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Biochemistry

CHBC10
1.
2.
3.
4.
5.
6.
7.

Lectures
Exercise lectures
Demonstration visualization
Computer-exercise Bioinformatics
Computer-exercise Visualization
Tests/exams 2x (make up 10% of final grade)
Exam (80% of final grade):

(obligatory)
(obligatory)
(obligatory)

Covers only what has been discussed during lectures/slides (Nestor)


Lectures will cover all advised to attend lectures!
Exercise lectures : assignments, mimick exam questions, test and apply
obtained knowledge
book: essential

Marco Fraaije

Biochemistry

CHBBBIOCH - Biochemie - RU
Groningen

Biochemistry

J.M. Berg, J.L. Tymoczko, L. Stryer: Biochemistry (7th Edition, 2010, W.H. Freeman)
2687 gram!!! Compact textbook, full of information!!! >1100 paginas!!!
Very complete book, ~50% will be covered in this course, other courses also depend
on this book
Use the website http://bcs.whfreeman.com/berg7e for illustrative movies.
Wikipedia and other websites or books also offer excellent material, be creative!

Biochemistry - Topics
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Chapter 14
Chapter 15
Chapter 28
Chapter 29
Chapter 30
Chapter 31
Chapter 32

Introduction
Proteins
Exploring proteins and proteomes
Genetic information, transcription, translation
Exploring genes and genomes
Exploring evolution and bioinformatics
Hemoglobin, allostery
Enzymes: basic concepts and kinetics
Catalytic strategies
Regulatory strategies (general aspects)
Carbohydrates
Lipids and cell membranes
Membrane channels and pumps
Signal-transduction pathways (general aspects)
Metabolism: basic concepts and design
DNA replication, repair and recombination
RNA synthesis and processing
Protein synthesis
Control of gene expression prokaryotes
Control of gene expression eukaryotes

Items that are not part of the lectures: see sheets on Nestor!!!

CHBBBIOCH - Biochemie - RU
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Content of BIOCHEMISTRY
Central dogma

Functions

 Proteins

 Proteins
ligand-binding, transport
allosteric effects
 Enzymes

structure
research techniques

 DNA RNA protein


DNA structure, transfer of
information
replication DNA DNA
transcription DNA mRNA
translation mRNA eiwit
regulation
research techniques

function, kinetics
katalytic mechanisms

 Membranes
lipids, bilayers
Membrane proteins

 Carbohydrates
 Metabolism
 Signaaltransduction

Schedule
Schedule BIOCHEMISTRY (CHBC-10), 2013-2014
lectures
Exercise lectures
Computer exercises
Datum

Marco Fraaije / Dick Janssen


Marco Fraaije / Willem Dijkman / Misun Lee / Alrik de Voogd
Dirk-Jan Slotboom / Marco Fraaije

Tijd

Zaal

Activiteit

Leerstof

Di 4-2

9:00-10:45

11.0080

lecture 1

H0 Intro, H1 Biochemistry

Di 4-2

13:00-15:00

16.0116

Groep
MF
A

Wo 5-2

9:00-10:45

11.0022

lecture 2

Wo 5-2

13:00-15:00

16.0116

werkcollege

Vrij 7-2

9:00-10:45

61.0267

lecture 3

H3 Protein analysis

H2 Proteins

Di 11-2

9:00-10:45

H4 DNA-RNA-protein (H28-31)

Demonstration!!!

11.0080

lecture 4

Di 11-2

13:00-15:00

16.0116

exercise 1

Wo 12-2

9:00-10:45

11.0022

lecture 5

Wo 12-2

13:00-15:00

16.0116

exercise 1

Vrij 14-2

9:00-10:45

61.0267

lecture 6

Vrij 14-2

14:00-16:00

Hal 03

exam 1

H1-H5

Di 18-2

9:00-10:45

11.0080

lecture 7

H7 Hemoglobin, H8 Enzyme kinetics

Di 18-2

13:00-15:00

16.0116

exercise 2

Wo 19-2

9:00-10:45

11.0022

lecture 8

Wo 19-2

13:00-15:00

16.0116

exercise 2

Do 20-2

9:00-11:00

18.-152

exercise

H1-H4

MF
all MF/AV/ML
MF
MF
A WD/ML

H5 DNA technology
H1-H4

DBJ
B WD/ML

H6 Bioinformatics

H5-H7

MF
MF
A WD/ML

H8 Enzyme kinetics
H5-H7

MF
B WD/ML
B

Do 20-2

9:00-11:00

18.-156

Vrij 21-2

9:00-10:45

61.0267

lecture 9

H9 Catalysis

Di 25-2

9:00-10:45

11.0080

lecture 10

exercise
H10 Enzyme regulation, H11 Carbs

Di 25-2

11:00-17:00 16.303/310

computer

Bioinformatics (obligatory)

