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CEN 551 Biochemical Engineering. Instructor: Dr. Christine Kelly. Review chapter 3, 4, 5 Section 4.6 - Regulation. Schedule. Today 1/27: chapter 3 and 4 review, chapter 5 Thursday 1/29: chapter 6 and 7 Tuesday 2/3: review for exam 1 Thursday 2/5: exam 1 (chapters 1-7).

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cen 551 biochemical engineering

CEN 551 Biochemical Engineering

Instructor: Dr. Christine Kelly

Review chapter 3, 4, 5 Section 4.6 - Regulation

schedule
Schedule
  • Today 1/27: chapter 3 and 4 review, chapter 5
  • Thursday 1/29: chapter 6 and 7
  • Tuesday 2/3: review for exam 1
  • Thursday 2/5: exam 1 (chapters 1-7)
michaelis menten kinetics6
Michaelis-Menten Kinetics
  • When v= 1/2 Vmax, [S]= Km so Km is sometimes called the half-saturation constant and sometimes the Michaelis constant
damkohler number da
Damkohler number (Da)

maximum reaction rate

maximum diffusion

V’m

kL[Sb]

Da>>1 diffusion limiting

Da<<1 reaction rate limiting

Da =

Sb = bulk substrate

kL = mass transfer coefficient

Da =

vocabulary from chapter 3
Vocabulary from Chapter 3

Write down vocabulary from chapter 3 that you think I expect you to know without looking in the text or notes.

slide10
Michaelis-Menten kinetic equation and shape of the plot

Factors that can cause denaturation of enzymes

Activation energy

Rapid equilibrium assumption

Quasi-steady state assumption

Types of inhibition

How does temperature affect enzyme kinetics

What are immobilized enzyme

Advantage/disadvantage of immobilized enzyme

Process in converting reactants to products in immobilized systems

what kind of open book problems am i likely to ask
What kind of open book problems am I likely to ask?
  • Here is some data, what are the Michaelis-Menten parameters?
  • Here is some data, what type of inhibition is exhibited?
  • Here is some data, are the immobilized enzyme kinetics mass transfer or reaction limited?
  • Here is some data, what is the activation energy?
  • Derive one of the inhibition rate expressions – using rapid equilibrium and/or quasi steady state assumption.
  • Derive batch rate equation using Michaelis-Menten kinetics.
  • Derive second order differential equation describing substrate concentration within an porous support.
rna post processing eucaryotes
RNA Post Processing (Eucaryotes)

exon intron exon

intron degraded before translation

mRNA rejoined

metabolic regulation controlling the rates of reactions in the cell
Metabolic Regulation: Controlling the rates of reactions in the cell.

1. Genetic level (control of transcription). Controlling the amount of enzymes. Most common in procaryotes.

2. Enzymatic level (control of product formation). Controlling activities of enzymes. Most common in eucaryotes.

genetic level control
Genetic Level Control
  • Feed back repression- end product blocks transcription.
  • Induction- metabolite (reactant) induces transcription.
  • Constitutive expression: genes transcribed continuously (always on).
  • Catabolite Repression: several operons influenced by the presence of glucose. If glucose presence, most operons for other sugar metabolism are regulated off.
genetic level control33

PROMOTER

OPERATOR

GENES

Genetic Level Control

Activator binding site

  • Repressor: molecule that binds to operator – when bound, transcription off.
  • Activator: binds to activator binding site, when bound transcription on.
  • Inducer: binds to repressor or activator – results in transcription on.
  • Corepressor: binds to repressor – results in transcription off.
slide39

If tryptophan low, the repressor does not bind tryptophan and thus cannot bind to operator. RNA polymerase can bind to the promoter.

If tryptophan high, the repressor binds tryptophan, binds to the operator, where it blocks the binding of RNA polymerase to the promoter.

Repression

slide40

lac

operon

slide41

Lac Operon

http://www.people.virginia.edu/~rjh9u/lacoperonanim.html

enzymatic level control
Enzymatic Level Control
  • Enzymes are transcribed and translated.
  • Feedback inhibition of allosteric enzymatic reactions.
allosteric enzymes
Allosteric Enzymes

allosteric inhibitor changes the conformation of the enzyme, distorting the active site and reducing the ability to catalyze the reaction.

types of feedback enzyme inhibition
Types of Feedback Enzyme Inhibition
  • Isoenzymes: two allosteric enzymes that carry out the same reaction, but are inhibited by different compounds.
  • Concerted: single enzyme has two allosteric inhibitor sites, each of which cause complete inhibition.
  • Sequential: more than one allosteric enzyme in sequential reactions.
  • Cumulative: single enzyme has two or more allosteric inhibitor sites – requires all inhibitors to achieve complete inhibition.
differences between enzyme and genetic level control
Differences Between Enzyme and Genetic-Level Control
  • Enzyme level control is fast and relatively quick to reverse, inefficient since unneeded enzymes are produced.
  • Genetic level control is slow and relatively slow to reverse, efficient for long time control.
transport
Transport
  • Energy-independent transport
    • simple (passive) diffusion of small and hydrophobic molecules
    • facilitated diffusion of larger molecules
  • Energy-dependent transport
    • occurs against a concentration gradient
    • uses transmembrane proteins
slide50

The relative permeability of a synthetic lipid bilayer to different classes of molecules. The smaller the molecule and, more important, the fewer its favorable interactions with water (that is, the less polar it is), the more rapidly the molecule diffuses across the bilayer. Note that many of the molecules that the cell uses as nutrients are too large and polar to pass through a pure lipid bilayer.

concepts and terms i expect you to know without looking at the book
Concepts and terms I expect you to know without looking at the book
  • 5’ and 3’ end of DNA
  • Replication enzyme (copies DNA)
  • Primer
  • Okazaki Fragment
  • Gene
  • Transcription enzyme (reads DNA, makes RNA)
  • Types of RNA
  • operon
slide53
Promoter
  • Intron
  • Ribosome
  • Codon
  • Anticodon
  • Glycosylation
  • Secretion signal – differences in secretion
  • 2 types of regulation/control
  • Induction/inducer
  • Repression/repressor
  • Catabolyte repression
slide54
Feedback inhibition
  • Allosteric enzyme
  • 2 types of transport
  • Electron transport pathway
  • NADH
  • ATP
  • Glycolysis
  • TCA/citric acid cycle
  • Specific growth rate
  • Phases of batch growth
  • Monod equation
slide55
Maintenance
  • Endogenous metabolism
  • Translate the code and reverse
  • Derive model of batch and CSTR growth
questions
Questions
  • Translate the following code:

GACGAUGACAAAGGGCCGU

  • Write the mRNA and DNA code for the following polypeptide:

Thr-Lys-Gly-Arg

types of problems
Types of Problems
  • Given data, find parameters
  • Given parameters, predict value of variables