Living systems Flashcards
(134 cards)
1
Q
what is biotechnology
A
the use of biological processes to create useful products
2
Q
What is the process of creating a biotech product from raw materials?
A
- Raw material upstream processing fermentation downstream processing
3
Q
examples of biotech products
A
wine, cheese, vinegar, insulin and citric acid
4
Q
red biotech?
A
the pharmaceutical branch which uses bacteria to produce drugs e.g. disease preventation
5
Q
White biotech?
A
- White biotech is the aid of living organisms and enzymes e.g. biofuels to biodiseal
6
Q
Green biotech?
A
- Green biotech is the use of agriculture such as plants less suspectible to pests e.g. water purification
7
Q
What is cell growth
A
essential element of fermentation for the growth of a organism
8
Q
Growth is an orderly increase of…
A
cellular constituents
9
Q
what does optimising the environment for growth require?
A
balancing the economic feasibility of maintaining a suitable chem environment
10
Q
What does growth depend on?
A
the ability to form new protoplasm from the nutrients available
11
Q
What does cell growth involve
A
An increase in the cell mass and number of ribosomes and cell division
12
Q
Methods of measurement of cell mass
A
- Direct physical measurement of weight after centrifugation
- Direct chemical measurement of chemical component
- Indirect measurement of chemical activity
- Turbidity measurements to determine amount of light scattered by suspension of cells
- Microscopic count
- Viable cell count
13
Q
Lag phase
A
after inoculation of cells the population remains unchanged so no cell division occurs but the metabolic activity may increase
14
Q
expo phase
A
cells divide by binary fission at constant rate
15
Q
stationary phase
A
exhaustion of available nutrients and space growth stops
16
Q
death phase
A
population declines
17
Q
What is a closed system
A
It is a batch culture where there is a lack of input and output of materials once batch medium has been inoculated, a discontinous process which environment and organisms are changing continually
18
Q
What is an open system
A
It is a continous culture which is capable of obtaining steady state where there is balanced input growth substrate and ouput of organisms
19
Q
equation for increase in cell mass
A
ln x = ln x0 + n ln 2
*n= t/td, ie no of generations = total time/doubling time
20
Q
equation for increase in cell mass in terms of specific growth rate
A
ln x = ln x0 + µt
or 2=exp(ut) doubling
t=generation time
21
Q
What is a growth limiting substrate
A
nutrient medium containing one limiting substrate at low concentrations
22
Q
what limits cell synthesis
A
nutrient concentration in culture vesssel
23
Q
Monod kinetics eq for specific growth rate
A
µ = µmax . s/(Ks + s)
24
Q
Lineweaver burke plot
slope?
x intercept?
y intercept?
A
ks/umax
-1/ks
1/umax
plot is /u v 1/s
25
what is cell yield coefficent
amount of cell mass produced per unit amount of substrate consumed
26
Yield factor eq
Yfg= - deltaF/deltaG
```
f= moles produced
G= moles consumed
```
27
observed biomass yield
Y'xs=-DeltaX/deltaSG
X=biomass produced
SG= mass of substrate
28
what is a continuous culture
a continuous feed of influent solution containing substrate and nutrients and a drain of effluent solution containing cells and metabolites
29
what is a chemostat
allows control of rate of growth which can be used to optimise the production of products
30
What is a primary metabolite
produced at high flow/dilutuion rate stimulating cell growth
31
What is a secondary metabolite
produced at low flow/dilution maintaining cell numbers
32
What two parameters are controlled in a chemostat and why?
Dilution rate and influent substrate conc. By controlling the dilution rate we can control the specific growth rate. By controlling the substrate conc we can control number of cells produced or cell yield in chemostat
33
dx/dt=?
ux-Dx
u=d is steady state
u>D utilization of substrate exceeds supply so slow growth
U
34
critical dilution eq
Dc=Umax(s/(s+Ks))
35
Why do we have critical dilution
when a chemostat is operating at Dc , if the dilution rate is increased further, the growth rate will not be able to increase (since it is already at µmax ) to offset the increase in dilution rate.
