Higher Biology: Metabolism in Microorganisms - Education Scotland

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Dec 11, 2012 (4 years and 8 months ago)

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NATIONAL QUALIFICATIONS CURRICULUM SUPPORT



















Biology


Unit 2, Part 3: Metabolism in

Microorganisms




Teacher’s

Notes



[HIGHER]



2

UNIT 3, METABOLISM AND SURVIVAL

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© Learning and Teaching Scotland 2011


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Acknowledgement

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Qualifications support programme for Biology.


© Learning and Teaching Scotland 2011


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UNIT 2: METABOLISM IN MICROORGANISMS

(H, BIOLOGY)

3


© Learning and Teaching Scotland 2011





Contents


(b)

Genetic control of metabolism

4

(i)

Genetic variation

4


(b)

Genetic control of metabolism

7

(ii)

Recombinant DNA technology

7


(c)

Ethical considerations in the use of microorganisms

11




METABOLISM IN MICROORGANISMS

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© Learning and Teaching Scotland 2011

Investigating metabolism in microorganisms


(
b
)

Genetic control of metabolism


(i)

Genetic variation


Links to prior/prerequisite knowledge

SCN 3
-
14b

SCN 4
-
14c

Student
s have already studied
mutations in Unit 1 (see
Section
3, The Genome)
and so should be aware that physical changes to the DNA of a cell or a change in
the number of
chromosomes can arise naturally.

They should also be familiar
with the concept of improvement through mutat
ion si
nce

polyploidy
crops are
discussed

in Unit 1.

New content areas



Examples of mutagenic agents and their effect on genetic material.



Transfer of DNA between bacteria, uptake of DNA by bacteria from their
enviro
n
ment
.



Production of new genotypes by sexual r
eproduction between existing strains
of fungi and yeast
.

Background information



Mutations may arise naturally by physical change
s

to the DNA of a cell or a
change in the number of copies of an entire gene or chromosome. When such
a change in genotype pro
duces a change in phenotype, the organism affected
is called a mutant.

In natural conditions, mutations arise spontaneously and at
random.



While they occur rarely, the

frequency

of
mutation

can be increased by
exposure to mutagenic agents such as mustard g
as and various types of
radiation.

E
xposure to natural
mutagens

such as ultraviolet (UV) light, to
industrial or environmental mutagen
s such as benzene or asbestos can all
cause mutations.

For geneticists, the study of mutagenesis is important
because muta
nts reveal the genetic mechanisms underlying heredity and gene
expression.



Genetic
transformation

is the uptake of
DNA from the environment.

The cell
is genetically altered as a

result of direct uptake, incorporation and
expression

of DNA

from its surroundings
. Transformation occurs most commonl y in
bacteria and in some species occurs naturally.
Bacteria capable of being
transformed are said
to be competent.
Transformation is
thought to be a
significant cause of increased
drug resistance

when one bacterial cell acquires
resistance and quickly transfers the resistance genes to many other cells.
The

METABOLISM IN MICROORGANISMS

UNIT 2: METABOLISM IN MICROORGANISMS

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© Learning and Teaching Scotland 2011

main method of cell
-
to
-
cel l
t ransfer i s

conj ugat i on.
Bact eri al conj ugat i on

i s
t he t ransfer of genet i c mat eri al bet ween bact eri al cel l s by di rect cel l
-
to
-
cel l
cont act or by a bri dge
-
l i ke connect i on bet ween two cel l s.

Duri ng conj ugat i on
t he
donor

cell provi
des a genetic element that is most often a
plasmid
. The
plasmid transferred is often beneficial to the recipient. Benefits may include
antibiotic resistance
.



A
fungus

is a member of a large group of
eukaryotic

organisms that includes
microorganisms such as
yeasts

and
moulds
. Although many species of fungi
and yeasts reproduce asexually, many also carry out sexual reproduction and
therefore have the ability to in
crease genetic variation. During this process,
meiosis forms genetically varied spores
that

are then released from the fungi
by

specialised

mechanical or physiological mechanisms.

Identification of key concepts



Mutations

are rare but their incidence can
be increased by exposure to
mutagenic agents
.



Mutagenic agents can be chemical
,

such as asbestos or mustard gas, physi cal
,

such as several forms of radiation
,

or biological
,

such as bacteria phage
.



Mutations may be of benefit to the species or may introdu
ce characteristics of
commercial value.



Recombinant DNA technology allows deliberate alteration of a genome. This
may invol ve the

addition
,
modification
or

deletion of one

or

more
genes in a
cell. As a result the cell may receive an additional property, fo
r example the
ability to make a new protein.



