Perspectives in Biochemistry

Course Overview
BIOC1600 (Perspectives in Biochemistry)

9:30am-10:20am Thursdays + 9:30am-11:20am Mondays

Grand Hall (CPD-LG.01), Centennial Campus

Prof. Julian A. Tanner [email protected]

Dr. Brian Wong [email protected]
Dr. Joanna Ho [email protected]
Dr. Bonny Yuen [email protected]
Welcome!

HKU Education Aims:

The undergraduate curriculum enables students to develop capabilities in:

1.Pursuit of academic/professional excellence, critical intellectual enquiry and

life-long learning
2. Tackling novel situations and ill-defined problems
3.Critical self-reflection, greater understanding of others, and upholding personal
and professional ethics
4.Intercultural understanding and global citizenship
5.Communication and collaboration
6.Leadership and advocacy for the improvement of the human condition

BIOC1600 is a small step towards these greater aims of your next 4 years.

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 BIOC1600 Course Objective 1

Teach a biochemical perspective

on the Basic Sciences

Biology Physics Chemistry

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 BIOC1600 Course Objective 2

Promote deep learning by integrated

practical and collaborative tasks

Two collaborative
laboratory practicals Collaborate on group project and
are incorporated into in Monday learning sessions
the course

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 BIOC1600 Course Objective 3
Inspire with a view of the great discoveries
and future challenges for biochemistry

AlphaFold neural network – new approach to solve AI algorithm to solve RNA structures through
protein structures computationally from Google’s machine learning
DeepMind (27 August, 2021)
(26 August, 2021)

You will begin to interact with the primary literature where real science occurs and
is changing every day. Reading assignments to highlight classic primary articles,
group project to interact with contemporary literature.
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 BIOC1600 Course Objective 4

Help you transit from School to University Level

Study

• Developing independent self-directed study skills

• Teamwork
• Confidence to communicate

(Moodle also has the formal course objectives / learning outcomes)

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Who will teach the course?
Professor Julian Tanner is Associate
Director of the School of Biomedical
Sciences at HKU.

I am director of the BBiomedSc

programme, help oversee years 1-2 of
MBBS as Assistant Dean, and co-authored Faculty of Medicine
“Essentials of Chemical Biology”, pitched (photoshopped??)
for final year/postgraduate study.

My research topics are chemical biology,

DNA nanotechnology and directed
evolution.

A DNA aptamer we
discovered that may
have applications for
malaria diagnosis
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 • Dr. Brian Wong is a Principal
Lecturer in the School of
Biomedical Sciences

I have been teaching at HKU for over 10 years. I am

also one of the course selection advisor for the
Biochemistry major.

My main area of teaching is molecular biology.

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 Dr. Bonny Yuen
• Lecturer in the School of
Biomedical Sciences.
• Involved in the following
courses:
• BIOC1600
• BIOC3601
• CCST9009

Research interest: Toxicology

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 Dr. Joanna Ho
Lecturer,
School of Biomedical Sciences

Dr. Ho will mainly be involved in

the practical teaching.

I taught for 2 years in the biochemical technique courses in HKUST and

have been teaching the medical biochemistry labs in HKU for 8 years.

My education background is in applied biochemistry and biomedical

sciences.

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Moodle will be our page for posting all course powerpoints,
lectures, course information.

Accessible via HKU Portal then click through My Learning

tab.

Click through to BIOC1600 Perspectives in Biochemistry

[2022]

Use of Moodle is compulsory.

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From Atoms to Amino Acids

Prof. Julian A. Tanner

School of Biomedical Sciences
[email protected]

BIOC1600 Lecture 1

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 Week 1 Learning Outcomes
On completing week 1 study, students should be able:

• To categorise elements from periodic table important for

biochemistry

• To illustrate the electronic structure of the atom including

understanding s orbitals, p orbitals and hybrid orbitals particularly
with relevance to bonding around carbon

• To summarize the bonding around atoms important to biochemistry

with understanding of difference between sigma and pi bonds and
effects on bond rotation

