Important elements to life (CHNOPS):

• Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

• Living organisms are made up of chemicals based mostly on the element carbon

• Carbon is unparalleled in its ability to form large, complex, varied molecules

  • A compound containing carbon is an organic compound

• Trace elements- very small amounts but essential to function

  • Iron (Fe), sodium (Na+), potassium (K+), copper (Cu), Iodine (I)

• Important molecules of all living things fall into 4 main classes:

  • Carbohydrates (energy)- Carbon

  • Lipids (long-term energy)- Carbon, Phosphorus

  • Proteins (muscles)- Carbon, Sulfur, Nitrogen

  • Nucleic acids (store/transmit genetic information)- Carbon, Nitrogen, Phosphorus

Carbon

• Why carbon?

• Abundant, versatile in bonds, tetravalent- makes 4 bonds to get stable = infinite variety

  • Valence electrons—electrons on outermost energy level

  • Valence—number of covalent bonds an element can make

    • Carbon-4, Hydrogen- 1, Oxygen- 2, Nitrogen- 3

• *STRUCTURE affects molecule function

  • Ex) Ismoers- molecules with the SAME molcular formula but different structures/order—emergent property a property that only occurs at a specific level

    Three kinds of isomers:

    • Structural- same chemical formula different order/arrangement

      

    • Cis-Trans- same formula, different positioning around a double bond

      • Cis- Xs arranged on the same side of a double bond

      • Trans- Xs arranged on opposite sides of the double bond

        

    • Enantiomers- same formula, mirror image positioning around a central carbon due to an asymmetric carbon attached to 4 different atoms

      • Left-handed and Right-handed variations

        

    • Biological processes tend to use one or two of the enantiomer forms

      • Ex. R-Ibuprofen vs S-Ibuprofen (works to reduce pain)

• Hydrocarbons- organic molecules consisting of only carbon and hydrogen

  • *ORGANIC substances have hydrocarbons

    • Many organic molecules such as fats have hydrocarbon components

    • Hydrocarbons can undergo reactions that release a large amount of energy

• Chemical groups most important to life:

  • Carbs: Hydroxyl group, Carbonyl group

  • Amino Acids/Proteins: Carboxyl group, amino group, hydroxyl group

  • Nucleic Acid: Phosphate group, Hydroxyl group (sugar), Carbonyl group (nitrogen base)

  • Lipids: Hydroxyl group (glycerol), Carboxyl group (fatty acid chains), Methyl group (fatty acid chains)

• Each functional group participates in chemical reactions in a characteristic way

  

1.2 Elements of Life

• Living systems require a constant input of energy

  • Law of conservation of energy: energy cannot be created nor destroyed only TRANSFORMED

  • Living systems follow the laws of energy

  • Living systems need constant input of energy to grow, reproduce, maintain organization

  • Living systems mainly use energy stored in chemical bonds

• Living systems require an exchange of matter

  • Atoms/molecules from the environment needed to build new molecules

  • Carbon is used to build all 4 biological molecules (carbs, proteins, nucleic acids, lipids)

  • Nitrogen used to build proteins and nucleic acids

  • Phosphorus used to build nucleic acids and some lipids

• Carbon is used to build macromolecules

  • Carbon’s unique ability to bond w/ other carbon atoms creating carbon skeletons other atoms can attach to

  • Enables creation of large and complex molecules

  • Carbon contains molecules that can be used to store energy

  • Carbon containing molecules can be used to form basic cell structures

  

1.3 Intro to Biological Macromolecules

• Monomers: Chemical subunits used to create polymers

  • Monomers have specific chemical properties allowing them to interact with one another

  • Covalent bond is formed between two interacting monomers

• Polymers: macromolecule (large moelcule) made of many monomers

  • Polymers are specific to the monomers they consist of

  • Ex. Monosaccharide → Carbohydrate (Polysaccharide) ; Amino acid → Protein; Nucleotide → Nucleic Acid; Fatty Acid → Lipids (lipids don’t have true monomers)

• Dehydration Synthesis reactions (Condensation reactions) form covalent bonds

  • Dehydration synthesis reactions create macromolecules

  • Subcomponents of a water molecule (H and OH) are removed from interacting monomers and a covalent bond forms

  • The H and OH join to form a molecule of water, water is a byproduct of this reaction

