The Building Blocks

Structure

1. Atom is the smallest unit of matter that has the chemical properties of an element

2. Atoms contain protons and electrons and neutrons

   1. Exception to this is hydrogen, which has no neutrons

3. Protons and neutrons have roughly the same mass: one atomic mass unit (amu) or Dalton

4. Electrons are not considered in atomic mass

5. Dimer- a molecule consisting of two identical molecules linked together

6. Most of the volume of an atom (more than 99%) is empty space

   1. Solid objects do not pass through each other because electrons around atoms repel each other

Number and mass

1. Atomic number is the number of protons

2. Number of protons and neutrons is the mass number

3. Atomic mass is the calculated mean of the mass number for its naturally occurring isotopes (often contains fraction)

Isotopes

1. Different forms of an element with different numbers of neutrons

2. Some isotopes emit neutrons, protons, and electrons

   1. These are radioactive isotopes, or radioisotopes

Electron shells and the Bohr model

1. Bohr model shows central nucleus and circular orbitals at specific distances

2. Octet rule: with the exception of the innermost shell, atoms are more stable energetically when they have 8 electrons in their valence shell

3. Electrons don’t orbit the nucleus like in Bohr’s model, but are found in electron orbitals

4. Each electron shell has subshells

   1. Subshells are designated s, p, d, and f with 1, 3, 5, and 7 orbitals respectively

      1. Orbitals can hold two electrons

   2. The nth shell will have n subshells

5. when adding an electron, it goes to the highest unfilled shell-- when more than one unfilled shells are present, add it to the one that has two fewer subshells filled than the one below it

6. Subshells are more stable when half full or full

7. All orbitals will get their first electrons before any get their second

8. Electron configuration is written as the highest shell, that shell’s subshell, and that subshell’s electrons

   1. For example, Neon (10 electrons) would be written as 1s2 2p2 2p6

Chemical reactions and molecules

1. Reactions occur when atoms bond or break apart

2. Substances before the reaction are called the reactants and the substances after the reaction are called the products

3. An arrow can be used to show a reaction

   1. E.g. 2H2O2 (hydrogen peroxide) → 2H2O (water) + O2 (oxygen)

4. Molecules with more than one type of element are called compounds

5. Molecules with one type of element are called homonuclear molecules

6. Some reactions are reversible

   1. When the concentration of product goes beyond a certain threshold, some of these products will be converted back into reactants

   2. Back and forth continues until equilibrium is reached

   3. This back and forth can be denoted with a double-headed arrow

7. Law of mass action-- rate of chemical reaction is proportional to the masses of the reacting substances

Ions and ionic bonds

1. Atoms form ions when they gain or lose electrons to become more stable

   1. Cations are positive ions formed by losing electrons

   2. Anions are negative ions formed by gaining electrons

      1. Anions have their elemental name altered to end in “-ide”

   3. This movement of electrons is called an electron transfer

      1. These can usually only happen simultaneously

   4. Ionic bonds are formed between ions with opposite charges

Covalent bonds and other bonds/interactions

1. 3 pairs of electrons may be shared at most

2. The more covalent bonds, the stronger the connection between atoms

3. Covalent bonds are bonds formed when electrons are shared

Metallic bonds

1. Metallic atom-- has a bunch of electrons on the outer shell that atom is “willing to give”

2. When many metallic atoms come together, they donate their electrons in a “shared electron pool,” making the atoms positive

3. The positive atoms become attracted to the negative “electron pool”

4. Metallic bonds make metals conductive and malleable

London dispersion forces

1. Weak attractions between atoms or molecules of any kind; depend on temporary imbalances in electron distribution

2. Because electrons are constantly moving, there will be moments where electrons are clustered together, forming a partial negative charge in one part and a partial positive charge in the other

3. A molecule with this imbalance can cause a similar charge redistribution in a nearby second molecule, and the molecules will attract because of the temporary charges

Hydrogen bonds and London dispersion forces are both examples of van der Waals forces-- intermolecular interactions that don’t involve covalent bonds or ions