Di 25-2

A WD/AV

MF
MF

13:00-15:00

16.0116

exercise 3

H8-H11

Wo 26-2

9:00-10:45

11.0022

lecture 11

H12 Membranes, H13 Transport

Wo 26-2

11:00-17:00 16.303/310

computer

Bioinformatics (obligatory)

H8-H11

B WD/AV

Wo 26-2

MF

13:00-15:00

16.0116

exercise 3

Vrij 28-2

9:00-10:45

61.0267

lecture X

Vrij 28-2

14:00-16:00

Hal 01

exam 2

Di 4-3

9:00-10:45

11.0080

lecture 12

Di 4-3

11:00-17:00 16.303/310

computer

Di 4-3

13:00-15:00

16.0116

exercise 4

H12-H14

WD/AV

Wo 5-3

9:00-10:45

11.0022

lecture 13

H15 Metabolism

MF

Wo 5-3

MF
H6-H11
H13 Transport, H14 Signal transduct.
Visualisation (obligatory)

B MF

11:00-17:00 16.303/310

computer

Wo 5-3

13:00-15:00

16.0116

exercise 4

H12-H14

WD/AV

Vrij 7-3

11:00-12:45

61.0267

lecture 14

Overview

MF

Do 10-4

14:00-17:00

Hal 01

EXAM 3

CHBBBIOCH - Biochemie - RU
Groningen

Visualisation (obligatory)

MF

A MF

all

Next wednesday
We will visit the visualisation center of the RUG
Biomolecules will be shown and explained in 3D
Where: Zernikeborg
When: see group&time below

13:00

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Bart Louwers
Ellen Kampinga
Simon Stegink
Danil Buwalda
Jasper Pol
Jasper Bos
Pieter Smit
Renske de Vries
Tamara Idema
Matthijs Dijkstra
Mimi Zhao
Hidde Schijen
Alfred Rodenboog
Hanneke Siebe
Paco Visser
Lon Zandstra

13:20
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13:40

Wouter de Looff
Yannick Onstenk
Vangelis Vasilikos
Patrick Paalman
Taco Tjalma
Sander van der Veen
Wybren Kalsbeek
Bart Brouwer
Eva Doting
Sam Leemeyer
Elisabet Keisia Sumarjadi
Jurjan Bruggink
Axel Kees
Jesse Heijkoop
Lucas van Kleef
Chaline van Aartrijk
Nick Patsos

s2552841
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Mees Hoff
Jacques Hille
Akua Henaku
Fabian Grnewald
Coen Analbers
Martine Schouten Hoogendijk
Joni Gallagher
Matthijs van Akker
Dylan Siepel
Frank de Boer
Ivaylo Angelov
David van Schagen
Jorn de Jong
Winfried de Haas
Stijn Spoormans
Hendrik Swart

Next wednesday
We will visit the visualisation center of the RUG
Biomolecules will be shown and explained in 3D
Where: Zernikeborg
When: see group&time below

14:00
s2556677
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s2311313
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Marit Velsma
Marten Boerma
Marthieu Keizer
Kemba Krallmann
Christian Bhmer
Jisk de Vries
Jorik Melsen
Theo Oehlmann
Wisse Looijenga
Ingmar Loohuis
Jowan Zink
Mathijs Steenhuis
Kenny Zuur
Elvera van der Kooi
Roos van Lier
Harmen Sikkema

CHBBBIOCH - Biochemie - RU
Groningen

14:20
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Hans Beukers
Valrie Vugteveen
Tom Knobbe
Pieter Blom
Jesus Rodriguez Comas
Gydo Kempenaar
Wouter Sipma
Marlinde Koops
Laura Boetje
Tim de With
Katharina Wegner
Jarno de Witte
Emmy Slager
Priscilla Pieters
Bas Fluitman
Rogier Ketelaars
Luke Duigan Slater

14:40
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Natasha Witto
Rian Lenting
Sarah Mitchel
Thijn Kortenbach
Hao Wu
Jacco van der Wal
Rob Lammers
Sanne de Wit
Mees Brenninkmeijer
Christina Verbruggen
Katrin Heinzerling
Annemarie Maan
Jens Teuben
Patrick Bosch
Willem van der Wouden
Iwan Hidding
Daem Vorster