36
what is maintence energy
the level of energy required to maintain a cell
37
purpose of a fermentor
control temp and ph
reduce evapouration
minimise the use of labour
maximise computer control
38
scales of operation for a fermentor/bioreactor
laboratory 20L
pilot plant 5000L
production 20,000L
39
Most important factor in fermentor design
height to diameter ratio
40
why do we implement impellers in bioreactors
to reduce bubble size hence increase surface area for oxygen transfer
41
What is genetic engineering
the direct manipulation of an organisms genes using biotechnology to change the genetic make up if cells
42
what is metabolic engineering
the direct improvement of cellular properites through direct modifications of biochem reactions
43
what are plasmids
self replicating pieces of DNA
44
what is gene cloning
genes are inserted into a plasmid then added to bacteria for replication
45
Steps of gene cloning
1. Isolate the plasmid
2. Isolate gene of interest
3. Insert the gene into the plasmid
4. Bacteria will take it through transformation
5. Cells divide along with the plasmid and form a clone of cells
46
Why is bacteria grown in a culture
to produce copies of the isolated gene of interest
47
what is Metabolism
the summation of chemical reactions in a organism
48
what are autotrophs
organisms that use co2 as their sole carbon
49
what are chemotrophs
life forms that obtain their energy by injecting carbon
50
Phototrophs
i.e. plants via sun
51
Chemotrophs
oxidation of co2 and lipids
52
anabolism
construction path
53
Catabolism and how it works
degradation path, it is the breakdown of macromolecules into building blocks then the oxidation of building blocks to produce acetyl coA which is further oxidised to co2 and water
54
gycolysis under aerobic conditions
pyruvate further oxidises and enters the krebs cycle
55
gycolysis under anaerobic conditions
pyruvate is converted into a reduced end product
lactate in muscle) = homolactic fermentation. In yeast = alcoholic fermentation yield ethanol and CO2
56
As cells have limited quantities of NAD+ what should happen?
it must be recycled after reduction to NADH
57
what happens to NAD+ under aerobic conditions
oxidised in mitochondria
58
what happens to NAD+ under anaerobic conditions
NADH is replenished by reduction of pyruvate
59
what is pathway flux
Is the rate at which input metabolites are processed to form output metabolites
60
what are enzymes?
catalysts that preform a wide variety of biochemical reactions in the cell
61
How do enzymes differ from chemical catalysts
they catalyse under mild conditions
have a high degree of specificity
enzyme activity is regulated in the cell
62
oxidases
oxidation reduction
63
what enzyme involves the transfer of function groups
Transferases
64
what enzyme involves the hydrolysis of reactions
hydrolysis
65
lyases
group elimination of double bonds
66
isomerases
isomerisation
67
what enzyme involves bond formation
ligases
68
what is catalytic potential equal to
enzyme activity
69
how do enzymes bind to substrates
through a series of non covalent bonds
70
how is enzyme activity measured
substrate depletion, product production and can also be measured by coupling with an enzymatic reaction to others which transforms the product into a more detectable analyte
71
enzyme catalysed reaction
E+s--> ES--> E+P
| where [s] is high enough to convert E to ES so the second step is the rate limiting step
72
reaction velocity eq
```
vo=vmax[S]/Km+S
km=[S] when v0=vmax/2
enzymes with low km achieve max catalytic efficency
Km varies with temp, ph and enzyme
at high [S] vo approaches vmax
```
73
eadie hofstee plot parameters
V vs V/[S]
slope= -km
y-vmax
x=vmax/km
74
Detergent enzymes and their conditions
proteases, lipases and amylases are added to detergents where they catalyse the breakdown of chemical bonds on the addtion of water
Condtions --> ph 9-11, 60 degrees
75
proteases
remove protein stains such as blood, grass and egg. Hydrolyse the protein and break them down into more soluble polypeptides
76
Amylases
remove residue of starch foods such as mash potato
77
cellulose
modify the structure of cellulose fibrils such as those found on cotton
78
Lipases
remove fatty stains such as lipstick
79
detergents should be produced using?
