Advance
Biochemistry
Introduction
Goals
• To cover aspects of biochemistry unique and important to plants

Sometimes will involve bacterial biochemistry
• To see some of the many biochemical pathways critical to plants
• To learn about regulation
Overall plan
Cell and Cellular Constituents
Metabolism
Mode of regulation
Applied Biochemistry
http://www.sigmaaldrich.com/img/assets/
4202/sigma_metabolic_path-new.pdf
Cell
 Unit from which living organisms are built
 It consists of a plasma membrane surrounding the cytoplasm, in
which a variety of structures may be present
Two basics types of Living Cells
Prokaryotic : Cells that have no internal, membrane-bounded
structures and no clearly defined nucleus
Eukaryotic : Cells that contain a nucleus surrounded by a
membrane, the nuclear envelope
Eukaryotic cells
 They have developed an internal system of membranes that
separates the cells into distinct areas, called organelle
 The organelles have specific biochemical function and allow more
ordered and directed metabolism to occur
 Multicellular eukaryotic organisms have evolved cells with very
specialized functions and structures which often associated in large
numbers to form clearly identifiable tissue
Component of eukaryotic cells
Plasma membrane
Cytoplasm
Nucleus
Cell walls
Ribosomes
Endoplasmic reticulum
Vacuoles and specialized vesicles
Mitochondria
Chloroplasts
Cytoskeleton
Plasma membrane
 a selectively permeable barrier that control the movement of
molecules into and out of the cells
Transport of essential nutrient required for growth and metabolism
 Hormone/receptor interactions
Cell recognition
Cytoplasm
 This is composed of the cytosol
 Glycolysis
Gluconeogenesis
 pentose phosphate pathways
 polysaccharide breakdown
Complex lipid breakdown
Fatty acid synthesis
Protein breakdown
Amino acid synthesis
Nucleus
 DNA synthesis
 RNA synthesis
 RNA processing
Cell walls
 it determines to a great extent the morphology and to some extent the
function of the cell
 It may directly involved in regulating cell expansion
Ribosomes
 Responsible for the synthesis of proteins
Endoplasmic reticulum
 It is divided in two parts: rough and smooth
 The rough ER is due to the present of ribosomes required for the synthesis of protein
 it is the site of synthesis of proteins destined to be secreted from the cell
 In the smooth ER occurs fatty acid elongation and desaturation, complex of lipid
synthesis and detoxification reactions
 Of the layer of smooth ER stacked golgi apparatus which is the site of carbohydrate
synthesis, glycoprotein synthesis, and packaging of cell product
Vacuoles and specialized vesicles
 vacuoles:
 Stored materials separated from the main biochemical process of the cells
 Pigment, toxic and waste material may be accumulate
 Maintenance of turgor
 Peroxisomes:
 Fatty acids oxidation,
 amino acids oxidation,
 Photorespiration
Mitochondria
 TCA cycle
Fatty acid oxidation
Amino acid oxidation
 gluconeogenesis
Synthesis of organelle protein
Chloroplasts
 Photosynthesis
Fatty acid synthesis
Complex lipid synthesis
Synthesis of some amino acids
Synthesis of organelle protein
Calvin cycle
Light reaction
Reduction of nitrate and sulphate
Part of photorespiration
Methods of regulation
 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 (Post-translational
regulation)
• Phosphorylation


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 nonregulatory
• Prenylation

Fanesylation (3 isoprenoids, 15 C) CaaX C-terminus
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



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





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?






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.