  • Ex. Dehydration Synthesis creates carbonhydrates

    • Carbohydrate monomers have hydroxides (OH) and hydrogen atoms (H) attached

    • One monomer loses an entire hydroxide while the other will only lose the hydrogen to form hydroxide

    • A covalent bond will form where the hydroxide/hydrogen atom were REMOVED

    • Hydroxide and hydrogen join forming a water molecule

      

  • Dehydration synthesis creates proteins

    • Each amino acid has an amino group (NH2) terminus and a carboxyl group (COOH) terminus

    • A hydroxide is lost from the carboxyl group and hydrogen atom is lost from the amino group of another amino acid

    • A covalent bond/peptide bond forms between the monomers where the hydrogen/hydroxide were removed

    • The hydroxide and hydrogen atoms form a water molecule

      

• Hydrolysis reactions cleave covalent bonds

  • Polymers are hydrolyzed (broken down) into monomers during a hydrolysis reaction

  • Covalent bonds between the monomers are cleaved (broken) during a hydrolysis reaction

  • A water molecule is hydrolyzed into subcomponents (H and OH) and each added to a different monomer

  • Ex. Proteins undergo hydrolysis reactions

    • Covalent bonds between amino acids can be cleaved (broken)

    • A water molecule is hydrolyzed and each subcomponent of water (H and OH) will be bonded to different amino acids

    • Result in separate amino acid monomers

      

1.4 Properties of Biological Molecules

• Living organisms are organized in a hierarchy of structural levels

  • At every level of organization function is related to structure

  • A change in the structure reesults in a change in the function

  • Properties determined by structure and function of molecules

• Nucleic Acids

  • **DO NOT CONFUSE W/ AMINO ACIDS

  • Nucleic acids—polymers comprised of monomers called nucleotides

  • Basic structure containing 3 subcomponents: 5-carbon (pentose) sugar, a phosphate group, a nitrogen base

  • Store biological information in the sequence of nucleotides

  • Ex. DNA vs. RNA

Deoxyribose (sugar)	Ribose (sugar)
Nitrogen bases: Thymine, Adenine, Guanine, Cytosine	Nitrogen bases: Uracil, Adenine, Guanine, Cytosine

• Amino acids- monomers that make up proteins

  • Have directionality with an animo (NH2) group and carboxyl (COOH) group

  • Polypeptide- primary structure; consists of a specific order of amino acids → determines the overall shape and function of the protein

  • R-group- group of atoms attached to the central carbon differs amino acids from one another

    • R-groups can be Hydrophobic, Hydrophilic, or Ionic

  • Protein can have different amino acids in the polypeptide allowing the protein to have regional differences in structure/function

• Carbohydrates

  • Complex carbohydrates can have monomers whose structures determine the properties and functions of the carbohydrate

• Lipids

  • Nonpolar macromolecules DO NO HAVE TRUE MONOMERS comprised of subunits (fatty acids and glycerol)

    • Fatty acid components determine structure/function based on SATURATION

      • Saturated: no double bond; Unsaturated: double bond between a carbon group

    • Specialized phospholipids- contain BOTH hydrophilic (polar head)+ hydrophobic (nonpolar tail) regions determine interactions with other molecules

      

  • Cell membranes contain lipids + proteins

    • Phospholipids and some membrane proteins have both hydrophilic/hydrophobic regions

    • Hydrophilic regions can interact with each other and the water environments (facing outwards)

    • Hydrophobic regions can interact with each other but NOT water environments (facing inwards)

1.5 Structure and Function of Biological Macromolecules

• Directionality in subunits influences structure of nucleic acid polymers

  • Linear sequence of all nucleic acids characterized by a 3’ hydroxyl and 5’ phosphate of the sugar in the nucleotide

    • Ex. DNA is nucelic acid plymer containing TWO strands each in an antiparallel 5’-3’ direction

    • Adenine - Thymine base pairs have TWO hydrogen bonds; Guanine - Cytosine held together by THREE hydrogen bonds

      • More hydrogen bonds = more stable the molecule’s structure is

      

    • Linear sequence of nucleotides encodes biological information

      • Any change in sequence may change encoded information

  • Synthesis:

  • Nucleotides can only be added to the 3’ end

    • Covalent bonds used to connect free nucelotides to the strand

    • Antiparallel Structure effect of replication: Since nucleotides can only be added to the 3' end, new nucleotides are added to the DNA strand moving from the 5' to 3' direction (leading strand)

    • Meanwhile, on the opposite strand, since nucleotides are still added from the 5' to 3' direction yet the strand runs opposite starting from the 3' to 5' direction, it replicates starting from the opposite direction (lagging strand)

      ---

      Thus, short segments called Okazaki fragments are created that are later joined together.