• To assign molecular geometries and bond angles for common

bonds in biochemistry

• To build an amino acid using a model and understand its

stereochemistry based on underlying chemical principles
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 An introduction to the wonders of
biochemistry and the cell
https://www.xvivo.net/animation/influenza-a/ Influenza A lifecycle

https://www.youtube.com/watch?v=-q82IrNWbKc&t=106s Cellscape

https://www.youtube.com/watch?t=12&v=uHeTQLNFTgU Inner Life of a Cell | Protein Packing

Powering the cell:
http://www.youtube.com/watch?v=RrS2uROUjK4
mitochondria
https://www.youtube.com/watch?v=FzcTgrxMzZk The Inner Life of the Cell
Wonders of integrated
biochemistry and cell biology –
this video depicts how
illustrating mechanisms that
allow a white blood cell to sense
its surroundings and respond to
an external stimulus.

“If I have seen further it is by standing on the shoulders of Giants.”

Isaac Newton to Robert Hooke in 1676
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 Biochemistry is underpinned and was born
from chemistry

The first ‘biochemical’ experiment?

The first time an organic

compound was produced from
inorganic reactants.

After Friedrich Wohler synthesized urea in 1828 he wrote to Berzelius:

"I cannot, so to say, hold my chemical water and must tell you that I can make
urea without thereby needing to have kidneys, or anyhow, an animal, be it
human or dog“
"The great tragedy of science, the slaying of a beautiful hypothesis by an ugly
fact.“
- the synthesis of urea was the birth of biochemistry.
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 Further major steps towards biochemistry as
a discipline
•Emil Fischer (1852-1919) demonstrated biological
catalysts (enzymes) and proved structures of sugar –
Nobel Prize 1902 (we will learn Fischer projection in
BIOC1600!)

•Eduard Buchner (1860-1917) showed fermentation

could be carried out using yeast extracts – Nobel Prize
1907

The first protein structures

solved were haemoglobin and
myoglobin by Max Perutz and
John Kendrew in 1958 (1962
Nobel prize)

Understanding of function is
underpinned by understanding of Haemoglobin Myoglobin
structure
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 The most recent stage of the death of
‘vitalism’ occurred a few years ago with first
self-replicating synthetic cell

Synthetic Mycoplasma
mycoides bacteria.

Source: J. Craig Venter Institute

https://www.ted.com/talks/craig_venter_unveils_synthetic_life

Craig Venter

http://www.sciencemag.org/content/329/5987/52.abstract

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 The hierarchical organisation of life
Focus of BIOC1600

Subatomic particles Eg. Protons, neutrons, electrons

Atoms / Elements Eg. Carbon, oxygen, sulfur

Molecules Eg. Water, DNA, proteins, sugars, lipids

Subcellular organelles Eg. the nucleus, the Golgi apparatus

Cells Eg. A neuron, a red blood cell

Tissues Eg. the epithelium, muscle tissue

Organs Eg. The liver, the kidney

The human body You or me.

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 So which elements are
important in biochemistry?

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Use chat
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The outermost electrons determine how atoms interact

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 Recap of some basic bonding of atoms important for biochemistry

Oxygen forms 2 bonds, Single bonds rotate.

nitrogen forms 3 bonds and Double bonds are planar and
carbon forms 4 bonds, cannot rotate.
phosphorus forms 5 bonds,
sulphur forms 2 bonds. But why?
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 For biochemistry at university
level we need to understand
bonding around carbon

We need to stop thinking like this! And start thinking like this

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 Which best describes your acquaintance with
orbitals?

A: Never heard of “orbital”, aren’t electrons like planets in

orbit around sun?
B: Heard the word, don’t know what it means
C: Yeah, something to do with fuzziness and uncertainty.
D: Yeah I know why there are 8 electrons in second shell, 1
s orbital and 3 p orbitals each with 2 electrons.
E: Sure, I can solve Schrodinger’s equations to prove that
weird dumbbell on the p orbital.

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 Some terrible schematic representations of
carbon and hydrogen

Reminder!:
•Protons are positively charged
and in the nucleus of the atom
•Neutrons are uncharged in the
nucleus of the atom
•Electrons are negatively
charged and in orbitals around
the nucleus

But these are poor representations! From quantum mechanics we cannot consider
electrons in “orbit” (Heisenberg uncertainty principle – the location and momentum
of an atomic particle cannot be simultaneously determined).