1. Some textbooks use van der Waals forces only to refer to London dispersion forces

Water

1. Polarity

   1. The oxygen molecules in water are electronegative, causing a slightly positive charge on hydrogen and slightly negative charge on oxygen

   2. Opposite charges in water form hydrogen bonds

   3. Water attracts/dissolves other polar molecules (hydrophilic) and repels/does not dissolve nonpolar molecules (hydrophobic)

2. States

   1. Hydrogen bonds give water unique characteristics

      1. Freezing water pushes the molecules apart, making ice less dense than water

      2. Causes a layer of ice to rise to the top of water, which insulates and protects life in the water from freezing

      3. Ice crystals from freezing can rupture membranes

3. Heat Capacity

   1. Hydrogen bonds cause high specific heat

      1. Specific heat-- amount of heat absorbed/lost for one gram of substance to change one degree celsius

      2. One calorie-- the specific heat of water

      3. Kilocalorie-- 1,000 calories

      4. 
         

   2. High heat capacity disperses heat in bodies of animals

4. Heat of vaporization

   1. Water requires a lot of energy to become a gas due to hydrogen bonds

   2. As a result, water acts as a heat sink

   3. Below the boiling point, individual water molecules with enough energy can still evaporate

   4. Evaporative cooling-- as liquid evaporates, the surface that remains cools; used by many organisms (sweat) to maintain homeostasis of body temperature

5. Solvent properties

   1. Water’s polarity allows ions and polar molecules to dissolve easily, so it is often referred to as the “solvent of life” or “universal solvent”

   2. Molecules with charge will form hydrogen bonds with and be surrounded by water, forming a sphere of hydration or hydration shell

      1. This keeps molecules separated or dispersed in the water

   3. Reactions with water molecules can disrupt ionic compounds in the process of dissociation (atoms breaking off from molecules to form ions)

   4. Mole - SI unit of an amount of a substance

   5. Molarity - number of moles of solute per liter of solution

6. Cohesive and adhesive properties

   1. Cohesion-- attraction to molecules of its own kind

      1. Hydrogen bonds allow for surface tension, which causes the formation of droplets and allows things like bugs and paper clips to float on the surface of water

   2. Adhesion- attraction to different molecules

      1. Forms a concave meniscus on glass

      2. Observed when water “climbs” a thin glass capillary tube

         1. This “climbing” is called capillary action

   3. Transports water from roots to rest of plant

   4. Insects stay afloat on water because of surface tension

7. Buffers, acids, and bases

   1. pH

      1. Litmus tests acidity or alkalinity

      2. In pure water, when water becomes hydrogen ions and hydroxide ions, hydroxide stays bound to other molecules because of hydrogen bonds and hydrogen ions form H3O with other water molecules

      3. Negative of the base 10 logarithm of the concentration of hydrogen ions is the pH

      4. Near-neutral pH is maintained in blood and in human cells

   2. Acids and bases

      1. Acids increase the concentration of hydrogen ions (lower pH) usually by having one of its own hydrogen ions dissociate

      2. bases lower the concentration of hydrogen ions (higher pH) by providing hydroxide ions or another anion to combine with hydrogen ions

      3. Stronger acids more readily give hydrogen ions, like hydrochloric acid, which dissociates into hydrogen and chloride ions, unlike tomato juice and vinegar do not completely dissociate and are weak acids

      4. Strong bases readily take up hydrogen ions, like sodium hydroxide and many other household cleaners that rapidly give up hydroxide ions, unlike sea water, with a pH near 8.0

      5. Lower than 7 on the pH scale is acidic and higher than 7 on the pH scale is alkaline

      6. High acidity in stomach causes cells to constantly be replaced in the stomach

   3. Buffers

      1. Buffers absorb excess hydrogen ions or hydroxide ions to maintain a near neutral pH

      2. Buffer in human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3–), and carbon dioxide (CO2)

         1. Bicarbonate combines with hydrogen ions and become carbonic acid

         2. Carbonic acid becomes water and carbon dioxide, and carbon dioxide is exhaled

         3. Carbonic acid can combine with excess dioxide ions to make bicarbonate

Carbon

1. Hydrocarbons

   1. Organic molecules made entirely of carbon and hydrogen

   2. Covalent bonds between the atoms store a lot of energy, allowing it to be used as fuel when burned (oxidized) e.g. methane (CH4)

