biochemistry focus: 1. biological structures interaction, organization and coordination of...
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BIOCHEMISTRYFocus:
1. Biological Structures
Interaction, organization and coordination of biomolecules
Chemical and 3D structures of biomolecules
Synthesis and degradation of biomolecules
2. Metabolism
Energy production, utilization and conservation
anabolism vs catabolism
3. Genetic Information
Transmission, expression and storage of genetic information
BIOCHEMISTRYDefinition:
the study of the chemistry of life
“The basic goal of the science of biochemistry is to determine how the collections of inanimate molecules that constitute living organisms interact with each other to maintain and perpetuate life.”
Lenhinger, Principles of Biochemistry
Biology and ChemistryBackground
Biology Prokaryotes vs EukaryotesOrganelle Functions
Chemistry Bonds
The tree of life
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Biomolecules
The Chemical Building Blocks of Life
Biologically important molecules
•Molecules that are important to cells!• Organic Compounds- made mostly of carbon, hydrogen and oxygen
Biomolecules – the building blocks of living cells
a. Carbohydratesb. Lipidsc. Proteinsd. Nucleic Acids
Organic Molecular Structure of Living Systems
These biomolecules or organic molecules are polymers.Most are macromolecules
Macro means largeA polymer consists of many identical subunits connected together
How are polymers made?
They are formed by a process called condensation – where units are linked and a water molecule is removed.
CondensationIt’s not just for the water cycle anymore
Macromolecules are constructed by covalently bonding monomers by condensation reactions where water is removed from the functional groups of the monomers
Dehydration synthesis (water is removed) A hydroxyl (-OH) from one monomer and a
hydrogen (-H) from another are removed Anabolic reaction
How are polymers broken down? They are broken down by adding a
water molecule through a process called hydrolysis.
Hydrolysis
Hydrolysis is the reverse of condensation Results in the break down of polymers Hydration reactions add water and break
bonds releasing energy
Macromolecules in Organisms
There are four categories of large molecules in cells:
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Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbohydrates Monosaccharides
Five carbon: Ribose Six carbon: glucose and fructose
•Disaccharides–Sucrose (table sugar)–Lactose (milk sugar)–Maltose (grain sugar)
•Polysaccharides–Starch–Cellulose–Glycogen
Molecular structure of various forms of glucose.
Monosaccharides:Called simple sugars
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Include glucose, fructose, & galactoseHave the same chemical, but different structural formulas
C6H12O6
Rings
In aqueous (watery) solutions, monosaccharides form ring
structures
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3. Polysaccharides These are macromolecules that have a
few hundred or thousands of monosaccharides linked together
They store a lot of energy and also provide structural support for cells
Examples: Starches – potatoes, wheat, corn, rice,
fruits of grasses Glycogen – animal starch – stored in
muscles and livers of vertebrates Cellulose – plant fiber – in cell walls – the
fiber in our diet Chitin – in exoskeletons of invertebrates
Polysaccharides
Complex carbohydrates
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Composed of many sugar monomers linked togetherPolymers of monosaccharide chains
Starch Starch is an example of a polysaccharide in plants
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Plant cells store starch for energy
Potatoes and grains are major sources of starch in the human diet
Cellulose chains Starch chain
GlycogenGlycogen is an example
of a polysaccharide in animals
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Animals store excess sugar in the form of glycogen
Glycogen is similar in structure to starch because BOTH are made of glucose monomers
cellulose
amylose (a starch)
glycogen
Dietary Cellulose
Most animals cannot derive nutrition from fiber
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They have bacteria in their digestive tracts that can break down cellulose
LIPIDS A diverse group of organic molecules
that are insoluble in water (nonpolar) and will only dissolve in nonpolar solvents like chloroform and benzene
Made of glycerol and fatty acids 3 groups
Fats Phospholipids Steroids
fats…….
Stores energy (actually stores 2x the energy as polysaccharides like starches)
Cushions vital organs in animals Insulates against heat loss Two types
Saturated fat – no double bonds between carbon atoms, solid at room temp, mostly animal fats – bacon, butter, lard
Unsaturated fats – one or more double bonds between carbon atoms, liquid at room temp, most plant fats – corn oil, olive oil
Triglycerides
Triglyceride
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Glycerol Fatty Acid Chains
Types of Fatty Acids
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Single Bonds in Carbon chain
Double bond in carbon chain
Fats in Organisms
Most animal fats have a high proportion of saturated fatty acids & exist as solids at room temperature (butter, margarine, shortening)
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Fats in Organisms
Most plant oils tend to be low in saturated fatty acids & exist as liquids at room temperature (oils)
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phospholipids……..
Major part of cell membranes “a phospholipid bilayer”
hydrophobic tails
hydrophilichead
steroids……
Cholesterol is an important steroid in the cell membrane – provides strength
Some develop into to vertebrate sex hormones
SteroidsThe carbon skeleton of steroids is bent to form 4 fused rings
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Cholesterol is the “base steroid” from which your body produces other steroids
Estrogen & testosterone are also steroids
Cholesterol
TestosteroneEstrogen
Lipids & Cell Membranes Cell membranes are
made of lipids called phospholipids
Phospholipids have a head that is polar & attract water (hydrophilic)
Phospholipids also have 2 tails that are nonpolar and do not attract water (hydrophobic)
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Proteins
Proteins are polymers made of monomers called amino acids
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All proteins are made of 20 different amino acids linked by peptide bond in different orders
Proteins are used to build cells, transport things across membrane,act as hormones & enzymes, and do much of the work in a cell
Amino group (basic)
Carboxyl group (acidic)
R group (20 kinds with distinct properties)
Linking Amino AcidsCells link amino acids together to make proteins
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The process is called condensation or dehydrationPeptide bonds form to hold the amino acids together
Carboxyl
Amino Side
Group
Dehydration Synthesis
Peptide Bond
•They are very folded and coiled.
