important biological molecules

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Overview: The Molecules of Life All living things made of 4 classes of biological molecule: carbohydrates, lipids, proteins nucleic acids Macromolecules - large molecules composed of thousands of covalently connected atoms Molecular structure and function are inseparable © 2011 Pearson Education, Inc.

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Macromolecules are polymers, built from monomers Polymer - long molecule consisting of many similar repeating units (building blocks) ……. called monomers 3 of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids © 2011 Pearson Education, Inc.

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Dehydration reaction: building a polymer Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond. Longer polymer 1 2 3 4 1 2 3

Wingdings:

Hydrolysis: breaking down a polymer Hydrolysis adds a water molecule, breaking a bond. 1 2 3 4 1 2 3

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Carbohydrates - fuel and building material Carbohydrates - sugars and polymers of sugars Simplest carbohydrates = monosaccharides ( monomer single sugars) serves as major fuel for cells and a building material Carbohydrate macromolecules (“complex carbs”) = polysaccharides ( polymers of many sugar building blocks) used for storage and structure © 2011 Pearson Education, Inc.

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Sugars Monosaccharides - molecular formulas are usually multiples of CH 2 O Glucose ( C 6 H 12 O 6 ) is the most common monosaccharide (others include, ribose, fructose) Monosaccharides are classified by……… location of the carbonyl group (C=O)…… The number of carbons in the carbon skeleton © 2011 Pearson Education, Inc.

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Figure 5.3a Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Glyceraldehyde Trioses: 3-carbon sugars (C 3 H 6 O 3 ) Dihydroxyacetone

Overview: The Molecules of Life:

Figure 5.3b Pentoses: 5-carbon sugars (C 5 H 10 O 5 ) Ribose Ribulose Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Macromolecules are polymers, built from monomers:

Figure 5.3c Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Hexoses: 6-carbon sugars (C 6 H 12 O 6 ) Glucose Galactose Fructose

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Figure 5.4 1 2 3 4 5 6 6 5 4 3 2 1 1 2 3 4 5 6 1 2 3 4 5 6 In aqueous solution - many sugars form rings

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Figure 5. UN04 Disaccharide - join two monosaccharides covalent bond is a glycosidic linkage

Carbohydrates - fuel and building material:

Polysaccharides - polymers of sugars for storage and structure The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages © 2011 Pearson Education, Inc. Starch Glycogen Cellulose Chitin

Sugars:

Chloroplast Starch granules Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose Starch - storage polysaccharide of plants made entirely of glucose monomers

Figure 5.3a:

Mitochondria Glycogen granules Humans and other vertebrates store glycogen mainly in liver and muscle cells Glycogen - storage polysaccharide in animals

Figure 5.3b:

polymer of glucose, like starch, but cellulose has different glycosidic linkages Cell wall Cellulose – structural polysaccharide major component of plant cell walls

Figure 5.3c:

 Glucose  Glucose 4 1 4 1 difference is based on two different ring forms of glucose: alpha (  ) and beta (  ) Starch and cellulose are both polysaccharides of glucose but have different glycosidic linkages

Figure 5.4:

Figure 5.7b Starch : 1–4 glycosidic linkage of  glucose monomers Cellulose : 1–4 glycosidic linkage of  glucose monomers 4 1 4 1

Figure 5. UN04:

Figure 5.7 Starch: 1–4 linkage of  glucose monomers Cellulose: 1–4 linkage of  glucose monomers  Glucose  Glucose 4 1 4 1 4 1 4 1 Starch polymers with  glucose are helical Cellulose - H on one strand can bond with OH groups on other strands Cellulose polymers with  glucose are straight

Polysaccharides -:

Cell wall Microfibril Cellulose microfibrils in a plant cell wall Cellulose molecules  Glucose monomer Figure 5.8 Parallel cellulose molecules are grouped into microfibrils which form strong building materials for plants

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Enzymes that digest starch by hydrolyzing  linkages can NOT hydrolyze  linkages in cellulose Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores , from cows to termites, have symbiotic relationships with these microbes © 2011 Pearson Education, Inc.

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Figure 5.9a CHITIN – polysaccharide that provides structural support exoskeleton of arthropods cell walls of many fungi

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LIPIDS - a diverse group of hydrophobic molecules Lipids – are NOT polymers The unifying feature of lipids is having little or no affinity for water Lipids are hydrophobic because  they consist mostly of hydrocarbons, which form nonpolar covalent bonds biologically important lipids are……… fats phospholipids steroids © 2011 Pearson Education, Inc.

