein
sequence Redundant/degenerate – in terms of the genetic code
• Reading frame – How you break up a DNA or mRNA sequence into
successive codons – there are three reading frames (assuming we are
looking at the coding strand). This affects the sequence of the protein that is
produced.
• Open reading frame – from the start codon to the stop codon/the part of
the gene that encodes the protein
• Point mutation – a base is changed to a different base
• Deletion mutation – one or more bases have been lost
• Silent mutation – the DNA or RNA mutation has no affect on the protein
sequence (because of redundancy in the genetic code)
• Frame shift mutation – a deletion mutation that changes the reading frame
of the gene – any protein sequence after the deletion will be nonsense.
From
Molecules to
Ecosystems
Biol1XX7 – 2021
Lecture 5A - Copying DNA:

DNA Replication

WARNING
the Act.
Knox References
Biology-2e Stryer
Chapter 10 5.3.1 DNA polymerases
14.3 Basics of DNA Replicat 27 DNA replication overview
ion 27.2.5 The separation of DN
14.4 DNA replication in prok A strands
aryotes 27.4.1/2/3/5 Mechanisms
https://www.youtube.com/w
atch?v=0Ha9nppnwOc
Start Here
1. Outline the general mechanism for copying DNA to DNA
before cell division -replication.
2. List the unique problems associated with replication and
describe the strategies used by the cell to overcome
these, including unwinding DNA, and leading versus
lagging strand replication.
3. Describe the general functions of proteins that are
required for DNA-replication
29
Glossary
• Ligase – enzyme, joins pieces of • Semi-conservative DNA replication –
DNA DNA contains one older and one newly
• Helicase – enzyme, unwinds DNA replicated strand
• Topoisomerase/gyrase – enzyme, • Supercoiling – overwinding DNA
that relieves supercoiling • Replication fork – structure where
• Primase – RNA polymerase that DNA is being replicated on the lagging
makes primers for replication and leading strands
• ssBP/single stranded binding proteins
– bind to ssDNA and protect from
tangling/reforming dsDNA
• Initiation – polymerisation starts
• Chain elongation – main phase of
polymerisation
• Termination – polymerisation stops
• Okazaki fragments – DNA fragments
being generated on the lagging strand
30
From
Molecules to
Ecosystems
Biol1XX7 – 2021
Lecture 5B - Copying DNA:

RNA Transcription

WARNING
the Act.
Textbook References
Biology-2e Stryer
15.2 Prokaryotic transcriptio 5.4.2-4 Gene Expression
n 28.0.1 Overview of RNA syn
16.1 Regulation of gene exp thesis
ression 28.1 Prokaryotic transcriptio
16.2 Prokaryotic gene regul n
ation (introduction). (Intro-28.1.7)
Start Here
1. Outline the general mechanism for copying DNA to RNA
- transcription.
2. List the unique problems associated with transcription
(including unravelling DNA, and making multiple copies
of small sections of the genome at different frequencies)
and describe the strategies used by the cell to
overcome these.
3. Describe the general functions of proteins that are
required for RNA transcription
4. Compare and contrast the differences between making
DNA and RNA
33
Glossary
• Promoter – DNA sequence near start site of transcription, bound by sigma
factor which recruits RNA polymerase II complex
• RNA polymerase II complex – collection of proteins that make an RNA
copy of DNA
• Sigma Factor – common bacterial transcription factor
• Transcription factor – protein that binds DNA and regulates transcription
• Transcription bubble – local unwinding of DNA for transcription
• Transcriptional activator – molecule that increases transcription
• Transcriptional repressor - molecule that decreases transcription
• Transcription start site – DNA sequence where transcription begins
34
From
Molecules to
Ecosystems
Biol1xx7 – 2021
Lecture 6A – Making Proteins:

Protein Synthesis (Translation)

WARNING
the Act.
Text References
Biology-2e Stryer
15.5 Ribosomes and Prot 5.4.5 Protein Synthesis
ein Synthesis 29.1 Introduction/29.1.3
29.2.1-4 aatRNA
synthetases
29.3 Ribosomes
29.4.4 Termination
Start Here
1. Explain the unique problems associated with converting
the information as a nucleic acid sequence to an amino
acid sequence.
2. Outline the unique problems associated with protein
synthesis, with particular reference to the unfavourable
thermodynamics of peptide bond formation and the
requirement for order. Describe the strategies used by
cells to overcome these problems.
3. Describe the general functions of proteins and RNA
molecules that are required for Protein synthesis
37
Glossary
aa – abbreviation for amino acid Peptidyl transferase – enzyme
aa-tRNA synthetase – enzyme that component of the ribosome that
binds tRNA and charges it with the transfers the activated amino acids from
correct, activated amino acid tRNA to the growing peptide chain
Anticodon – sequence in tRNA that Ribosome – RNA-protein complex that
recognises the codon in mRNA catalyses peptide bond formation and
Codon – sequence of 3 bases that guides correct sequence assembly in
specifies a given amino acid protein translation
Genetic Code – set of codons and Start Codon – Codon that signals the
corresponding amino acids start of protein synthesis – encodes Met
mRNA/tRNA/rRNA – messenger Stop Codon – Codon that signal the
(encodes proteins), transfer (links end of translation; no tRNAs recognise
mRNA to correct amino acid) and these codons
ribosomal (forms the ribosome) RNA Release/terminal factor – protein that
binds the stop codon to terminate
translation
38
From
Molecules to
Ecosystems
Biol1xx7 – 2021
Lecture 6B – Making Proteins:

