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Biochemistry (20 Photosynthesis and Carbohydrate Synthesis in Plants…
Biochemistry
20 Photosynthesis and Carbohydrate Synthesis in Plants
Evolution of Oxygenic Photosynthesis
Carbon-Assimilation Reactions
Carbon Dioxide Assimilation Occurs in Three Stages
Introduction
Photosynthetic organisms use ATP and NADPH from light-dependent reactions to synthesize thousands of components that make up the organism
Plants can reduce CO2 to produce trioses, precursors to cellular components
Green plants have enzymatic machinery in their chloroplasts to perform
CO2 assimilation
conversion of CO2 to simple, reduced compounds
CO2 / carbon fixation
is the incorporation of CO2 into the three-carbon triose phosphate
3-phosphoglycerate
ATP Synthesis by Photophosphorylation
Photorespiration and the C4 and CAM Pathways
Photochemical Reaction Centers
Biosynthesis of Starch, Sucrose, and Cellulose
Light Absorption
introduction
photophosphorylation
resembles oxidative phosphorylation because an electron transfer chain enables proton pumps to generate a transmembrane potential to power ATP synthesis
H2O is the electron donor and NADPH is formed, opposite of oxidative phosphorylation
electrons/protons move in opposite direction from oxidative phosphorylation
water is a poor electron donor, so photosynthesis needs the energy input from light to create a good electron donor
and
a good electron acceptor
electrons flow from donor through membrane-bound carriers, including
quinones
and iron-sulfur proteins
cytochromes
while protons are pumped across the membrane
electron transfer/proton pumping is catalyzed by membrane complex like complex III in mitochondria
p 595 fig 3
Chloroplasts Are the Site of Light-Driven Electron Flow and Photosynthesis
chloroplasts
perform
light-dependent reactions
and carbon-assimilation reactions
outer membrane is permeable to small molecules and ions
inner membrane encloses the
stroma
, analogous to the matrix in mitochondria
aqueous phase containing most enzymes required for carbon-assimilation reactions
Integration of Carbohydrate Metabolism in Plants
Introduction
ATP synthesis coupled to the light-driven flow of electrons to oxygen
Anabolic pathways
use chemical energy in the form of
ATP and
NADH
to synthesize cellular components from percursors
or NADPH
are generally reductive
Catabolism and anabolism are balanced, and proceed simultaneously in steady state
photosynthesis
CO2 + H2O + light/ATP/NAD(P)H ==> CH2O + O2
respiration
CH2O + O2 ---> CO2 + H2O + ATP
This chapter begins with photosynthesis
then covers the conversion of trioses from the Calvin cycle to sucrose and starch
and finally how carbohydrate metabolism is integrated in a plant cell and the plant body
analogous to glycogen synthesis in animals
plant cell wall cellulose synthesis
encompasses two processes
light-dependent reactions (LDR)
light energy :arrow_forward: ATP and NADPH
and
carbon-assimilation/fixation reactions (CAR/CFR)
Calvin cycle
ATP/NADPH reduce CO2 to form triose phsphates
photorespiration is an unproductive side reaction, plants can avoid this
oxygenic photosynthesis evolved about 2.5 billion years ago
Chapter 8 - 14
14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
Gluconeogenesis
Feeder Pathways for Glycolysis
Pentose Phosphate Pathway of Glucose Oxidation
Glycolysis
Fates of Pyruvate under Anaerobic Conditions: Fermentation
13 Bioenergetics and Biochemical Reaction Types
12 Biosignaling
11 Biological Membranes and Transport
Membrane Dynamics
Solute Transport across Membranes
The Composition and Architecture of Membranes
10 Lipids
Lipids as Signals, Cofactors, and Pigments
Working with Lipids
Structural Lipids in Membranes
Storage Lipids
introduction
fats and oils are derivatives of fatty acids
comes from hydrocarbon derivatives
this section covers structures and nomenclature of fatty acids
triacylglycerols and waxes are two types of FA containing compounds
Fatty Acids Are Hydrocarbon Derivatives
FA are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons long
branched and unbranched, saturated and unsaturated, rings, or hydroxyl groups
nomenclature specifies chain length and number of double bonds
length:bonds palmitic acid is 16:0
oleic (octadecenoic) acid is 18:1
the carboxyl carbon is the first carbon
double bonds are designated delta:small_red_triangle: with superscript number representing the lower numbered carbon
the most commonly occurring FA have an even number of carbons in an unbranched chain of 12 to 24 carbons
the even number comes from biosynthesis with acetate units
in most monosaturated FA the double bond is at C9, and any additional double bonds are at C12 and C15
arachadonic acid is an exception at C5,8,11, and 14
double bonds are almost never conjugated; always separated by a methylene group
double bonds are always cis