      

  • Direcitonality and protein structure:

    • Proteins comprise linear chains of amino acids that have a directionality with the amino + carboxyl groups

    • New amino acids added to carboxyl group connected by covalent bonds at the carboxyl group of the growing peptide chain

  • Elements of protein structure

    1. Primary structure- determined by sequence of amino acids held by covalent (peptide) bonds

    2. Secondary structure- local folding of amino acid chain into alpha-helices/beta-sheets

    3. Tertiary structure- overall 3D shape of the protein and often minimizes free energy; various types of bonds between R-groups stabilize protein

    4. Quaternary structure- arises from interactions between multiple polypeptide units

• Directionality and structure of carbohydrates

  • Carbodydrates comprise linear chains of sugar monomers connected by covalent bonds

    • Small directional changes in compnents (i.e. direction of OH group) can result in functional differences

  • Carbohydrate polymers can be linear or branched

    • Starch and glycogenboth function in energy storage (starch-plants; glycogen-humans/vertebrates)

    • Cellulose provides support and strength to cell walls

      

Carbon (Textbook ch. 3.1)

• Carbon has 4/8 valence electrons in its outer shell and a valence of 4 → enables carbon to form large, complex molecules

  • Valence: the number of covalent bonds an atom can form

    • Carbon-4, Oxygen-2, Nitrogen-3, Hydrogen-1

• Carbon can bond to various atoms including other carbon atoms to form carbon skeletons of organic carbon

• Shapes of carbon bonds:

Carbohydrates (Textbook Ch. 3.3)

• Monomer- Monosaccharides

• Molecules Involved: Carbon, Hydrogen, Oxygen

• Characteristics of carbohydrates/sugars:

  • Carbon skeleton (C-C-C-C); ranges from 3-7 carbons long

  • Carbonyl group (C=O)

  • Multiple hydroxyl groups (OH)

  • 6 carbons—Hexoses; 5 carbons—Hexoses; 3 carbons—Trioses;

• Major nutrients for cells

  • Cells extract energy from glucose molecules by breaking them down

  • Carbon skeletons of monosaccharides raw material for synthesis of other types of small organic molecules (amino acids)

• Examples: Glucose (C6H12O6), Galactose, Fructose, Ribose, Glyceraldehyde

• Macromolecules-

  • Dissacharides- 2 monosaccahrides joined by glycosidic linkage (covalent bond formed through a dehydration reaction)

    • Must be broken into monosaccharides to be used for energy

  • Examples: Sucrose (glucose + fructose); Lactose (galactose + glucose); Maltose (glucose+glucose)

    

• Polysaccharides- many sugar building blocks joined by glycosidic linkages

  • Structure/function determined by sugar monomers and position of glycosidic linkages

  • Storage Polysaccharides: serve as storage material—hydrolyzed to provide sugar monomers for cells

    • Examples:

    • Starch stores energy—withdrawn by hydrolysis reaction breaking bonds between glucose monomers

    • Glycocen—stored in animal liver/muscle cells breakdown of glycogen releases glucose

  • Structural Polysacchrides

    • Serve as building material for structures to protect the cell/organism

    • Examples:

    • Chitin- used by anthropods to build exoskeletons/fungi cell walls

    • Cellulose- forms plant cell walls

    • Starch vs. Cellulose

      • Starch and cellulose similar in structure except all glucose monomers in starch are in the alpha (α) configeration while cellulose is all in the beta (β) —making every other one appear “upside down”

      • Enzymes that digest starge by hydolysizing (α) linkages unable to for cellulose →

        • Few organisms can digest cellulose unless microorganisms in gut of animals like cows can hydrolyze cellulose

    
  

Lipids (Textbook Ch. 3.4)

• Characteristics of Lipids:

  • NO true monomers or polymers; not big enough to be considered macromolecules

  • Shared characteristic: HYDROPHOBIC molecules—low solubility in water

    • Consist of mostly hydrocarbon (CH) regions

  • Purposes: Stores energy (long-term), insulates body, cushions organs (cell membrane)

  • Molecules involved: Carbon, Hydrogen, Oxygen, Phosphate* (Nitrogen?)