Bacillus
80
what was the first cost effective detergent and what was it based on?
lipases based on the use of rDNA technology. it has made is possible to alter the dna sequence randomly or at specific sites of lipase enzyme in order to change the amino acid sequence
81
what properties of lipase has protein engineering improved?
substrate specificity
thermostability
proteases stability
82
enzyme production process
gene+plasmid-->recombinant plasmid --> bacterial transformation --> protein
83
steps of enzyme production
screening - choosing appropriate micro organism
modification - improving microbial stain
lab scale - determine optimum conditions
pilot plant - large scale
84
upstream processing
cell factory(bioreactor) sepration of cells (centurifgation) enzymes secreted from cells downstream processing
enzymes secreted in cells --> enzymes inside cells --> cell lysis --> downstream
85
downstream processing
LL extraction chromatography purified enzyme three by producs(solid, liquid formulation and the reaming enzyme is imbolized)
86
biomass -> .....->biofeul
sugars
87
examples of biomass
cereal crops and lignocellulose
| proteins and carbs
88
why is biomass not compatible with existing engines
it is a solid whereas conventional feuls are gases and has a low energy density and high moisture and oxygen content
89
examples of biofeuls
gasoline, hydrogen gas and propane
90
production of bioethanol
extraction of sugar cane --> saccharification of corn --> pre treatment
```
(grains)milling
(water and enzymes)saccharification
(yeast and sugar)fermentation
(mash from fermentation)distillation
can be dehydrated to bioethanol
```
91
what is milling
| disadvantages
mechanical crushing of cereal grains to release starch
| time consuming, expensive and slow
92
saccharification
heating and addition of water and enzymes for conversion into fermentable sugar
93
fermentation
of the mash using teast converting bioethanol and c02
94
saccharification of starch
starch is mixed with water at 60 degrees for 5-10mins
starch dissolves in water to form mash
liquefication of mash by adding amylase at 80 degrees for 2 hours to degrade starch
saccharification of glucoamylase added at 65 degrees for 30 mins to produce glucose
95
common microbes in glycolysis fermentation
saccharmyces cerevisae and zymommonis mobillis
96
fermentation process
1) in yeast fermentation glucose solution is obtained from starch saccharification and is cooled to 32 degrees
2) yeast culture is added and glucose is metabolised to ethanol and co2
3) some of the released energy and glucose are utilised by the yeast cells to support growth the rest of the energy becomes heat to fermentation
97
normal inoculation ratio for fermentation
5-10% 6-8hrs
98
how long does active fermentation last
12 hours then fermentation activity slows down due to less glucose being available
99
what happens during slow fermentation
cells do not grow anymore biochem reactions are limited by substrate conc
100
sources for bioethanol production
corn farm in us and brazil
| 60% is based on sugar cane conversion
101
three constituents for lignocellulose
celluose, hemi-cellulose and lignin which enhances strength and compactness
102
what is the structure in lignocellulose like
complex structure due to strong linkages between molecules
103
advantages of using lignocellulose
increases available surface area
reduces particle size
pre treatment leads to solubising hemi-cellulose and increasing enzymatic hydrosybility of cellulose
104
biological pre treatment
```
fungi and bacteria
slow
no chemicals
solubises micro-organisms
brown white and soft rot fungi
white and soft rot both attack cellulose and lignin but white is more effective for pre treatment
```
105
Chemical pre treatment
dilute sulfric acid can acheive high reaction rates
| but there is high costs and neutralisation is required
106
Alkaline pre treatment
can disrupt lignin structure and decrease crystalinity
| but there is less sugar degradation and naoh can be recovered
107
why are advanced biofeuls good
can drop into existing infrastructure because they have similar properties to petroleum but requires large biorefineries to produce high yields
108
what leads to corrosion
ethanol
109
what is the main challenge in isobutanol production
is using native hosts to convert feedstocks into advanced bio fuels to overcome regulation of biofuel pathways to improve yields.