Some sp
ecies of bacteria are able to

carry out transformation
that

involves
uptake of DNA from thei r environment or another cell. The most common
form of transformation is called conjugation and involves direct
contact
between two cells. DNA can then be transferred from a donor cell to a
recipient cell.



Many species of fungi are able to reproduce sexually and therefore increase
variation. This is most commonl y achieved by the production of genetically
varied spor
es
that

are dispersed from the fungi and fuse with other sexual
spores.

Identification of particular areas of difficulty

The i
dea of sexual spores produced by fungi is
probably

a new concept and many

available sources of information

on this topic
are

ve
ry advanced and

involve
challenging vocabulary.

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Links to websites
,
animations
, P
ower
P
oints
,
audio or video files etc

http://www.bbc.co.uk/learningzone/cli
ps/mutations
-
and
-
genetic
-
diseases/10653.html

http://www.microbiologyonline.org.uk/about
-
mi crobiology/introducing
-
microbes/fungi


http://highered.mcgraw
-
hill.com/sites/dl/free/0072835125/126997/animation6.html


http://www.microbeworld.org/index.php?option=com_content&view=article&id=
123&Itemid=118

http://www.bbc.co.uk/learningzone/clips/genetic
-
engineerin
g
-
and
-
insulin
-
production/4200.html

Co
-
operative Learning Activities 3 and 4

Other useful information to stimulate interest





METABOLISM IN MICROORGANISMS

UNIT 2: METABOLISM IN MICROORGANISMS

(H, BIOLOGY)

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© Learning and Teaching Scotland 2011

(b)

Genetic control of metabolism


(ii)

Recombinant DNA technology


Links to prior/prerequisite knowledge



Refer to Organisa
tion of DNA in
prokaryotes
and
eukaryotes
in

Unit 1 to
remind students about the existence of circular chromosomes.



Students will
probably

be aware of the use of genetic engineering for the
production of
insulin
,
factor
VIII

and
human growth hormone
,

and s
hould
therefore be familiar with the role of plasmids and the process at a basic
level.

New content areas



Use of
recombinant
DNA
technology
to create enzymes
, genetically modified
food
s

and
pharmaceuticals and its future role in gene therapy.



Examples of

species commonly used for genetic engineering
,

such as
E.

coli
,

and reasons for their suitability.



When the gene for a protein is cloned, it is placed on a plasmid adjacent to a
region where the expression of genes can be controlled easily.



Structure of
plasmids/vectors.



Use of endonucleases and ligase during the process of genetic engineering
.



Yeast as an alternative to bacteria.

Background information



The field of genetic engineering involves the isolation, manipulation and
expression of genetic mater
ial.
Genetic engineering is a rapidly growing
technology and it is thought that it will have profound effects on our
everyday lives. Some examples of how it may affect us are:

-

In the field of medicine it may improve the diagnosis and cure of
hereditary def
ects and disease.

-

It is being used for the development of new drugs and vaccines for use by
humans and animals.

-

In agriculture it is being used to improve food production.

-

It is being used to monitor and reduce environmental pollution.



The process commonly

utilises bacterial cells and their plasmids. Foreign
genes can be inserted into isolated plasmids
,

which are returned to the
bacterial cells. The cells reproduce, cloning the recombinant DNA as the
cells replicate their plasmids. Under suitable conditions
, the bacterial culture
will produce the protein encoded by the foreign gene.



Genetic engineering requires three biological ‘tools’.



Enzymes to cut DNA
:
The f i rst st ep i n many genet i c engi neeri ng
processes is t he i sol ati on of DNA f rom cel l s. When puri f ied

DNA has
METABOLISM IN MICROORGANISMS

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UNIT 2: METABOLISM IN MICROORGANISMS

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© Learning and Teaching Scotland 2011

been obtained it is cut into smaller fragments using
restriction
endonucleases. These enzymes were discovered in the late 1960s and
work by cutting up DNA.
The
y

recognise

and cut short specific
sequences (between
four

and
eight

base pairs) within
DNA. One of the
most commonly used restriction enzymes is called EcoR1. It recognises
the following
six
-
base pair DNA sequence:


5′
GAATTC
3′

3′
CTTAAG
5′



EcoR1 then cuts the DNA sequence as follows:




5′
G

AATTC
3′



3′
CTTAA

G
5′



When EcoR1 cuts DNA it produces two double
-
stranded fragments, but
the cuts do not occur at the same position. Instead the cut is staggered
by four

nucleotides, so that the DNA fragments have single
-
stranded
overhangs (known as sticky ends). If another piece of DNA is cut with
the same enzyme and so has the same sticky ends, the pieces of DNA
can be j oined together by base pairing between the sticky
ends. Genes
of interest and suitable vectors are treated with the same endonucleases
to create complementary sticky ends
,

which are then combined using
DNA ligase to form recombinant DNA.


