Transcript Plant Biochemistry Biochemistry/Botany 621

Advance
Biochemistry
Introduction

Goals
• To cover aspects of biochemistry unique and
important to plants

Sometimes will involve bacterial biochemistry
• See some of the many biochemical pathways
critical to plants (Structures will be shown!)
• Hear about techniques important in plant
biochemistry

Molecular biology, mass spectrometry etc.
• Major emphasis on regulation

Grading
• Three one hour exams (in class, Tuesdays) (90
points each)
• 30 points for homework assignments
Textbook and reading
• Biochemistry &Molecular
Biology of Plants, ASPB
• Plant Biochemistry and
Molecular Biology by Hans-Walter
Heldt
• Readings from original literature
(PDFs supplied for UW-Madison
licensed materials)
Overall plan

Cell and Cellular Constituents
Cell structure and functions
Water and solutions
Carbohydrates
Fatty acids and lipids
Amino acids and protein
Enzymes
Vitamins and minerals

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Metabolism
Strategy for Processing of Nutrients in Plants
Applied Biochemistry
Overall plan

Photosynthesis
• Carbon metabolism, Electron transport
• Nitrogen, reduction and metabolism
• Carbon end products

Cell constituents
• Membranes, Cell walls

Cellular metabolism
• Ion pumps
• Protein turnover

Symbiotic nitrogen fixation
Regulation of Metabolism

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Plant cells do a wide range of
biochemistry
Regulation of metabolism
• Stoichiometric requirements (e.g. amino
acids)
• Avoid waste (energy that is needed
when it is needed)
• Directionality of metabolism

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Most reactions are reversible
The cytoplasm as a soup, how does
anything get done?
http://www.sigmaaldrich.com/img/assets/
4202/sigma_metabolic_path-new.pdf
Plant and animal biochemistry
sometimes differ
Methods of regulation
1.
2.
3.
Properties of enzymes
Compartmentation
Gene expression
Methods of regulation

Properties of enzymes
• Affinity for substrate, inherent catalytic
capacity
• Feedback
regulation/feedforward/loopgain
• Allosteric effects, competitive versus
non-competitive inhibition

Fructose 2,6-bisphosphate as an example
• Redox control of enzymes (vicinal
cysteines can become cystine)
• pH and Mg regulation

Especially chloroplast enzymes
Methods of regulation

Properties of enzymes (Posttranslational regulation)
• Phosphorylation

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Protein kinases and phosphatases
Turns enzymes on or off, can affect
sensitivity to effectors (SPS)
• Fatty acids

Palmitic acid in a regulatory way, myristic
acid is non-regulatory
• Prenylation
Anchoring proteins to
membranes
Buchannan et al. (ASPB book) Fig. 1.10 page 9
Methods of regulation

Cellular compartmentation
• Hallmark of eukaryotic cells
• Oxygen reactions mostly in
mitochondria and chloroplasts
• Chloroplasts – more generally
plastids – are what make plants
unique


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Cell walls, vacuoles also distinctive but
not unique
Plastids are biochemical powerhouses
I hope this course will leave you
The family of plastids
Buchannan et al. Fig. 1.44
Endosymbiosis



Well accepted that chloroplasts and
mitochondria were once free living
bacteria
Their metabolism is bacterial (e.g.
photosynthesis)
Retain some DNA (circular
chromosome)
• Protein synthesis sensitive to
chloramphenicol
• Cytosolic P synthesis sensitive to
Phylogeneti
c location of
chloroplasts
and
mitochondri
a
DNA for chloroplast proteins
can be in the nucleus or
chloroplast genome
Buchannan et al. Fig. 4.4
Import of
proteins
into
chloroplas
ts
Buchannan et al. Fig. 4.6
Biochemistry inside plastids


Photosynthesis – reduction of C, N,
and S
Amino acids, essential amino acid
synthesis restricted to plastids
• Phenylpropanoid amino acids and
secondary compounds start in the
plastids (shikimic acid pathway)
• Site of action of several herbicides,
including glyphosate
• Branched-chain amino acids
Biochemistry inside plastids
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Carotenoids – source of vitamin A
Thiamin and pyridoxal, B vitamins
Ascorbic acid – vitamin C
Tocopherol – vitamin E
Phylloquinone (an electron accepttor
in PS I – vitamin K)
Photorespiration is highly
compartmentalized
Buchannan et al. Fig. 1.40
Methods of regulation

Gene expression
• Normally slow relative to metabolic
control that will be discussed most of
the time in this course
• Allows metabolism to be changed in
response to environmental factors
• Transcriptional control most common

Sometimes variation in transcription rate
not reflected in enzyme amount
• Translational control also found

No change in mRNA levels but changes in
Gene structure relevant to metabolic
regulation
Promoters
Exploring metabolism by
genetic methods

Antisense – what happens when the
amount of an enzyme is reduced
• not clear how antisense works

Knockouts
• Often more clear-cut since all of the enzyme is
gone
• Use of t-DNA, Salk lines

Overexpression
• Use an unregulated version of the protein or
express on a strong promoter
• Sometimes leads to cosuppression

RNA interference
• 21 to 26 mers seem very effective in
regulating translation
What do we expect for the
reaction of metabolism to
changes in amount of an
enzyme?
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Is subtracting 50% likely to give exactly
the opposite result as adding 50%?
Are there threshholds?
Are there optimal amounts?
Are there compensatory pathways?
Are there compensatory regulatory
mechanisms?
Kacser H, Porteous JW. Control of
metabolism: what do we have to
measure. Trends Biochem.Sci.