•The function of the protein depends on the structure of the protein
Levels of Protein Structure
Proteins as Enzymes
Many proteins act as biological catalysts or enzymes
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Thousands of different enzymes exist in the body
Enzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction
Enzymes
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Their folded conformation creates an area known as the active site.
Enzymes are globular proteins.
The nature and arrangement of amino acids in the active site make it specific for only one type of substrate.
Enzyme + Substrate = Product
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Nucleic Acids
Two types - DNA and RNA These store and transmit hereditary
information Made of chains of nucleotides which are
made of a sugar, a nitrogenous base and a phosphate group
The sequence of the bases in the DNA or RNA determines the type of protein that is made
Bases in DNA and RNA
DNA Adenine Guanine Cytosine Thymine
• RNA– Adenine– Guanine– Cytosine– Uracil
BasesEach DNA nucleotide has one of the following bases:
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Thymine (T) Cytosine (C)
Adenine (A) Guanine (G)
–Adenine (A)
–Guanine (G)
–Thymine (T)
–Cytosine (C)
Nucleic Acids
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Nitrogenous base(A,G,C, or T)
Phosphategroup
Thymine (T)
Sugar(deoxyribose)
Phosphate
BaseSugar
Nucleic acids are polymers of nucleotides
Nucleotide
RNA – Ribonucleic Acid
Ribose sugar has an extra –OH or hydroxyl group
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It has the base uracil (U) instead of thymine (T)
Nitrogenous base(A,G,C, or U)
Sugar (ribose)
Phosphategroup
Uracil
Nucleotide – Nucleic acid monomer
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Comparing DNA and RNA
DNA stands for deoxyribonucleic acid – the plans for the actual proteins Remember proteins are used to build
cells and control processes in cells (enzymes)
RNA stands for ribonucleic acid – it is a copy of the DNA used for transferring a copy of the DNA to the ribosomes where the proteins are actually made
Comparing DNA and RNA
DNA is a double helix- a twisted ladder RNA is a single helix – one side DNA contains the bases Adenine,
Guanine, Cytosine and Thymine RNA contains the bases Adenine,
Guanine, Cytosine and Uracil DNA contains the sugar deoxyribose RNA contains the sugar ribose
DNA
Two strands of DNA join together to form a double helix
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Basepair
Double helix
Nucleotides, DNA, and RNA
Figure 2-18: RNA and DNA
ATP – Cellular Energy
ATP is used by cells for energy Adenosine triphosphate Made of a nucleotide with 3
phosphate groups
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Cellular Fuel
Monosaccharides are the main fuel that cells use for cellular work
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ATP
In Mitochondria
In Cytosol
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Macromolecules
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Macromolecules
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Carbohydrate Biomolecules: Carbon, Hydrogen & Oxygen
Figure 2-13-1: Carbohydrates
Carbohydrate Biomolecules: Carbon, Hydrogen & Oxygen
Figure 2-13-2: Carbohydrates
Lipids: Mostly Carbon and Hydrogen; little Oxygen
Figure 2-14: Lipids and lipid-related molecules
Combination Biomolecules Lipoproteins (blood transport molecules) Glycoproteins (membrane structure) Glycolipids (membrane receptors)
Figure 2-19: Chemistry summary
Nucleotides, DNA and RNA Composition
Base Sugar Phosphate
Transmit and store Information (genetic code) Energy transfer molecules
ATP Cyclic AMP NAD & FAD
metabolism is categorized into two types
Catabolism (biodegradation): larger molecules (nutrients and cell constituents) are broken down (often via exergonic reactions) to salvage (reuse) their components or/and to generate energy.
Anabolism (biosynthesis): The generation of biomolecules from simpler components (often via endergonic reactions).
metabolism is categorized into two types
Catabolism (biodegradation): larger molecules (nutrients and cell constituents) are broken down (often via exergonic reactions) to salvage (reuse) their components or/and to generate energy.
Anabolism (biosynthesis): The generation of biomolecules from simpler components (often via endergonic reactions).
Classification of organisms based on trophic (“feed”) strategies
Autotrophs—synthesize all cellular components from simple inorganic molecules (e.g, H2O, CO2, NH3, H2S).
Heterotrophs—Derive energy from oxidation of organic compounds (made by autotrophs).
Chapter 5
Metabolism in various living organisms allow carbon, oxygen and nitrogen to be cycled in the biosphere.
The cycling of matter is driven by the flow of energy in one direction through the biosphere!
Metabolism allows the cycling of C/O and the flow of energy in the biosphere
H2O
glucose
Producers Consumers
Metabolism also allows the cycling
of N in the biosphere
(NH4+)
NO3-
NO2-