   3. May exist as linear chains, rings, or combinations of both

   4. May be single, double, or triple bonds

2. Isomers

   1. Isomers are molecules that share the same chemical formula but differ in the placement of their atoms and/or chemical bonds

   2. Structural isomers differ in the placement of their covalent bonds

   3. Geometric isomers differ in how covalent bonds are made to the surrounding atoms, especially carbon-to-carbon double bonds

      1. Same side of a double bond is a cis configuration

      2. Opposite sides of a double bond is a trans configuration

3. Enantiomers

   1. Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are mirror images (e.g. below)

4. Stereoisomers

   1. Stereoisomers are molecules that share the same chemical structure and bonds but have a different organization of atoms around one carbon

Functional Groups

1. Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules

2. Found along the “carbon backbone” of macromolecules-- chains/rings of carbon atoms with occasional substitutions of elements like nitrogen or oxygen

   1. These molecules with other elements in their carbon backbone are substituted hydrocarbons

3. Functional groups can participate in specific chemical reactions

4. Examples

   1. Hydroxyl (R-O-H | Polar)

   2. Methyl (R-CH3 | Nonpolar)

   3. Carbonyl (R-C*-R’ *--O | Polar)

   4. Carboxyl (O--C*-OH *-R | charged and ionized to release hydrogen ions)

   5. Amino (H-N*-H *-R | takes hydrogen ions to form NH3+)

5. Hydrogen bonds are important in folding properly into and maintaining the shape for functioning

Synthesis of Biological Macromolecules

1. Condensation reaction - molecules covalently bond through the loss of a small molecule

2. Dehydration synthesis - condensation reaction where a water molecule is lost

   1. Biological macromolecules-- large molecules necessary for life that built from smaller organic molecules

   2. Four major classes of biological macromolecules

      1. Carbohydrates

      2. Lipids

      3. Proteins

      4. Nucleic acids

   3. Most macromolecules made from single subunits called monomers

   4. Monomers combine with each other using covalent bonds to form larger molecules called polymers, releasing water molecules as byproducts

      1. This reaction is known as dehydration synthesis

      2. In this reaction, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water

      3. e.g. an electronegative oxygen in a glucose molecule may bond with an electropositive carbon atom in another glucose molecule; the hydrogen bonded to the oxygen may separate and the hydroxyl bonded to the carbon may separate, and the two may combine to make water

         1. Alternatively, a water molecule may pick up the oxygen’s hydrogen atom and form a hydronium ion (H3O+)

3. Hydrolysis

   1. Polymers break into monomers through hydrolysis

   2. Hydrolysis is a reaction in which a water molecule is used to break down another compound

   3. The polymer is broken into two components, one that gains a hydrogen atom and one that gains a hydroxyl molecule from a split water molecule

   4. Specific enzymes catalyze (speed up) dehydration and hydrolysis reactions

   5. Dehydration reactions form new bonds and requires energy while hydrolysis reactions break bonds and release energy

Carbohydrates

1. Molecular Structures

   1. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch

   2. Carbohydrates can be represented by the stoichiometric formula (CH2O)n where n is the number of carbons in the molecule

   3. Classified into 3 subtypes

   4. Monosaccharides

      1. Monosaccharides are simple sugars; the most common is glucose

      2. Usually has 3-7 carbons

      3. Most monosaccharide names end with “-ose”

      4. If it has an aldehyde group (R-C*-H *--O, i.e. it has its carbonyl group on the end) it is known as an aldose

      5. If it has a ketone group (R-C*-R *--O i.e. it has its carbonyl group internally) it is known as a ketose

      6. Depending on the number of carbons, they may also be known as trioses (3), pentoses (5), or hexoses (6)

      7. Chemical formula for glucose (used as energy by humans and plants), galactose (part of milk sugar) and fructose (found in fruit) is C6H12O6, these all have the same chemical formula but differ structurally and chemically from each other