Tips!!!
1. Biochemistry is not so tough (yet, quite a number of students fail each
year!) The course is very concentrated, treat many topics, a large part of
the textbook should be read and absorbed. This is essential to understand
general concepts and serves are a basis for future (bio)chemical courses.
2. Attend the lectures and bring the book and print-outs of the sheets. Write
down notes!
3. During the exercise lectures questions will be treated that are similar to
exam questions attend and participate !!!
4. De computer practicals (bioinformatics & visualization) should be attended!
5. During or after each lecture: clickerquestions, participate!
6. I am always willing to help, also outside lectures: m.w.fraaije@rug.nl
7. There are 2 in-between-exams (each counts for 10% of final grade): 14&28 Feb
8. Use links & tips provided during the lectures
9. Ask-ask-ask-ask-ask-ask

after the lecture course: practical!


you are going to make
a recombinant organism by DNA technology

CHBBBIOCH - Biochemie - RU
Groningen

after the lecture course: practical!


you are going to make
a recombinant organism by DNA technology

Biochemistry studies the molecular basis of life


 Biological processes:
Photosynthesis, creating biomass by plants with the use of light and CO2
light-energy capture
biosynthese
Genetics, all information of an organism in 1 cell, in its DNA
Metabolism, energy, motion, sensing

 Results (examples):
Chemical processes for basal metabolism for each organism are known
Common (bio)chemical processes: the same chemical processes apply for all
living organisms
Complex biological processes are beter understood: morphogenesis, central
nerve system, immune system, evolution
Influence on medical sciences: knowledge, diagnostics, therapy, predictions
New applications, example: biotechnology

CHBBBIOCH - Biochemie - RU
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Simple view on biology: life, cell division = growth






The essence of any living being is growth, and replication


Cells continuously divide & grow (or specialize)
All required (chemical!) processes are catalysed by enzymes




enzymes are proteins, built from amino acids


enzymes are produced by & in the cells, DNA is used as manual (code)

Cell division includes duplicating genetic information (=DNA): replication of DNA!


A cell requires synthesis of an enormous number of different molecules/polymers
for building the cell: biosynthesis

biosynthesis depends on energy, which is supplied as ATP (fuel of every living organism)
the cell de cell needs to produce ATP; the energy for this often comes from oxidation
(sort of combustion/burning, we do it gently using lungs) of for example carbohydrates

Simple view on biology: the cell


 Organisms are composed of cells, that can divide & grow
 A cell is 1-10 m in size and can be regarded as a droplet of fluid
(cytoplasma), that is surrounded with a (cell)membrane (lipide bilayer)
 Some organisms (e.g. bacteria) are uni-cellular
 Multi-cellular organisms develop starting from a single cell
 Cells can specialize, for example in humans:

Muscle cells
Red and white blood cells
Brain cells (billions! miljarden)
Liver cells
etc., etc.
Eukaryotic cells contain
a nucleus, which
contains genetic
material (DNA)

www.natuurinformatie.nl
nl.wikipedia.org/wiki/Cel_(biologie)

CHBBBIOCH - Biochemie - RU
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The cell
1
2
3
4
5
6

1: Nucleus (contains DNA, transcription for synthesis of RNA takes place)


2: Ribosomes (protein synthesis)
3: Cell membrane (border of a cell, is a lipid bilayer, also contains transport proteins)
4: Endoplasmic reticulum (transports compounds within a cell)
5: Mitochondrium (ATP production for general energy supply)
6: Golgi-apparatus (storage, transport and secretion of proteins to the outside)

In the cell: cytoplasma

 DNA, carrier of all information


eukaryotic cells contain DNA in the nucleus
Prokaryotes do not have nuclei (no organelles)

 ribosomes for protein synthesis


 lots of enzymes: catalytic proteins that synthesize
and degrade compounds
 the compounds that are formed/degraded
(nucleotides, fatty acids, sugars, amino acids, etc.)
are used as building blocks for polymers (DNA,
proteins, etc.)
Scale/Complexity!
cell: 1-10 m
enzyme: 5-50 nm
Euroborg
soccer ball

CHBBBIOCH - Biochemie - RU
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glucose
ping-pong
ball

Biochemistry: why?
 Fundamental knowledge of the (chemical) basis of life
 Elucidate the molecular mechanisms of diseases
 Develop & produce medicines
 Learn from nature how to do chemistry
 Essential for all forms of biotechnology

insuline

Biochemistry: why?
 Fundamental knowledge of the (chemical) basis of life
 Elucidate the molecular mechanisms of diseases
 Develop & produce medicines
 Learn from nature how to do chemistry
 Essential for all forms of biotechnology
 Essential for new areas of science: Nanotechnology, Industrial
Biotechnology, Systems Biology, Synthetic Biology...
DNA
synthese

DNA double helix

CHBBBIOCH - Biochemie - RU
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Biochemistry: why?