Protein Structure

WARNING
the Act.
Text Book References
Biology-2e Stryer
3.4 Protein Structure; 3.3 Protein Secondary Struc
Denaturation and Protein ture
Folding 3.4 Tertiary Structure
3.5 Quaternary Structure
15.5 3.6 Protein Folding
Protein folding, modification
and targeting
Start Here
1. Describe the differences between primary, secondary,
tertiary and quarternary structure of proteins.
2. Appreciate that the protein sequence defines the protein
fold and function, and that protein molecules are held
together by the combination of many bonds.
3. Demonstrate how 3D protein structure is related to
function using the example of the alpha helix in DNA
binding proteins.
41
Glossary
• Alpha Helix– form of protein • Sidechain – functions groups which
secondary structure that forms a right distinguish amino acids from each
handed helix other
• Beta Strand –extended form of protein • Polypeptide – protein or peptide
secondary structure Beta Sheet – • Primary structure – protein sequence
Assembly of beta strands • Protein Folding – process of forming
• Beta turn – form of protein secondary tertiary structure
structure, often formed between beta • Quaternary structure – arrangement
strands in a beta sheet of folded protein subunits
• Secondary structure – local • Tertiary structure – overall fold of a
interactions in the polypeptide chain protein (or protein subunit)
with defined hydrogen bonding
patterns and backbone bond angles
42
From
Molecules to
Ecosystems
Biol1XX7 -2021
Lecture 7A - Enzymes and Thermodynamics:

Equilibrium and Thermodynamics vs Kinetics
WARNING
the Act.
1. Understand the difference between potential and kinetic
energy
2. Explain the concept of equilibrium and how it relates to
energy
3. Explain the difference between the thermodynamic and
kinetic properties of a reaction.
44
Textbook references
Biology-2e Stryer
6.2 Potential, Kinetic, Free, 8.1 Enzymes
and Activation Energy
6.3 The Laws of thermodyna
mics
6.5 Enzymes
Start Here
Glossary
• Activation energy/barrier – The • Kinetic energy – energy
energy required to initiate a association with movement
reaction • Potential energy – see chemical
• Chemical energy – energy stored energy
in bonds • Product – result of a reaction
• Energy – capacity to do work • Thermodynamics – measures
• Entropy – measure of disorder and transitions of intrinsic energy
• Equilibrium – rates of forward • Transition state – high energy
and reverse reactions are the state that has to be bypassed to
same; concentrations of form products
substrates and products don’t • Substrate – starting compound of
change; overall energies are a reaction
balanced.
• Kinetics – how quickly an event
happens; rates
46
From
Molecules to
Ecosystems
Biol1XX7 – 2021
Lecture 7B - Enzymes and Thermodynamics:

Enzymes

WARNING
the Act.
Knox References
Biology-2e Stryer
6.5 Enzymes 8.1 Enzymes
6.4 8.2.1/3 Enzymes:
ATP: Adenosine Triphosphat energy,rates vs equilibrium
e 2.3.1 ATP
Start Here
1. Explain how enzymes act as catalysts, including what
effect they have on reaction rates and final
concentrations of substrates and products of a reaction.
2. Appreciate how enzymes can be used experimentally
(in combination with the labs).
3. Understand that enzymes combine to form enzymatic
pathways that are important for living organisms.
4. Describe how a secondary reaction can drive
equilibrium and provide energy for an unfavourable
interaction.
49
Glossary
• Activation energy – The energy • Pyrophosphate (PPi) – released
required to initiate a reaction by hydrolysis of NTPs into NMPs;
• Catalyst – speeds up reaction spontaneously forms phosphates
rates (not used up/doesn’t affect (2Pi); provides energy for
equilibrium) unfavourable reactions
• Enzyme – biological (usually • Reaction rates – speed of a
protein) catalyst reaction
• Substrate – molecule on which an
enzyme reacts
50

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Summary of LOs/Text

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

Stryer – if you want more

Lecture 3A – Biopolymers: The basic structure of DNA and

Prof Jacqui Matthews

Prof Jacqui Matthews

Lecture 4A – The Central Dogma of Molecular Biology

Lecture 4B – The Central Dogma of Molecular Biology:

Lecture 5A - Copying DNA:

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

Lecture 5B - Copying DNA:

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

Lecture 6A – Making Proteins:

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

Lecture 6B – Making Proteins:

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

Lecture 7A - Enzymes and Thermodynamics:

Lecture 7B - Enzymes and Thermodynamics:

Prof Jacqui Matthews COMMONWEALTH OF AUSTRALIA

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