  • Ex. Fats, Phospholipids, Steroids

• Fats

  • Purpose: Energy storage (stores more than carbohydrates)

  • Triglycerides/Triacylglycerol: Three fatty acid tails bind to a molecule of glycerol

    • Glycerol- 3 carbons bearing a hydroxyl (OH) group; a type of alcohol

    

    • Fatty Acid- long carbon skeleton (16-18 C atoms) with one end part of a carboxyl group (COOH) and the rest consisting of a hydrocarbon chain (C-H)

      • Nonpolar hydrocarbon (C-H) bonds cause fatty acids to be hydrophobic

  • Large molecules assembled from smaller molecules through dehydration reactions

    • Fatty acid molecule joined to glycerol via dehydration synthesis → esther linkage—bond between a hydroxyl (OH) and carboxyl group (COOH)

  

  • Saturated Fats: Only contain single carbon bonds in hydrocarbon chains of fatty acid tails

    • Solids at room temperature (b/c molecules packed closer together) Ex. Butter, lard

  • Unsaturated Fats: Contain double bonds in one or more hydrocarbon chains of fatty acids (usually cis double bonds = kink/bend in hydrocarbon chain)

    • Liquids at room temperature Ex. Vegetable oil

  • *Trans Fats: Synthetically convert unsaturated to saturated fats by adding hydrogen → produces unsaturated fats with trans double bonds

  

• Phospholipids

  • Phosphate-containing polar (hydrophilic) head connected to glycerol and TWO nonpolar (hydrophobic) fatty acid tails

    • Head: Negatively charged phosphate group attached to glycerol may be attached to another charged molecule such as choline

  • Purpose: Makes up cell membranes (phospholipid bilayer)

    • Assemble into a double-layered sheet with polar heads facing outwards towards the water and fatty acid tails shielded from water

      

• Steroids

  • All have carbon skeleton with 4 rings; difference in chemical groups attached to the rings

  • Cholesterol

    • Component of animal cell membranes + precursor other steroids are synthesized from

    • Synthesized in the liver and obtained from diet

      

Proteins (Textbook Ch. 3.5)

• Protein- biologically functional molecule made up of one of more polypeptides folded and coiled into a 3D structure

  • Made of monomer amino acids linked together via peptide bonds (covalent bond) → polymer = polypeptide

• Protein Functions:

Enzymatic Proteins (Enzymes)- Catalysts that speed up and chemical reactions; regulate metabolism Ex) Digestive enzymes- catalyze the hydrolysis (breakdown) of bonds in food	Storage Proteins- Storage of amino acids Ex) Ovalbumin- protein of egg white source of amino acid for embryo	Hormonal Proteins- coordination of organism’s activities Ex) Insulin causes other tissues to take up glucose → regulate blood sugar concentration
Contractile and motor proteins- Movement Ex) Actin + myosin responsbile for muscle contractions	Defensive proteins- Protects against disease Ex) Antibodies	Transport proteins- transport of substances Ex) Hemoglobin; Transport proteins tansport molecules across membranes (active transport)
Receptor proteins- cell response to chemical stimuli Ex) Receptors in nerve cell membrane detect signaling molecules released by other nerve cells	Structural proteins- support and bind parts together Ex) Collagen + elastin provide a fibrous framework in animal connective tissues

• Amino Acids

  • All contain an amino group (NH2) and carboxyl group (COOH) attached to a central alpha (α) carbon

  • Differs in the side chain/R-group that determine the unique characteristics of the amino acid

  • Chains of amino acids have a directionality, with an amino acid end (N-terminus) and a carboxyl end (C-terminus)

    

• 20 total types of amino acids:

• Nonpolar R group (hydrophobic)

  • Hydrocarbon (CHx) on the outside

  

• Polar R group (hydrophilic)

  • Hydroxyl (OH) or animo group (NH2) and Oxygen on the outside

  

• Acidic amino acids have side chains usually negative (-) in charge due to prescence of carboxyl group (COOH) that usually dissociates (ionizes) at cellular pH

• Basic amino acids have amino groups (NH2) in side chains generally positive (+) in charge

  

• Polypeptides

  • Polypeptide- a polymer of many amino acids linked by peptide bond formed by dehydration synthesis