         1. These 3 monosaccharides are isomeric hexoses (6 carbons and different structures)

         2. Glucose and galactose are aldoses while fructose is a ketose

         3. Monosaccharides in aqueous solutions are usually found in ring forms

            1. Glucose in a ring form can have two different arrangements of the hydroxyl group around the anomeric carbon (carbon that becomes asymmetric in the process of ring formation)

               1. If the hydroxyl group is below the anomeric carbon/plane, it is in the alpha (a) position

               2. If the hydroxyl group is above, it is in the beta (b**)** position (image for reference)

   5. Disaccharides

      1. Form when two monosaccharides undergo a dehydration reaction

      2. The hydroxyl group of one monosaccharide combines with the hydrogen of another, releasing a water molecule and forming a covalent bond known as a glycosidic bond, which can be the alpha or beta type

      3. A glycosidic bond is an oxygen bonded to the carbons of two sugars

      4. Common disaccharides include lactose (found in milk), maltose (formed by dehydration synthesis between two glucose molecules) and sucrose (table sugar), the most common and composed of glucose and fructose

   6. Polysaccharides

      1. Polysaccharides are long chains of monosaccharides linked by glycosidic bonds

         1. Chain may be branched or unbranched, may contain different types of monosaccharides

      2. Primary examples include starch, glycogen, cellulose, and chitin

      3. Starch

         1. Stored form of sugars in plants made of a mixture of amylose (linear chain structure) and amylopectin (branch chain structure), two polymers of glucose

         2. Plants can synthesize glucose, and the excess glucose is stored as starch in different plant parts including the roots and the seeds

         3. The starch in the seeds provides food for the embryo as it germinates and can also act as a food source for humans and animals

         4. Starch consumed by humans is broken down by enzymes into smaller molecules like glucose and maltose, which is then absorbed by the cells

         5. Made of glucose monomers joined by a 1-4 or a 1-6 bonds glycosidic bonds

            1. The numbers refer to the carbon number of the two residues that join to form the bond (right-most carbon is 1, counting clockwise, left-most is 4)

      4. Glycogen

         1. Glycogen is the storage form of glucose in humans and other vertebrates and is made of glucose monomers

         2. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells

         3. When glucose levels in the blood decrease, glycogen is broken down to release glucose in a process called glycogenolysis

      5. Cellulose

         1. The most abundant natural biopolymer

         2. Cell wall of plants is mostly made of cellulose; provides structural support to the cell

         3. Wood and paper are mostly cellulosic in nature

         4. Made of glucose monomers linked by b 1-4 glycosidic bonds

         5. Every other glucose monomer in cellulose is flipped over and the monomers are packed tightly as extended long chains, giving cellulose rigidity and strength, which is important to plant cells

         6. The b 1-4 linkage can’t be broken down by human digestive enzymes, but herbivores like cows and buffalos can with the help of specialized flora in their stomach to digest plant material rich in cellulose