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Fatty acid Glycerol Glycerol - 3-carbon alcohol with a hydroxyl group (OH) attached to each C Fatty acid - a carboxyl group (CHO 2 ) attached to a long carbon skeleton Fats: constructed from two types of smaller molecules

Figure 5.7b:

Figure 5.10 3 dehydration reactions in the synthesis of a fat Fatty acid Glycerol Ester linkage

Figure 5.7:

Figure 5.10b Fat molecule - triacylglycerol or triglyceride Ester linkages

Figure 5.8:

Figure 5.11 Saturated fat Unsaturated fat Stearic acid oleic acid Cis double bond causes bending. Unsaturated fatty acids - one or more double bonds……fluid at room temp Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds….. solid at room temp

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Hydrogenation - process of converting unsaturated fats to saturated fats by adding hydrogens Hydrogenating vegetable oils creates unsaturated fats with trans double bonds trans fats may contribute even more than saturated fats to cardiovascular disease © 2011 Pearson Education, Inc.

Figure 5.9a:

major function of fats is energy storage mammals store their fat in adipose cells Adipose tissue cushions vital organs and provides insulation © 2011 Pearson Education, Inc. some unsaturated fatty acids are not synthesized in the human body and must be supplied in the diet

LIPIDS - a diverse group of hydrophobic molecules:

Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails Hydrophilic head Hydrophobic tails 2 fatty acids and a phosphate group attached to a glycerol two fatty acid tails are hydrophobic phosphate group and its attachments form a hydrophilic head Phospholipids:

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Hydrophilic heads Hydrophobic tails WATER WATER When phospholipids are in water they self-assemble into a bilayer bilayer Phospholipids - the major component of all cell membranes Hydrophilic heads bilayer

Figure 5.10:

Steroids: Cholesterol (important steroid) - a component in animal cell membranes and a template for steroid hormones © 2011 Pearson Education, Inc. lipids characterized by a carbon skeleton consisting of four fused rings

Figure 5.10b:

Proteins : diversity of structures, and variety of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include: structural support storage transport cellular communications movement defense against foreign substances © 2011 Pearson Education, Inc.

Figure 5.11:

Figure 5.15b Storage proteins Ovalbumin Amino acids for embryo Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

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Figure 5.15c Hormonal proteins Function: Coordination of an organism’s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration High blood sugar Normal blood sugar Insulin secreted

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Figure 5.15d Muscle tissue Actin Myosin 100  m Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Phospholipids::

Figure 5.15e Defensive proteins Virus Antibodies Bacterium Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria.

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Figure 5.15f Transport proteins Transport protein Cell membrane Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes.

Steroids: :

Figure 5.15g Signaling molecules Receptor protein Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Proteins: diversity of structures, and variety of functions:

Figure 5.15h 60  m Collagen Connective tissue Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

Figure 5.15b:

Enzymatic proteins Enzyme Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Function: Selective acceleration of chemical reactions Enzymes - proteins that acts as a catalyst to speed up biochemical reactions Enzymes can perform their functions repeatedly workhorses that carry out the processes of life

Figure 5.15c:

Proteins are made of Polypeptides Polypeptides – polymer chains built from a set of 20 amino acids (monomers) Protein - a biologically functional molecule that consists of one or more polypeptides © 2011 Pearson Education, Inc.

Figure 5.15d:

Side chain (R group) Amino group Carboxyl group  carbon 20 Amino acids differ in their properties due to differing side chains (R groups) Amino Acids are Monomers

Figure 5.15e:

Figure 5.16 Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine ( I le or I ) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Polar side chains; hydrophilic Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged side chains; hydrophilic Acidic (negatively charged) Basic (positively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

Figure 5.15f:

Figure 5.16a Nonpolar side chains = hydrophobic amino acids Side chain Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine ( I le or I ) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

Figure 5.15g:

Figure 5.16b Polar side chains = hydrophilic amino acids Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q)

Figure 5.15h:

Figure 5.16c Electrically charged side chains = hydrophilic amino acids Acidic (negatively charged) Basic (positively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

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Polypeptide = polymer of amino acids linked by peptide bonds Polypeptides range in length from a few to more than a thousand monomers (amino acids) Each polypeptide has a unique linear sequence of amino acids © 2011 Pearson Education, Inc.

Proteins are made of Polypeptides:

Figure 5.17 Peptide bond New peptide bond forming Side chains Back- bone Amino end (N-terminus) Peptide bond Carboxyl end (C-terminus) Dehydration Reactions

Amino Acids are Monomers:

Groove Groove A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape A protein’s structure determines its function sequence of amino acids determines a protein’s three-dimensional structure

Figure 5.16:

Four Levels of Protein Structure Primary structure - its unique sequence of amino acids Secondary structure (found in most proteins) - consists of coils and folds in the polypeptide chain Tertiary structure - determined by interactions among various side chains (R groups) Quaternary structure - a protein consisting of multiple polypeptide chains © 2011 Pearson Education, Inc.

