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-