Rothemund 2006

Biochemistry: why?

Kjems 2009

CHBBBIOCH - Biochemie - RU
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10

Biochemistry: why?
 Fundamental knowledge of the (chemical) basis of life
 Elucidate the molecular mechanisms of diseases
 Develop & produce medicines
 Learn from nature how to do chemistry
 Essential for all forms of biotechnology
 Essential for new areas of science: Nanotechnology, Industrial
Biotechnology, Systems Biology, Synthetic Biology...
DNA
synthese

DNA double helix

Biochemistry
1.
2.
3.
4.
5.
6.
7.

Lectures
Exercise lectures
Demonstration visualization
Computer-exercise Bioinformatics
Computer-exercise Visualization
Tests/exams 2x (make up 10% of final grade)
Exam (80% of final grade)

(obligatory)
(obligatory)
(obligatory)

Why?

CHBBBIOCH - Biochemie - RU
Groningen

11

Biochemistry
1.
2.
3.
4.
5.
6.
7.

Lectures
Exercise lectures
Demonstration visualization
Computer-exercise Bioinformatics
Computer-exercise Visualization
Tests/exams 2x (make up 10% of final grade)
Exam (80% of final grade)
2012

CHBBBIOCH - Biochemie - RU
Groningen

(obligatory)
(obligatory)
(obligatory)

2013

12

Chapter 1: introduction
Biochemistry studies the molecular basis of life

Chapter 1: introduction
Biochemistry studies the molecular basis of life

CHBBBIOCH - Biochemie - RU
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13

Chapter 1: introduction
Biochemistry studies the molecular basis of life

Life has evolved: evolution

Detailed knowledge about many aspects


of the evolution of life

Different at macro-scale
Similar at nano-scale

CHBBBIOCH - Biochemie - RU
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14

Geological & Biochemical evidence:


common ancestor

Common feature of life: DNA

1940-1950: DNA carries information


1953: DNA structure determined (Watson & Crick)

DNA double helix

CHBBBIOCH - Biochemie - RU
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15

Common feature of life: DNA

1940-1950: DNA carries information


1953: DNA structure determined (Watson & Crick)

DNA double helix


two copies of information

Why does DNA form a defined helical structure?


long polymer of A, C, G en T
(nucleotides)
double helix

A base pairs with T base


C base pairs with G base
A-T base pairs are weaker than
G-C base pairs

double stranded & antiparallel (Watson and Crick, 1953)

CHBBBIOCH - Biochemie - RU
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16

Structure of DNA:
universal to life, carrier of genetic information
stacking of these
bases stabilizes
Watson & Crick
double helix

phosphate groups on
the outside, exposed to
polar solvent
stacking of aromatic
bases
hydrogen bonds
between bases

Matching DNA strands form a stable helix: why?!

each strand has all information


enzyme-catalyzed strand duplication
What interactions exist

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17

Atom interactions in DNA


Covalent bond
Strongest
(C-C : 356 kJ/mol or 85 kcal/mol)
Strength dependent on atom types (C=O : 730 kJ/mol)
Length around 1.5 (0.15 nm)
(C-C: 1.54 and C=C: 1.34 )
Length can change by e.g. resonance

C-C: 1.40 !

Atom interactions in DNA


Noncovalent bonds
Electrostatic:
Hydrogen bonds:

q1

Coulombs law
E = k q1 q2 / D r2

q2
H-bond donor

~ 5 kJ/mol

H-bond acceptor 4-20 kJ/mol

2.4 3.5

CHBBBIOCH - Biochemie - RU
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Hydrogen bonds

linear

donors: H atoms connected to O, N (side chains, main chain N-H in


proteins)
acceptors: carbonyl and amide O; carboxylate oxygens (pH dependent)
-helix: main chain C=O of residue n is acceptor of H bond from main
chain N-H of residue n+4

Atom interactions in DNA


Noncovalent bonds
Electrostatic:
Hydrogen bonds:

q1

q2
H-bond donor

van der Waals interactions

Coulombs law
E = k q1 q2 / D r2

H-bond acceptor 4-20 kJ/mol


2-4 kJ/mol

atom
H
C
N
O
S
P

CHBBBIOCH - Biochemie - RU
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~ 5 kJ/mol

v.d. Waals
contact dist.
1.2
2.0
1.5
1.4
1.85
1.9

19

Water is the solvent in biological systems


 Polar, specific interactions with
biomolecules
 Cohesive properties, ordered
structure, hydrogen bonds
 Solvent for polar compounds
 Reduction of electrostatic
forces, solvent shells around
charged groups
 Water-free microenvironments
for reactions involving polar
groups
 Non-polar groups associate in
water hydrophobic
attractions