110
what is isobutanol
a next generation product which builds on the foundation and provides additional solutions to various challenges not met by first generation products
111
advantages of isobutanol
- Isobutanol has more hydrocarbons then ethanol therefore has a better energy content and is less polar
- Absorbs less water
- Volatility
- good Phase separation
- Good platform molecule
- Good blend properties
112
what 3 pathways does the isobutanol pathway consist of
- Glycolysis to provide pyruvate
- Valine biosynthesis to metabolise pryruvate to KIV
- Ehrilich pathway which is required for degradation of KIV to isobutanol
113
why is a high activity of KDC essential is isobutanol production
it links valine metabolism and ehrilich pathway so is essential for high levels of isobutanol
114
How can we increase isobutanol production
by over expression of genetic engineering by increasing KDC and ADH.
115
Salmonella
distributed in domestic wild animals such as pigs and cattle
in humans it is generally contacted through consumption of contaminated food of animal orgin
symptoms - diarrhoea, fever and abdominal cramps
116
Listeria Monocybogenes
found in soil and water and animal digestive tracts
food with long shelf life under refridgeration
symptoms- gastroentritis, meningitis
onset 9-48hrs
duration
2-10 days
117
Campylobaceri-jeuni
distributed in warm blooded animals
symptoms - abdominal pain, diarrhoea and fever
onset 2-5 days
duration 2-10 days
118
Esherichia coli
```
found in cattle
food implicated with this are uncooked hamburger, dry cure salami, yogurt, cheese made from raw milk
symptoms - bloody diarhea
onset - 1-8 days
duration 5-10days
```
119
Staphyloccus aureus
```
found on skin and nose
foods at high risk of transmitting toxins are those that do not cook but handle such as sliced meat and sanwiches
symptoms - vomitting and diarrhoea
onset 6hrs
duration 24hrs
```
120
Bacillus cereus
found in rice
causes vomitting and diarrhoea
onset 8-16hrs
duration is 24hrs
121
Clostridium prefringens
commonly found in raw meat such as beef, poultry, gravy
symptoms - abdominal pain, stomach cramps followed by diarrhoea
onset 8-16hrs
duration 24hrs
122
Clastidium
anerobic bacteria so can only grow in the absence of oxygen
| onset 12-72 hours
123
what should be considered for foods that carry food borne pathogens
paesturization such as milk and fruit juices
124
standard sterilisation
| what eq can describe it
steam sterilisation for reactors 121 degrees for 15mins at 103kpa
arrhenius eq
125
Bacillus stearothermophilus
spores are commercially available for validation for steam sterilisation unit operations
126
number of viable organisms eq
Nt/No=exp(-kt)
127
sanatation
| control variables
reduction of the oppourtunity for bacterial contamination by removing it from process equipment
Control variables are cleaning agent conc, cleaning solution temp, time and velocity
Need uniform flow over tank surface which is function of application rate, surface and viscocity.
128
what does cooking do
Cooking kills viruses, bacteria, parasites and destroys toxins. Uncooked food contains viruses, live bacteria, parasites and toxins
129
what happens when re-heating food
if they do not reach 70 degrees bacteria will survive and toxins remains.
130
corrective action
reduce impact of an outbreak
131
preventive action
stop it from happening again by finding where it went wrong
132
method for cultivation
1. Rinse the seed(useful source for contamination) and remove the damaged seed
2. Soak for 8hrs
3. Rinse
4. Grow for 3 days at 15 degrees (ideal for salmonella growth)
5. Package
6. Distributed
133
are metabolic pathways reversible or irreversible?
irreversible – highly exergonic (ΔG = -ve) so reactions go to completion. This provides the pathway with direction.
134
Metabolite concentrations are a function of
Thermodynamics
| Reaction kinetics