            1. Certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase

            2. The appendix also contains bacteria that digest cellulose

            3. Cellulases break down cellulose into glucose monomers to be used for energy

            4. Termites can also break down cellulose because of other organisms in their body that secrete cellulases

      6. Chitin

         1. A polysaccharide-containing nitrogen

         2. Composes the exoskeleton of arthropods to protect internal body parts

         3. Made of repeating units of a modified sugar called N-acetyl-b-d-glucosamine

         4. Also a major component of fungal cell walls

Lipids

1. Sources of energy that power cellular processes, usually nonpolar and hydrophobic

2. Lipids are usually nonpolar because they are hydrocarbons that include mostly carbon-carbon/hydrogen-carbon bonds

3. Fats and Oils

   1. Purposes

      1. Cells store energy in the form of fats

      2. Lipids provide insulation, e.g. birds and mammals can keep dry with a protective layer over fur or feathers

      3. Lipids are the building blocks of many hormones and important in constructing cellular membranes

      4. Lipids include fats, waxes, phospholipids, and steroids

   2. Structure

      1. A fat molecule consists of mainly glycerol and fatty acids

      2. Glycerol is an organic compound (alcohol) with 3 carbons, 5 hydrogens, and 3 hydroxyl groups

      3. Fatty acids have long chains of hydrocarbons attached to a carboxyl group

      4. In a fat molecule, fatty acids are attached the glycerol’s carbons by dehydration synthesis with ester bonds through oxygen atoms

         1. Ester bonds - a carbon with a single bond to a carbon, a double bond to an oxygen, and a single bond to an oxygen bonded to another carbon (R-O-C*--O *-R)

      5. Fats are also called triacylglycerols/triglycerides because of their structure

         1. They have “acyl” in them because the (O--C-C) group connecting the glycerol to the hydrocarbon chain is called an acyl group

      6. Fatty acids are saturated if carbons have single bonds (“saturated” with hydrogen) while unsaturated fatty acids have double bonds

   3. Oils

      1. Unsaturated fats are typically liquid at room temperature and are called oils

      2. One double bond in the molecule is monounsaturated and more than one double bond is polyunsaturated

      3. Fats are only saturated when there are no double bonds

   4. Unsaturated fats and oils contain cis fatty acids

      1. Cis - hydrogens are in the same plane (causes a bend that prevents the acids from packing tightly, keeping them liquid at room temperature)

      2. Trans - hydrogens are on two different planes

   5. Trans Fats

      1. Trans fats are artificially hydrogenated to make them semi-solid and have a more desirable consistency

      2. Hydrogen gas is bubbled through oils which may double bonds from cis to trans

   6. Omega Fatty Acids

      1. Fatty acids not required but not synthesized by the human body are essential fatty acids and must be supplemented through the diet

      2. The two known essential fatty acids are omega-3 and omega-6

         1. omega-3 is polyunsaturated and the third carbon from the omega (w) carbon is connected to the fourth by a double bond

         2. Good sources of omega-3 are fish like salmon and tuna

      3. The furthest carbon away from the carboxyl group is numbered as the omega (w) carbon

4. Waxes

   1. Made of long fatty acid chains esterified to long-chain alcohols

   2. Because it’s hydrophobic, it covers some feathers and some leaves to prevent water from sticking to the surface

5. Phospholipids

   1. Major constituents of the plasma membrane (outermost layer of living cells)

   2. Composed of fatty acid chains attached to a glycerol or sphingosine backbone

   3. Differs from fats because there are only two fatty acids forming a diacylglycerol, the third carbon is occupied by a modified phosphate group

   4. A phosphate group attached to a diacylglycerol is a phosphatidate and becomes a phospholipid when modified by an alcohol

   5. Phospholipids are amphipathic, meaning it has a hydrophilic and a hydrophobic part (the phosphate head is hydrophilic and the lipid tail contains the hydrophobic fatty acids)

   6. phospholipids placed in water form a micelle, where the heads face the outside and the fatty acids face the interior

6. Steroids

   1. Steroids have a fused ring structure

   2. Hydrophobic and insoluble in water

   3. Steroids all have four linked carbon rings and several have a short tail (like cholesterol)

   4. Many steroids also have an -OH functional group, putting them in the alcohol classification

   5. Most common steroid is cholesterol, which is mainly synthesized in the liver and is used for many things like testosterone and Vitamin D

Proteins

1. Proteins are long chains of different sequences of the 20 amino acids that each contain an amino group (-NH2), a carboxyl group (OH-C--O), and a variable group

2. Amino acids are linked by a peptide bond formed through a dehydration reaction; a long chain of amino acids is a polypeptide

3. Changes in temperature, pH, and exposure to chemicals may change the protein, making it lose its function (denaturation)