Atom interactions in DNA


Noncovalent bonds
Electrostatic:
Hydrogen bonds:

q1

q2
H-bond donor

van der Waals interactions

Coulombs law
E = k q1 q2 / D r2

~ 5 kJ/mol

H-bond acceptor 4-20 kJ/mol


2-4 kJ/mol

Hydrophobic interactions

Force to lower amount


of caged waters

Hydrophobic effect (entropy-driven) drives protein folding

CHBBBIOCH - Biochemie - RU
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20

Atom interactions in DNA


Van der Waals interactions force double helix structure,
- stacking of aromatic rings of bases
Hydrogen bonds for buried polar groups
Electrostatic repulsion between phosphates

electrostatic
interactions

DNA obeys laws of thermodynamics


1. Energy can be neither created nor destroyed.
It can only change forms.
2. Total entropy of a system plus that of its surroundings
always increases.
G = H - TS : must be < 0 for things to happen!
G : free energy change
H : enthalpy change
S : entropy change

CHBBBIOCH - Biochemie - RU
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21

DNA strands can be melted by heat

ssDNA

melting temperature,
dependent on GC content

hybridisation

dsDNA

DNA_Unzip.mov.mov

DNA strands can be melted by pH


Titration (adding acid) brings down the pH, and protonates
carboxylate groups
H
amino groups
O
O
+

H3C

H3C

OH

What happens with DNA??!

CHBBBIOCH - Biochemie - RU
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22

High pH causes unfolding of double helix (melting)

H-bond donor
charge in interior 
of double helix

Henderson-Hasselbalch equation

pKa:

pH value at which the molecule


under consideration is 50% ionized

pI :

(isoelectric point) pH value at which


the (zwitterionic) molecule under
consideration has no net charge

pH = pK a + log([A ]/[HA])

What happens with DNA at low pH??!

Genomic revolution
1940-1950: DNA carries information
1953:
DNA structure determined (Watson & Crick)
>2000:
massive DNA sequencing becomes feasible!
human cell
Storage of DNA in nucleus
Long polymers!!! (how long?)
Organized in chromosomes (46)
3.000.000.000 basepairs
Sequenced in 2000
~ 25.000 genes
proteins

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Some insight into DNA organisation


(details in lectures 3,4,5)
chromosomen
mens: 23, elk in duplo (diploid)
man: 23=XY
vrouw: 23 = XX
gameten: haploid
bevruchting: fusie 2 gameten

Transcription and translation in prokaryotes and eukaryotes


(details in lectures 3,4,5)

prokaryotes: no nucleus, DNA in cytoplasm (e.g. bacteria)


eukaryotes: DNA in nucleus, mRNA exported to cytoplasm, ribosomes in cytoplasm
(yeast, plants, animals, man)

CHBBBIOCH - Biochemie - RU
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Flow of genetic information for protein synthesis


(details in lectures 3,4,5)
DNA  mRNA  protein


dsDNA
3' ---TACCGCGATCGGTCGCTA--- 5'
5' ---ATGGCGCTAGCCAGCGAT--- 3

template strand
coding strand

transcription: RNA polymerase makes mRNA copy of the coding strand


5' ---AUG GCG CUA GCC AGC GAU--- 3'

DNA

triplets

mRNA

Specific start signals (short sequences)

translation: ribosomes translate the mRNA and synthesize proteins

codons: three bases code for 1 amino acid (genetic code)


tRNA links codons to amino acids

protein
N-terminus Met-Ala-Leu-Ala-Ser-Asp-- C-terminus


DNA has 3 reading frames, 2 directions

Translation start signal: AUG


Translation stop signals: UAA, UAG, UGA

DNA determines what?


(details in other lectures)
The DNA sequence determines sequences of proteins
The amino acid sequence determines the folding of a protein
Folding provides function

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25

Genomic revolution
1940-1950: DNA carries information
1953:
DNA structure determined (Watson & Crick)
>2000:
massive DNA sequencing becomes feasible!
human cell
Sequenced in 2000
~ 25.000 genes
proteins
Challenges:
most genes with unknown protein function
most DNA is not encoding proteins (~3000 bp)
many mutations known: effect?
individual genomes...

Genomic revolution
DNA solves everything?
Health determined by:
genome sequence (genetic variation)
epigenetics
environment (e.g. food)

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genotype
phenotype

26

How to visualise molecular structures?


Common methods (p.22-23)

ball-and-stick

space-filling

standard
But what to do with DNA or protein???!! (p.61-62)
practical 4/5 March!

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