2.

A vector or transfer agent such as a plasmid
:
Cloni ng vect ors ca
n be
mani p
ul at ed so t hat t hey have t he
fol l owi ng charact erist i cs:

(a)

They can be cut wi t h rest ri ct i on enzymes and forei gn DNA
sequences (cut wi t h t he same rest ri ct i on enzymes) can be i nserted
i nt o t hem usi ng an enzyme cal l ed
DNA l i gase
.

(b)

Ant i bi ot ic resist ance
marker genes can be added t o t hem. These
genes code for prot ei ns that bre
ak down
ant i bi ot ics. If a cl oni ng
vect or i s i nsert ed i nt o a mi croorgani sm, t he mi croorgani sm gai ns
t he ant i bi ot ic resist ance

gene and so i s abl e t o grow i n t he
presence of t hi s anti bi
ot ic. The mi croorgani sm becomes resi st ant
t o t he anti bi oti c and can be easi l y i dent ifi ed.

(c)

Some cl oni ng vect ors cont ai n part of t he lac operon. Thi s is used
t o cont rol t he

expressi on of t he forei gn DNA
sequences. The
forei gn DNA i s t ranscri bed and t rans
lat ed onl y when t he l ac
operon i s swi t ched on.



Aft er a forei gn sequence of DNA has been i nserted i nt o a cl oni ng
vect or usi ng DNA l i gas
e, t he cl oni ng vect or i s mi xed
wi t h t he
mi croorgani sm i nt o whi ch i t i s t o be t ransformed. Some of t he
METABOLISM IN MICROORGANISMS

UNIT 2: METABOLISM IN MICROORGANISMS

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© Learning and Teaching Scotland 2011

microorganisms wil
l take up the cloning vector, some will not. To
separate the transformed microorganism from those that are not,
i
t

is
grown in media containing the antibiotic to which the transformed
microorganism has acquired resistance. The transformed
microorganism has

the cloning vector that has the antibiotic resistance
gene, so it is able to grow in the presence of the antibiotic.


Any microorganism that does not possess the cloning vector is unable
to grow in this medium.


The transformed microorganism is isolated f
rom the medium and
transferred to another medium where it is allowed to

reproduce and
grow in large quantities. Each new microorganism that is produced is
genetically identical to the original transformed microorganism. Each
genetically identical microorga
nism is called a
clone
. The process of
producing lots of genetically identical microorganisms is known as
cloning
.


3.

An appropriate host cell for the recombinant DNA
:

Transformation is
the name used to describe the process when a foreign sequence of DNA
(such as a gene or cDNA)

is introduced into microorganisms such as
bacteria and yeast. Two microorganisms that are commonly used in

transformations are the bacterium
E.

coli
and the yeast
S. cerevisiae
.
Both microorganisms are single
-
celled organisms that
have fast
reproduction rates and thus are quick growing. This makes them ideal
for large
-
scale production in industrial fermenters.



E.

coli
:

This is a prokaryote that is often used as a recipient for foreign
DNA.

Large sequences of foreign DNA can be ins
erted into
E.

coli
using a

plasmid. The DNA is transcribed and translated
,

and it is
possible for the

protein coded for
by the foreign DNA to account for
60% of the total

protein produced by the bacterial cell.
E.

coli
is

rel ati vel y easy t
o
transform. Whil
e there are many advantages of using
E.

coli
, there are some disadvantag
es


mainl y due to the fact
that it is
a prokaryote and the foreign protein produced may originally have
come from a eukaryote.


There are some
disadvantages
of
E. coli
.
The foreign pr
otein produced
is not always secreted easily from
E.

coli
. This may be due to
E.

coli
not being able to
carry out modifications to the protein after it is made,
for example addition of sugar groups. If the protein is

not
secreted by
the bacterium, it cause
s problems for the biotechnologist as
E.

coli
must be
harvested, the bacterial cells
broken open (lysed) and the
protein purified. This increases the production costs.
E.

coli
does n
ot
always fold the
foreign protein into its natural
three
-
di mensional

shap
e.
This causes the protein to be inactive.


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UNIT 2: METABOLISM IN MICROORGANISMS

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© Learning and Teaching Scotland 2011


S. cerevisiae
:

This is a eukaryote (yeast) that can be used instead of
E.

coli
as the

recipient for foreign DNA.

Since it is eukaryotic, it can fold
proteins into their
three
-
dimensional

shape
,

which allows the
proteins
t
o be active. Foreign proteins
made by
S. cerevisiae

are secreted from
the cell
because

S. cerevisiae
can carry out post
-
t ranslational
modificati
ons (eg it
can add sugar groups to proteins)
,

which allows the
proteins to cross the cell wall. Thus p
roteins secreted by
S. cerevisiae

can be extracted from the culture medium.