4. Types and functions

   1. Proteins have the most diverse range of functions of all macromolecules and their structures vary greatly, although they are all polymers of amino acids in a linear sequence

   2. Enzymes

      1. Produced by living cells and are catalysts in biochemical reactions like digestion

      2. Speeds up specific reactions by decreasing the amount of energy needed

      3. Each enzyme is specific for the substrate (a reactant that binds to the enzyme) it acts on and may help in breakdown, rearrangement, or synthesis reactions

      4. Enzymes that break down their substrate are catabolic, enzymes that build more complex molecules are anabolic, and enzymes that affect the rate of reaction are catalytic

      5. All enzymes increase the rate of reaction and so are organic catalysts

   3. Hormones

      1. Chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control specific processes

   4. Primary functions

      1. Digestive enzymes - catabolize nutrients into monomeric units

      2. Transport - carry substances in the blood or lymph

      3. Structural - make different structures e.g. cytoskeleton

      4. Hormones - coordinate activities

      5. Defense - protect from foreign pathogens

      6. Contractile - effect muscle contraction

      7. Storage - nourish the embryo/seedling during early development

5. Amino acids

   1. Amino acids have a central alpha (a) carbon bonded to an amino group (NH2), a carboxyl group (COOH), a side chain, and a hydrogen atom

   2. The side chain determines the nature of the amino acid (pH, polar/nonpolar)

   3. Amino acids are represented by a single uppercase letter or a three-letter abbreviation (Valine - V or val)

   4. Essential amino acids are necessary for proteins but not produced by the body

   5. The sequence and number of amino acids determine the shape, size, and function of the protein

   6. Amino acids are attached by a covalent bond known as a peptide bond, which is formed by a dehydration reaction

   7. Linked amino acids form peptides, and multiple amino acids linked form a polypeptide with an amino group at one end (N or the amino terminal) and a carboxyl group at the other (C or carboxyl terminal)

   8. After protein synthesis, proteins are modified through post-translational modifications that make it completely functional

   9. The carboxyl group will lose its hydrogen proton and the amino group will have gained a hydrogen proton

      1. A neutral molecule where parts have charges that balance each other out is called a zwitterion

6. Protein Structure

   1. Enzymes bind to a specific substrate at a site known as the active site (region of enzyme surface where substrate binds)

   2. Primary structure

      1. The sequence of amino acids in a polypeptide chain is its primary structure

      2. The sequence is determined by the gene encoding the protein; a change in the nucleotide sequence of the gene’s coding may affect protein structure and function

   3. Secondary structure

      1. The folding of the polypeptide in some regions is the secondary structure

      2. Formed by hydrogen bonds between amino hydrogen and carboxyl oxygen on the backbones

      3. The most common are the a-helix (spirally) and B-pleated sheet (zig-zaggy) structures, both of which are held by hydrogen bonds

   4. Tertiary structure

      1. The three-dimensional structure of a polypeptide is its tertiary structure

      2. This structure is partly because of chemical interactions on the chains, primarily interactions between R groups

      3. These interactions can counteract hydrogen bonds in standard secondary structures

      4. Produced by hydrophobic interactions, ionic bonds, covalent bonds, and van der Waals forces

   5. Quaternary structure

      1. Interactions between subunits of polypeptides form the quaternary structure

      2. Weak interactions between subunits stabilize the overall structure

7. Denaturation and protein folding

   1. Temperature, pH, and chemicals may change the protein structure

   2. When proteins lose their shape without losing their primary sequence, it is known as denaturation

   3. Denaturation is often reversible because the primary structure of the polypeptide is conserved if the denaturing agent is removed

   4. Chaperones

      1. Protein helpers that assist during the folding process

      2. They associate with the target protein and prevent aggregation of polypeptides that make up the complete protein structure