polyunsaturated fatty acids (PUFAs) have a double bond at C3 (from the methyl end)
the first carbon from the methyl end is omega :recycle: 1
Introduction
The common feature of lipids is their insolubility in water
Lipids are as diverse in their function as they are in their chemistry
fats and oils are stored energy
phospholipids and sterols are present in membranes
others are enzyme cofactors, electron carriers, pigments, protein anchors and chaperones, emulsifying agents, and hormones
This chapter introduces lipids of each type organized by function
can be organized into 8 categories of chemical structure
9 DNA-Based Information Technologies
8 Nucleotides and Nucleic Acids
Nucleic Acid Chemistry
Other Functions of Nucleotides
Nucleic Acid Structure
Some Basics
Chapter 1 - 7
7 Carbohydrates and Glycobiology
Carbohydrates as Informational Molecules: The Sugar Code
Polysaccharides
Working with Carbohydrates
Monosaccharides and Disaccharides
Glycoconjugates: Proteoglycans, Glycoproteins, and Glycosphingolipids
6 Enzymes
Enzyme Kinetics as an Approach to Understanding Mechanism
Examples of Enzymatic Reactions
How Enzymes Work
Regulatory Enzymes
An Introduction to Enzymes
5 Protein Function
Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobins
Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors
Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
4 The Three-Dimensional Structure of Proteins
Protein Tertiary and Quarternary Structure
Protein Denaturation and Folding
Protein Secondary Structure
Overview of Protein Structure
3 Amino Acids, Peptides, and Proteins
Working with Proteins
The Structure of Proteins: Primary Structure
Peptides and Proteins
Amino Acids
2 Water
Buffering against pH Changes in Biological Systems
Water as a Reactant
Ionization of Water, Weak Acids, and Weak Bases
The Fitness of the Aqueous Environment for Living Organisms
Weak Interactions in Aqueous Systems
1 The Foundations of Biochemistry
Physical Foundations
Genetic Foundations
Chemical Foundations
Evolutionary Foundations
Cellular Foundations
Bacterial and Archaeal Cells Share Common Features but Differ in Important Ways
Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study
Organisms Differ Widely in Their Sources of Energy and Biosynthetic Precursors
The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic
Organisms Belong to Three Distinct Domains of Life
Cellular Dimensions Are Limited by Diffusion
In Vitro Studies May Overlook Important Interactions among Molecules
Cells Are the Structural and Functional Units of All Living Organisms
Cells Build Supramolecular Structures
Introduction
Life arose about 4 billion years ago
Simple microorganisms with the ability to extract energy from chemical compounds, and, later, from sunlight
use simple compounds and elements to make more complex
biomolecules
Biochemistry
asks how inanimate molecules interact to maintain and perpetuate life governed solely by the physical and chemical laws that govern the nonliving universe
asks how the properties of living organisms arise from thousands of different biomolecules
describes in molecular terms the structures, mechanisms, and chemical processes of life
has applications in medicine, agriculture, nutrition, etc
What attributes distinguish organisms from inanimate matter?
A high degree of chemical complexity and microscopic organization
Systems for extracting, transforming, and using energy from the environment
Defined functions for each of an organism's components and regulated interactions among them
Mechanisms for sensing and responding to alterations in their surroundings
A capacity for precise self-replication and self-assembly
A capacity to change over time by gradual evolution
23 Hormonal Regulation and Integration of Mammalian Metabolism
Hormonal Regulation of Fuel Metabolism
Obesity and the Regulation of Body Mass
Tissue-Specific Metabolism: The Division of Labor
Obesity, Metabolic Syndrome, and Type 2 Diabetes
Hormones: Diverse Structures for Diverse Functions
Hormones Act through Specific High-Affinity Cellular Receptors
All hormones bind to highly specific receptors inside or outside target cells with high affinity
Different cell types have different combinations of receptors, different intracellular targets, different responses, to either the different or the same hormones
The Detection and Purification of Hormones Requires a Bioassay
Introduction
Hormones
are small molecules or proteins produced in one tissue, released into the bloodstream, and carried to other tissues, where they induce cellular activity
Nitric oxide (NO) acts locally, and short-lived, on neighboring cells
Nearly all processes in a complex organism is regulated by several hormones, including blood pressure and volume, electrolyte balance, development, sexual differentiation, reproduction, hunger, digestion, etc.
