The School of Biosciences

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The School of Biosciences
An international reputation for research and
teaching
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Biosciences Degrees
Biological Sciences
Human Biology
Biochemistry
Bioinformatics
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Resources for Schools

• We visit schools to give talks on scientific
  topics
• We also visit to talk about University Admissions
  and careers.
• We organise programmes of seminars, tours and
  practicals at Birmingham specific topics for both
  pupils and teachers.

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Protein structure and function
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Why is protein structure important?

• Determines enzyme action
• Changes response to environment
• Drug design

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Structure of a protein bound to DNA
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Nucleosome structure showing DNA packing in a
chromosome
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Structure of part of a ribosome, the cells
factory where proteins are made
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How do you measure enzyme structure?

• Predicted sequence
• X-ray crystalography

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Predicted sequence

• DNA sequencing gives us possibility of predicting
  protein sequence
• Can predict chain folding from amino acid
  properties
• Domains give idea of function

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Predicted sequence

• DNA sequencing gives us possibility of predicting
  protein sequence
• Can predict chain folding from amino acid
  properties
• Domains give idea of function

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Sequence prediction- an example

• Model plant Arabidopsis
• 24,000 genes

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Protein sequence can be predicted from DNA
sequence

• MLLETFANLA LVYNVFLLGL GLDLRMIKIK DIKPVIIAIV
  GLLAALLAGA GLYYLPSNGE ADKILAGCMY WSIAFGCTNF
  PDLARILADL KLLRTDMGHT AMCAAVVTDL CTWILFIFGM
  AIFSKSGVRN EMLPYSLAST IAFVLLCYFV IQPGVAWIFN
  NTVEGGQVGD THVWYTLAGV IICSLITEVC GVHSITGAFL
  FGLSIPHDHI IRKMIEEKLH DFLSGMLMPL FYIICGLRAD
  IGYMNRTVSV GMMAVVTSAS VMVKILSTMF CSIFLRIPLR
  DGLAIGALMN TKGTMALVIL NAGRDTKALD VIMYTHLTLA
  FLVMSMVVQP LLAIAYKPKK KLIFYKNRTI QKHKGESELC
  VLTCVHVLPN VSGITNLLQL SNPTKKSPLN VFAIHLVELT
  GRTTASLLIM NDEAKPKANF ADRVRAESDQ IAEMFTALEV
  NNDGVMVQTI TAVSPYATMD EDICLLAEDK QACFILLPYH
  KNMTSDGRLN EGNAVHAEIN QNVMSHAPCS VGILVDRGMT
  TVRFESFMFQ GETTKKEIAM LFLGGRDDRE ALAYAWRMVG
  QEMVQLTVVR FVPSQEALVS AGEAADEYEK DKHVDEESIY
  EFNFKTMNDP SVTYVEKVVK NGQETITAIL ELEDNNSYDL
  YIVGRGYQVE TPVTSGLTDW NSTPDLGIIG DTLISSNFTM
  QASVLVVQQY SSANRQTAEN NNQEPVQGKA KTDHEATPFM
  EDEDDEVEHQ YSMRR

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• Trans membrane regions are red
• Probably a membrane channel

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Hypothetical structure of the aquaporin
Adapted from Jung et al. 1994. Journal of
Biological Chemistry. 26914648
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Proteomics

• Proteins are separated on 2D gels

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Proteomics

• Robots pick spots from gels

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Proteomics

• Spots are digested and shot into MALDI or Q - TOF

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Proteomics

• Mass of fragments gives a fingerprint individual
  to each protein

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Proteomics

• Protein identified in databases
• ie Bioiformatics

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X-ray crystalography

• Pure protein is crystalised
• Diffraction of X-rays gives pattern
• which can be solved to give structure

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X-ray crystalography

• Pure protein is crystalised
• Diffraction of X-rays gives pattern
• Patter can be solved to give structure

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X-ray crystalography

• Pure protein is crystalised
• Diffraction of X-rays gives pattern
• which can be solved to give structure

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What do enzymes do for us?

• Enzymes in analytics
• Enzymes in personal care products
• Enzymes in DNA-technology
• Enzymes in fine chemical production
• Rare sugars
• Semi synthetic penicillins
• Lipase based reactions
• Asymmetric synthesis
• Enzymatic oligosaccharide synthesis
• DNA technology

• Detergents
• Starch
• Drinks
• Textiles
• Animal feed
• Baking
• Pulp and paper
• Leather

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Example of enzymes we use

• Fermentation
• Washing powder
• DNA and PCR - Taq
• Medicine
• Hygiene - false teeth and contact lenses
• Food - proteases, cellulases
• Textiles - designer jeans

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Molecular biology - Restriction enzymes
GAATTC CTTAAG
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Molecular biology Taq Polymerase

• Taq DNA polymerase I, is an invaluable tool in
  the field of molecular biology.
• It is widely used in PCR because of its
  thermostability.
• A member of the pol I family of DNA polymerases
• Isolated from the thermophillic bacterium Thermus
  aquaticus.

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Molecular biology Taq Polymerase

• To copy DNA an enzyme (DNA polymerase) is needed.
  
• The DNA polymerase of Thermus aquaticus is called
  Taq polymerase
• Taq polymerase is not destroyed at 90oC
• Forms the basis of PCR - DNA fingerprinting etc

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Catalase
Protease
Protease
Cellulase
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Enzyme kinetics

• Enzyme reaction rate declines with time

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Enzyme kinetics

• Important parameters are Km and Vmax
• Vmax - maximum rate of activity
• Km - related to efficiency of substrate binding

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Enzyme kinetics

• Km and Vmax can be estimated from a
  Lineweaver-Burk plot

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Enzyme kinetics

• Competitive inhibition increases Km - no effect
  on Vmax
• Inhibitor binds to enzyme
• produces enzyme inhibitor complex

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Enzyme kinetics

• Non competitive inhibitors
• Bind to the enzyme-substrate complex and block
  the catalytic step,
• They do not effect Km but decrease Vmax

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ENZYMES Mode of action of enzymes. Candidates
should be able to A. explain that enzymes are
globular proteins which catalyse metabolic
reactions. B. explain the mode of action of
enzymes in terms of an active site,
enzyme/substrate complex, lowering of activation
energy and enzyme specificity. C. describe and
explain the effects of pH, temperature, enzyme
concentration and substrate concentration on
enzyme action.
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D. follow the time course of an
enzyme-catalysed reaction, by measuring rates of
formation of products (for example using
catalase) or rate of disappearance of substrate
(for example using amylase). E. investigate the
effects of temperature, pH, enzyme concentration
and substrate concentration on the rate of
enzyme-catalysed reactions, and explain these
effects. F. explain the effects of competitive
and non-competitive inhibitors on the rate of
enzyme activity. G. use the knowledge gained in
this section in new situations or to solve
related problems.
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• Practical work
• should include experiments to investigate the
  effects of temperature, pH and enzyme
  concentration on enzyme activity using suitable
  enzymes
• illustrations of enzyme immobilisation using
  lactase
• the use of pectinase in the production of fruit
  juice.