      3. they disassociate from the protein after the process

      4. Folding is critical to protein process

Nucleic Acids

1. DNA and RNA

   1. Nucleic acids carry the genetic blueprint of a cell and instructions for cell functions

   2. Two main types

      1. Deoxyribonucleic acid (DNA)

      2. Ribonucleic acid (RNA)

   3. Genes

      1. Genes may carry information to make protein or RNA products

      2. Genome - the genetic content of a cell

      3. Genomics - the study of genomes

      4. DNA forms a complex with histone proteins to form chromatin - the substance of eukaryotic chromosomes, which may contain thousands of genes

      5. DNA controls genes by turning them “on” or “off”

   4. RNA

      1. RNA is mostly involved with protein synthesis and regulation

      2. DNA molecules never leave the nucleus, so messenger RNA (mRNA) are used to communicate with the rest of the sell

   5. DNA and RNA

      1. Made up of monomers known as nucleotides, which combine to form polynucleotides

      2. Nucleotides have three parts

         1. A nitrogenous base

            1. Organic molecules (they contain nitrogen and carbon)

            2. They are bases because they contain an amino group

            3. Four possible bases

               1. adenine (A) and guanine (G)

                  1. Classified as purines

                  2. Primary structure of a purine is two carbon-nitrogen rings

               2. Cytosine (C), Uracil (U), and Thymine (T)

                  1. Pyrimidines

                  2. Primary structure is a single carbon-nitrogen ring

                  3. Uracil replaces Thymine in RNA; they are very similar, but thymine has a methyl group

         2. A pentose sugar

            1. Deoxyribose in DNA and ribose in RNA

            2. On the second carbon (2’), ribose has a hydroxyl group and deoxyribose has a hydrogen

         3. A phosphate group

            1. Phosphate residue is attached to the hydroxyl groups of the 5’ carbon of one sugar and the 3’ carbon of the sugar of the next nucleotide, forming a 5’-3’ phosphodiester linkage

               1. Not formed by dehydration reaction like others

               2. Formed through the removal of two phosphate groups

   6. DNA Double-Helix Structure

      1. Sugars and phosphate lie on the outside of the helix, forming the DNA’s backbone

      2. Nitrogenous bases are stacked on the interior in pairs; pairs are bound by hydrogen bonds

      3. The two strands will run in opposite directions, making the 5’ carbon of one strand face the 3’ carbon of the other

         1. This is called antiparallel orientation

         2. It is important to DNA replication and nucleic acid interactions

      4. Base complementary rule - A pairs with T and G pairs with C; this is due to the way the hydrogen bonds form between the nitrogenous bases

      5. During DNA replication, each strand is copied, so the daughter DNA double helix contains one parental DNA strand and one newly synthesized strand

   7. RNA

      1. RNA is usually single-stranded and made of ribonucleotides linked by phosphodiester bonds

      2. A ribonucleotide contains ribose, a nitrogenous base, and the phosphate group

      3. Four main types of RNA

         1. Messenger RNA (mRNA)

            1. Carries messages from the DNA

            2. Base sequence is complementary to the sequence of the DNA it was copied from, but U replaces T

            3. Interacts with ribosomes and other machinery in the cytoplasm

            4. Read in sets of three bases known as codons

               1. Each codon codes for a single amino acid

               2. This allows the mRNA to be read and produce a protein product

         2. Ribosomal RNA (rRNA)

            1. A major constituent of the ribosomes mRNA bind on

            2. Ensures proper alignment of the mRNA and ribosomes

            3. Catalyzes the formation of peptide bonds between two amino acids

         3. Transfer RNA (tRNA)

            1. One of the smallest of the four types

            2. Carries the correct amino acid to the site of protein synthesis

            3. The base pairing between tRNA and mRNA allows for the correct amino acid to be inserted into the polypeptide chain

            4. tRNA has anticodons that pair with the codons on the mRNA

         4. microRNA

            1. Smallest RNA molecules

            2. Regulate gene expression by interfering with the expression of certain mRNA messages

      4. DNA and RNA comparison

DNA dictates the structure of mRNA in a transcription process, and RNA dictates the structure of protein in a translation process