this section covers detection and measuring of hormones and their interactions, with a representative selection of hormones
Coordination of metabolism is accomplished with the
neuroendocrine system
this section emphasizes hormone action, but most mechanisms are also applicable to neurotransmitter action
signals start from cells detecting a change in the organism's conditions, which then release chemical messengers that bind to other cells either near or far away
Neuronal signaling uses neurotransmitters as chemical messengers (like acetylcholine), which may travel only to the next adjacent neuron
In hormonal signaling, the chemical messengers are hormones, operating through the bloodstream between cells close or far apart
these two signaling mechanisms are very similar aside from this anatomical difference; a single molecule can act as both a neurotransmitter and a hormone (like epinephrine and norepinephrine, which act at particular synapses and at neuromuscular junctions, or in liver or muscle metabolism)
Introduction
To fully understand metabolic pathways, it is important to consider not only the context on the cellular level but also of the whole organism
Division of labor amongst many different cell types is one of the essential characteristics of multicellular organisms
Different cells have different metabolic requirements, and are met with hormonal and neuronal signals, optimizing allocation of fuel
This chapter focuses on specialization of metabolism in mammalian organs and tissues, and metabolism of the whole organism
First, the broad range of hormones and hormonal mechanisms
Then tissue-specific functions regulated by hormonal mechanisms
Nutrient distribution, role of the liver, metabolic cooperation between organs
insulin, glucagon, epinephrine in muscle, liver, and adipose tissue
other hormones in adipose, muscle, gut, and brain
long-term regulation of body mass
and finally, obesity in development of metabolic syndrome and diabetes
allosterism and cooperate activity
19 Oxidative Phosphorylation
Regulation of Oxidative Phosphorylation
Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis
ATP Synthesis
Mitochondrial Genes: Their Origin and the Effects of Mutations
The Mitochondrial Respiratory Chain
Mitochondrial Complexes Associate in Respirasomes
Other Pathways Donate Electrons to the Respiratory Chain via Ubiquinone
Electron Carriers Function in Multienzyme Complexes
The Energy of Electron Transfer Is Efficiently Conserved in a Proton Gradient
Electrons Pass through a Series of Membrane-Bound Carriers
respiratory chain consists of a series electron carrier prosthetic proteins
there are three types of electron transfers in oxidative phosphorylation
direct transfer, as in iron reduction
as a hydrogen atom H+ + e-
as a hydride ion :H-
In addition to NAD and flavoproteins, there are three other electron carriers
ubiquinone
iron-containing proteins
cytochromes
iron-sulfur proteins
Reactive Oxygen Species Are Generated During Oxidative Phosphorylation
Electrons Are Funneled to Universal Electron Acceptors
The
respiratory chain
is a series of electron carriers
electrons are generated from catabolic pathways
dehydrogenases
universal electron acceptors
NAD+/NADP+
respiratory chain
neither NADH nor NADPH can cross the inner mitochondrial membrane, but their electrons are sindirectly
FMN/FAD
flavoproteins
contain tightly bound FMN or FAD
2 more items...
most are specific for NAD+
Plant Mitochondria Have Alternative Mechanisms for Oxidizing NADH
Introduction
The matrix contains
pyruvate dehydrogenase
fatty acid beta-oxidation pathway
citric acid cycle enzymes
amino acid oxidation
The inner membrane segregates intermediates and enzymes of cytosolic and matrix-bound metabolic pathways
transporters carry pyruvate, fatty acids, and amino acids (and their alpha-keto derivatives) into the matrix for access to citric acid cycle machinery
Introduction
All oxidative, energy-yielding metabolism (catabolism) of carbohydrates, fats, and amino acids converge at this final stage of cellular respiration
Fats
Oxidation
Amino acids
Carbohydrates
Energy of oxidation drives ATP synthesis in oxidative phosphorylation, accounting for the majority of ATP synthesized
Oxidative phosphorylation occurs in the mitochondria with huge protein complexes
Chemiosmotic theory
transmembrane differences in proton concentration are the reservoir for energy extracted from biological oxidation
The mechanism of oxidative phosphorylation has three defining components
The free energy made by this exergonic electron flow is coupled to the endergonic transport of protons across a proton-impermeable membrane
The transmembrane flow of protons back down their concentration gradient through proton channels provides the free energy ATP synthesis, catalyzed by ATP synthase
Electrons flow from electron donors through a chain of membrane-bound carriers to a final electron acceptor with a large reduction potential, O2
This chapter begins with a description of of the mitochondrial electron transfer chain,
path of electron flow
proton movements accompanied with electron flow
functional complex organization
then the enzyme complex that capture by rotational catalysis the energy of proton flow in ATP and the regulatory mechanisms that coordinate oxidative phosphorylation with the many catabolic oxidation pathways
The role of mitochondria in metabolism is so critical to cellular and organismal function, to neuronal and muscular function, and body weight. Mitochondria also act in thermogenesis, steroid synthesis, and apoptosis
16 The Citric Acid Cycle
Reactions of the Citric Acid Cycle
Regulation of the Citric Acid Cycle
Production of Acetyl-CoA (Activated Acetate)
17 Fatty Acid Catabolism
Oxidation of Fatty Acids
Ketone Bodies
Digestion, Mobilization, and Transport of Fats
18 Amino Acid Oxidation and the Production of Urea
Nitrogen Excretion and the Urea Cycle
Pathways of Amino Acid Degradation
Metabolic Fates of Amino Groups
15 Principles of Metabolic Regulation
21 Lipid Biosynthesis
22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
24 Genes and Chromosomes
25 DNA Metabolism
26 RNA Metabolism
27 Protein Metabolism
28 Regulation of Gene Expression