Figure 5.16a:

Amino acids Amino end Carboxyl end Primary structure of transthyretin Primary structure – sequence of amino acids Primary structure is determined by inherited genetic information

Figure 5.16b:

Figure 5.20b Secondary structure Tertiary structure Quaternary structure Hydrogen bond  helix  pleated sheet  strand Hydrogen bond Transthyretin polypeptide Transthyretin protein

Figure 5.16c:

Hydrogen bond  helix  pleated sheet Hydrogen bond secondary structure – hydrogen bonds between repeating units of the polypeptide backbone

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Hydrogen bond Disulfide bridge Polypeptide backbone Ionic bond Hydrophobic interactions and van der Waals interactions Interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Tertiary structure - interactions between R (side) groups of amino acids

Figure 5.17:

Quaternary structure Transthyretin protein (four identical polypeptides) Quaternary structure – 2 or more polypeptides form a macromolecule

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Hemoglobin: Heme Iron  subunit  subunit  subunit  subunit Hemoglobin - a globular protein consisting of 4 polypeptides (two alpha and two beta)

Four Levels of Protein Structure:

A slight change in primary structure can affect a protein’s structure and ability to function Sickle-cell disease - a single amino acid substitution in the protein hemoglobin causes abnormal shaped RBC © 2011 Pearson Education, Inc. Normal RBC Sickled RBC

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Figure 5.21 Primary Structure Secondary and Tertiary Structures Quaternary Structure Function Red Blood Cell Shape  subunit  subunit     Exposed hydrophobic region Molecules do not associate with one another; each carries oxygen. Molecules crystallize into a fiber; capacity to carry oxygen is reduced. Sickle-cell hemoglobin Normal hemoglobin Sickle-cell hemoglobin Normal hemoglobin 1 2 3 4 5 6 7 1 2 3 4 5 6 7    

Figure 5.20b:

Normal protein Denatured protein De n tu r t on Re n t r t on a a i a u a i Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel Loss of a protein’s structure is called denaturation A denatured protein is biologically inactive

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The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. Polypeptide Correctly folded protein An unfolded poly- peptide enters the cylinder from one end. The cap comes off, and the properly folded protein is released. 3 2 1 Chaperonins –assist in the proper folding of proteins

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Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins

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Nucleic acids : store, transmit, and express hereditary information Genes – “units of inheritance” …… sequence of nucleic acid that codes the amino acid sequence of a polypeptide Genes are made of DNA © 2011 Pearson Education, Inc. Two types of nucleic acids….. Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) Nucleic acids - polymers made of monomers called nucleotides

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Figure 5.25-1 Synthesis of mRNA mRNA DNA NUCLEUS CYTOPLASM 1 DNA directs synthesis of mRNA  and thru mRNA  controls protein synthesis

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Figure 5.25-3 Synthesis of mRNA mRNA DNA NUCLEUS CYTOPLASM mRNA Ribosome Amino acids Polypeptide Movement of mRNA into cytoplasm Synthesis of protein 1 2 3 Protein synthesis occurs at ribosomes

Figure 5.21:

Figure 5.26ab Sugar- phosphate backbone 5  end 5 C 3 C 5 C 3C 3  end Polynucleotide, or nucleic acid Phosphate group Sugar (pentose) Nitrogenous base 5 C 3 C 1 C Nucleotide = nitrogenous base + sugar + phosphate group Nucleic acids are polymers - polynucleotides Each polynucleotide is built of monomers - nucleotides

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Nitrogenous bases Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Adenine (A) Guanine (G) Sugars Deoxyribose (in DNA) Ribose (in RNA) Pyrimidines Purines DNA - sugar is deoxyribose ; RNA - sugar is ribose Two categories of nitrogenous bases: Pyrimidines - have a single 6-membered ring Purines - have a 6-membered ring fused to a 5-membered ring

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Figure 16.5 Sugar–phosphate backbone Nitrogenous bases Thymine (T) Adenine (A) Cytosine (C) Guanine (G) DNA nucleotide 3  end 5  end Adjacent nucleotides are joined by covalent bonds between the –OH group on the 3  carbon of one nucleotide and the phosphate on the 5  carbon of the next nucleotide Creates a sugar-phosphate backbone

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double helix DNA Single stranded RNA RNA molecules usually exist as single polynucleotide chains DNA consist of two polynucleotides spiraling around an imaginary axis, forming a double helix

Nucleic acids: store, transmit, and express hereditary information:

3.4 nm 1 nm 0.34 nm Hydrogen bond 3  end 5  end 3  end 5  end T T A A G G C C C C C C C C C C C G G G G G G G G G T T T T T T A A A A A A Hydrophobic bases on interior and negatively charged Phosphate groups far away from each other on hydrophilic exterior DNA: double strand helix

Figure 5.25-1:

Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 5  3  5  3  Complementary base pairing The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) with thymine (T) guanine (G) with cytosine (C) sequence of bases along a DNA or mRNA is unique for each gene

Figure 5.25-3:

DNA and Proteins as Tape Measures of Evolution One DNA molecule includes many genes The linear sequences of nucleotides in DNA molecules are passed from parents to offspring Two closely related species are more similar in DNA than are more distantly related species Molecular biology can be used to assess evolutionary kinship © 2011 Pearson Education, Inc.

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