Ch 5- bio 151

Large Biological Molecules

• Macromolecules are large polymers composed of monomers
• Polymers are long molecules consisting of many similar building blocks
• Monomers are repeating units that serve as building blocks
• Carbohydrates, proteins, and nucleic acids are polymers
• Lipids are not polymers or macromolecules

Synthesis and Breakdown of Polymers

• Enzymes are specialized macromolecules that speed up chemical reactions like making or breaking down polymers
• Dehydration reactions occur when two monomers bond together through the loss of a water molecule, forming a new bond
• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of a dehydration reaction.

The Diversity of Polymers

• A cell has thousands of different macromolecules
• Macromolecules vary among cells within an organism
• Macromolecules vary more within a species
• Macromolecules vary even more between species
• A huge variety of polymers can be built from a small set of monomers

Carbohydrates

• Carbohydrates include sugars and polymers of sugars
• Monosaccharides are simple sugars
• Carbohydrate macromolecules are polysaccharides
• Polysaccharides are polymers composed of many sugar building blocks

Sugars

• Monosaccharides have molecular formulas that are typically multiples of CH2O
• Glucose (C6H12O6) is the most common monosaccharide
• Monosaccharides are classified by
  • the location of the carbonyl group (as aldose or ketose)
  • the number of carbons in the carbon skeleton

Structures of Monosaccharides

• Though often drawn as linear skeletons, in aqueous solutions many sugars form rings
• Monosaccharides serve as a major fuel for cells and as raw material for building molecules

Disaccharides

• A disaccharide is formed when a dehydration reaction joins two monosaccharides
• The covalent bond between two monosaccharides is called a glycosidic linkage

Polysaccharides

• Polysaccharides, the polymers of sugars, have storage and structural roles
• The architecture and function of a polysaccharide are determined by its sugar monomers and the positions of its glycosidic linkages

Storage Polysaccharides

• Starch, a storage polysaccharide of plants, consists of glucose monomers
• Plants store surplus starch as granules within chloroplasts and other plastids
• The simplest form of starch is amylose
• Glycogen is a storage polysaccharide in animals
• Glycogen is stored mainly in liver and muscle cells
• Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases

Structural Polysaccharides

• The polysaccharide cellulose is a major component of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
• The difference is based on two ring forms for glucose: alpha (α) and beta (β)
• Cellulose molecules are straight and unbranched
• Some hydroxyl groups on the monomers of cellulose can hydrogen-bond with hydroxyls of parallel cellulose molecules

Chitin

• Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods.
• Chitin also provides structural support for the cell walls of many fungi

Lipids

• Lipids are the one class of large biological molecules that does not include true polymers
• Lipids mix poorly, if at all, with water
• Lipids consist mostly of hydrocarbon regions
• The most biologically important lipids are fats, phospholipids, and steroids

Fats

• Fats are constructed from two types of smaller molecules: glycerol and fatty acids
• Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon
• A fatty acid consists of a carboxyl group attached to a long carbon skeleton
• Fats separate from water because water molecules hydrogen-bond to each other, thus excluding fats
• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
• The fatty acids in a fat can be all the same, or of two or three different kinds

Fatty acids

• Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
• Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
• Unsaturated fatty acids have one or more double bonds
• Fats made from saturated fatty acids are called saturated fats and are solid at room temperature
• Most animal fats are saturated.
• Fats made from unsaturated fatty acids are called unsaturated fats or oils and are liquid at room temperature.
• Plant fats and fish fats are usually unsaturated

Functions of Fats

• The major function of fats is energy storage
• Humans and other mammals store their long-term food reserves in adipose cells
• Adipose tissue also cushions vital organs and insulates the body

Phospholipids

• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head
• When phospholipids are added to water, they self-assemble into double-layered sheets called bilayers
• At the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing toward the interior
• The phospholipid bilayer forms a boundary between the cell and its external environment

Steroids

• Steroids are lipids characterized by a carbon skeleton consisting of four fused rings
• Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized
• A high level of cholesterol in the blood may contribute to cardiovascular disease