Instead we use the term orbital – a probability distribution of finding the electron.

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 Why 8 electrons in the second and
third shells?

First shell: 2 electrons in 1s orbital

Second shell: 2 electrons in 2s

orbital, 2 electrons in px, 2 electrons
in py, 2 electrons in pz = 8.

https://www.youtube.com/watch?v=VfBcfYR1VQo

Don’t worry you probably don’t know this! – we have an excellent task from
Royal Society of Chemistry to help your learning with this in your own time this
week – check Moodle!

Another learning resource Khan academy: goo.gl/vj0eM8

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When atoms bond covalently to each other their orbitals hybridize

CH4 (methane). Four sp3 orbitals

around C overlap with 4 single s
orbitals on each H. Each bond is
a single bond (sigma (σ) bond)
PS if you don’t know all the
Greek letters learn them as a
good first week assignment to
science at university!

Review in your own time on Moodle !

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Double bond is a sigma bond
and a pi bond

Outstanding science
learning resource!

goo.gl/gwtT8Q

Because of the pi bond the double bond cannot rotate –

critical as we start to think about protein structure and nucleic

acid structure.
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A typical biochemical molecule and its
functional groups

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 Week 1 Learning Outcomes
On completing week 1 study, students should be able:

• To categorise elements from periodic table important for

biochemistry

• To illustrate the electronic structure of the atom including

understanding s orbitals, p orbitals and hybrid orbitals particularly
with relevance to bonding around carbon

• To summarize the bonding around atoms important to biochemistry

with understanding of difference between sigma and pi bonds and
effects on bond rotation

• To assign molecular geometries and bond angles for common

bonds in biochemistry

• To build an amino acid using a model and understand its

stereochemistry based on underlying chemical principles
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Perspectives in Biochemistry
- Assessment

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 How will I be assessed?
Continuous Assessment [50%]
- Lab practical [20%]
- Group project [30%]

Examination [50%]
inspire transit

collaborate

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Continuous Assessment [20%]
• TWO laboratory group assessments (10%
each)

• Laboratory practical will be held in person in

Sassoon Road Campus in MDL1/LG19 on:
- 3 Oct (Mon) 9:00 am - noon
- 24 Oct (Mon) 9:00 am - noon
- 7 Nov (Mon) 9:30 – 11:20 am

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 Examination [50%]
The examination will be a Multiple
Choice Question examination held
during the examination period in
December.

We will provide practice questions

and guidance later in semester
regarding style and content.

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 Group Project [30%]
Aims to develop:
➢science communication
➢creativity
➢collaboration

Full details will be provided by Dr. Bonny Yuen.

Presentations will be at end of course at end of November
before examination period.

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 BIOC1600: Key Commitments

Consider each 6 credit course at HKU is at least 100 hours: we expect at

least 5 hours of independent study per week for this course outside of
the Monday afternoon learning session (reading / group project work /
Moodle etc.).

How to spend your 5 hours over the next week?

1.Powerpoints from Prof. JA Tanner and Dr. Brian Wong.
2.Other linked videos embedded in this powerpoint.
3.Refresh your knowledge of atomic theory, and update with orbital
concepts (see Khan Academy videos)
4.Structure of amino acids viewer (Dr Brian Wong will introduce).
5.Proteins Fundamental Chemical Properties PDF document (p. 1-6 for
this week, p. 7- 10 next week).

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 Should I get a textbook?
To help you develop your self-study skills for the school to
university transition, we will not be teaching from a single textbook.
For guidance on what you are expected to understand each week
please refer to weekly learning outcomes.
But go to the library ASAP – find resources to help your own
personal style of learning!

If you would like to buy a single

textbook to help with Biochemistry
learning both for this course and in
future we recommend Lehninger
Principles of Biochemistry 8th Edition
or Biochemistry Berg 9th Edition (but
please hold in mind much of both
these books is beyond scope of this
course).

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Queries about anything relating to BIOC1600 or the study of
biochemistry very welcome to

[email protected]

We hope you will have a great course and a great experience

over your next four years at the University of Hong Kong!

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