Identification of key concepts



Recombinant DNA technology allows the transfer of plan
t

or animal gene
sequences to
microorganisms to produce plant or animal proteins.



Useful gene
s that
that remove inhibitory controls or amplify specific
metabolic steps in a pathway can be introduced to increase yield.



Restriction endonucleases cut target sequences of DNA
,

leaving sticky ends.
Treatment of vectors with the same restriction endonucl
ease forms
complementary sticky ends
.



Ligase combines complementary sticky ends and seals foreign DNA into the
plasmid.



Suitable microorganisms for transformation include bacteria such as
E.

c
oli

and yeast such as
S.
cerevisiae
.

Identification of particu
lar areas of difficulty

Clear visual aids should be used to illustrate the action of endonucleases and the
production of sticky ends as students may find the concept difficult to
understand.
Th
e web l i nk bel ow
provi des

a narrat ed ani mat i on sequence.

Li nk
s t o websi t es
,
animations
, P
ower
P
oints
,
audio or video files etc

http://highered.mcgraw
-
hill.com/sites/0072437316/student_view0/chapter16/animations.
html#

(whole
series of
biotechnology
ani mations
)
.

Co
-
operative Learning Activities 1 and 5

Other useful information to stimulate interest

http://www.sciencedaily.com/ne
ws/plants_animals/genetically_modified/


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© Learning and Teaching Scotland 2011

(c)

Ethical considerations in the use of microorganisms


Links to prior/prerequisite knowledge

Student
s will have already discussed the ethics of stem cell research and
sources of stem cells (refer to 2

(ii) Res
earch and therapeutic value of stem
cells) and may have carried out the suggested
case study
related to this
outcome.

New content areas



Consideration of the hazards involved in genetic engineering processes.



The p
olicies and practices in place to contro
l risks associated with genetic
engineering.

Background information



The earliest concerns around genetic engineering were that genetic
manipulations could create hazardous new pathogens, which might escape
from the laboratory. This led to the introductio
n of formal guidelines
administered by agencies such as the Food and Drug Administration

(
FDA
)
in the US and the Medicines and Healthcare
products
Regulatory Agency

(
MHRA
) in the UK. Today governments throughout the world grapple with
how to promote the po
tential benefits of genetic engineering while ensuring
that its products are safe.



With new medical products the main cause for concern is the potential for
harmful side effects. Hundreds of new genetically engineered vaccines,
diagnostic kits and drugs aw
ait government approval. Before considered for
general marketing,
each

substance must pass exhaustive tests in laboratory
animals and humans.



In the case of environmental problems
,

such as oil spills or chemical wastes
that threaten our soil, water and ai
r
,

genetically engineered organisms may
be part of the solution, but their own impact on the environment must be
considered before they are widely used.



There have been concerns that genetically engineered crop plants could
potentially become ‘superweeds’
if they have been engineered to have
resistance to herbicides, disease or pests and escape into the wild to overrun
native species.



Concerns over
genetically modified

foods have been high profile in the
media and
the
issues raised have included
:

-

the
appear
ance of new allergens

-

increased antibiotic resistance

-

the
creation of brand new disease
-
causing organisms, made up of genetic
material from many different species
.

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© Learning and Teaching Scotland 2011



Ethical considerations as well as concerns about potential environmental and
health hazards
will
probably

slow the application of genetically engineered
products. There is always a danger that too much regulation will stifle
potential benefits,
but

the nature of the work clearly requires caution. The
challenge seems to lie in striking a safe but
productive balance.

Identification of key concepts



What are the risks associated with genetic engineering?



How are these risks managed?



What ethical issues have been raised?

Identification of particular areas of difficulty



While it is important that
s
tudent
s are able to form their own opinions on this
topic, they must also be able to appreciate the debate as a whole and
communicate the issues obj ectively.

Links
to
sources of further information

http://www.beep.ac.uk/content/index.php

Links to websites
,
animations
, P
ower
P
oints
,
audio or video files etc

http://www.who.int/foodsafety/publications/biotech/
20questions/en/index.html

http://www.mhra.gov.uk/index.htm

http://www.fda.gov/

http://www.geneticallymodified
foods.co.uk/

Other useful information to stimulate interest

http://www.hse.gov.uk/biosafety/gmo/index.htm

http://www.geneticallymod
ifiedfoods.co.uk/

DVD: Science in Focus, The Virtual Body: Genetic Engineering. Available to
buy at
www.channel4.com/learning

or to view on Teacher’s TV
(
http://www.teachers.tv/series/science
-
in
-
focus
-
t he
-
vi rt ual
-
body
)

Co
-
operative Learning Activity 2.