Proteins

• Proteins account for more than 50% of the dry mass of most cells
• Some proteins speed up chemical reactions
• Other protein functions include defence, storage, transport, cellular communication, movement, and structural support
• Enzymes are proteins that act as catalysts to speed up chemical reactions
• Proteins are all constructed from the same set of 20 amino acids
• Polypeptides are unbranched polymers built from these amino acids
• The bond between amino acids is a peptide bond
• A protein is a biologically functional molecule that consists of one or more polypeptides
• Amino acids are organic molecules with amino and carboxyl groups
• Amino acids differ in their properties due to differing side chains, called R groups

Polypeptides

• Amino acids are linked by covalent bonds called peptide bonds
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to more than 1,000 monomers
• Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

Protein Structure and Function

• The specific activities of proteins result from their intricate three-dimensional architecture
• A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape
• The sequence of amino acids determines a protein's three-dimensional structure
• A protein's structure determines how it works
• The function of a protein usually depends on its ability to recognize and bind to some other molecule

Levels of Protein Structure

• The primary structure of a protein is its unique sequence of amino acids
• Secondary structure consists of coils and folds in the polypeptide chain
• Tertiary structure is determined by interactions among various side chains (R groups)
• Quaternary structure results when a protein consists of multiple polypeptide chains

Protein Folding

• It is hard to predict a protein's structure from its primary structure
• Most proteins probably go through several stages on their way to a stable structure
• Diseases such as Alzheimer's, Parkinson's, and mad cow disease are associated with misfolded proteins

###Determining Protein Structure

• Scientists use X-ray crystallography to determine a protein's structure
• Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization
• Bioinformatics is another approach to prediction of protein structure from amino acid sequences

Nucleic Acids

• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
• Genes consist of DNA, a nucleic acid made of monomers called nucleotides
• There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA (mRNA)
• Through mRNA, DNA controls protein synthesis
• This process is called gene expression
• Each gene along a DNA molecule directs synthesis of a messenger RNA (mRNA)
• The mRNA molecule interacts with the cell's protein-synthesizing machinery to direct production of a polypeptide
• The flow of genetic information can be summarized as DNA → RNA → protein

Components of Nucleic Acids

• Nucleic acids are polymers called polynucleotides
• Each polynucleotide is made of monomers called nucleotides
• Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups
• The portion of a nucleotide without the phosphate group is called a nucleoside
• There are two families of nitrogenous bases: pyrimidines (cytosine, thymine, and uracil); and purines (adenine and guanine)
• In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose
• Nucleotide = nucleoside + phosphate group

Nucleotide Polymers

• Nucleotides are linked together by a phosphodiester linkage to build a polynucleotide
• A phosphodiester linkage consists of a phosphate group that links the sugars of two nucleotides
• These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
• The sequence of bases along a DNA or mRNA polymer is unique for each gene

Structures of DNA and RNA Molecules

• DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix
• The backbones run in opposite 5' → 3' directions from each other; an arrangement referred to as antiparallel
• One DNA molecule includes many genes
• Only certain bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)
• This feature of DNA structure makes it possible to generate two identical copies of each DNA molecule in a cell preparing to divide
• RNA, in contrast to DNA, is single-stranded
• Complementary pairing can also occur between two RNA molecules or between parts of the same molecule
• In RNA, thymine is replaced by uracil (U), so A and U pair

Genomics and Proteomics

• Once the structure of DNA and its relationship to amino acid sequence was understood, biologists sought to "decode" genes by learning their base sequences
• The first chemical techniques for DNA sequencing were developed in the 1970s and refined over the next 20 years
• It is enlightening to sequence the full complement of DNA in an organism's genome
• The rapid development of faster and less expensive methods of sequencing was a side effect of the Human Genome Project
• Many genomes have been sequenced, generating large sets of data
• Bioinformatics uses computer software and other computational tools to deal with the data resulting from sequencing many genomes
• Analyzing large sets of genes or even comparing whole genomes of different species is called genomics
• A similar analysis of large sets of proteins, including their sequences, is called proteomics

DNA and Proteins as Tape Measures of Evolution

• Sequences of genes and their protein products document the hereditary background of an organism
• Linear sequences of DNA molecules are passed from parents to offspring
• We can extend the concept of "molecular genealogy" to relationships between species
• Molecular biology has added a new measure to the toolkit of evolutionary biology