    • Formed between the carboxyl (C-terminus) and amino (N-terminus) groups bond between the C—N molecules → creates the polypeptide backbone

    

  • Protein shapes and functions

    • When a polypeptide is synthesized, the chain may spontaneously fold into different shapes

      • Globular proteins- spherical shaped; Fibrous proteins- shaped like long fibers

    • A protein’s structure shapes its function

      • Ex) Antibodies fit the exact shape of the foreign substance/virus the antibody binds to

      • Morphine mimics the shape of endorphin binding into receptor proteins on brain cells

  • Levels of Protein Structure

  • Primary structure: Linear sequence of amino acids in a protein (polypeptide backbone)

    • A different arrangement/order of animo acids = polypepide has completely different name/identity

    • Determines the protein’s shape—where an α helix can form, where β pleated sheets can exist, where disulfide bridges are located, where ionic bonds can form etc.

  • Secondary structure- held together by hydrogen bonds between the animo (NH2) and carboxyl (COOH) groups of the polypeptide backbone (primary structure)

    • Take the form of an alpha (α) helix or beta (β) pleated sheet

    • Alpha/(α) Helix

      • Each transthyrtin polypeptide has only one alpha helix region

      • Globular proteins have multiple stretches of alpha helixes separated by nonhelical regions (hemoglobin)

      • Fibrous proteins like alpha keratin have majority alpha helix formation

    • Beta/(β) Pleated Sheet

      • Make up core for many globular proteins and may dominate some fibrous proteins

  • Tertiary Structures: 3D structures stablizied by interactions between R-groups/side chains

  • 4 Types of Interactions:

    • Hydrophobic -Hydrocarbon (CHx) often clustered on the interior/core of the protein

      • van der Walls interactions (electric forces between neutral molecules) help hold together nonpolar side chains

    • Covalent- Disulfite bridges (S2)

    • Hydrophilic- Hydrogen Bonds (H—O)

    • Ionic- +/- charged side chains

      

  • Quartenary Structure- 3D protein structures made of TWO OR MORE polypeptide chains

    • Ex) Collagen, Hemoglobin

  • Hemoglobin- carries oxygen on red blood cells to the body

    • Consists of 4 polypeptide subunits—2 (α) subunits and 2 (β) subunits made primary of alpha helixes

    • Has a nonpolypeptite component called heme with an iron atom that binds oxygen

      

    • Sickle-Cell Disease and change in primary structure:

      • Caused by substitution of a polar/hydrophilic R-group amino acid (valine) for nonpolar/hydrophobic R-group (glutamic acid) → blood cell misshapen into a sickle shape

      • Don’t carry as much oxygen; gets stuck in blood vessels; can kill a person at a young age if left untreated

    • Denaturation- Changes in the shape of a protein

      • Causes: changes in pH, changes in salinity, high temperatures

        • Transfer from aqueous environment to a nonpolar solvent (ether/chloroform) → polypeptide chains refold so hydrophobic regions face outward

        • Chemicals disrupt bonds/interactions (hydrogen, ionic, disulfide bridges)

Nucleic Acids (Textbook ch. 3.6)

• Purpose: Store genetic information through 2 types—DNA & RNA

  • Gene Expression: Includes DNA replication, RNA synthesis, protein synthesis

• Molecules: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphate

• Nucleic acids are macromolecules—Monomers: nucleotides; Polymers: polynucleotides

• Structure of nucleic Acids:

  • Nucelotides have 3 components—nitrogenous base, five-carbon sugar/pentose, phosphate group

    • Deoxyribose-DNA; Ribose-RNA

    • Nitrogenous Bases: Adenine—Thymine(DNA)/Uracil(RNA); Guanine—Cytosine

      • Pyrimadine: One six-membered ring of carbon and nitrogen atoms

        • Cytosine, Thymine/Uracil

      • Purines: Larger than pyrimadines with a six-membered ring fused to a five-member ring

        • Adenine, Guanine

  

• Structure of DNA + RNA

  • Sugar-phosphate backbone- nucelotides link to one another via dehydration synthesis and joined by a phosphodiester linkage—phosphate group covelently links sugars of 2 nucelotides

  • Phosphate attached to the 5’ carbon and hydroxyl group on a 3’ carbon end

    • Directionality 5’ → 3’

  • Sequence of bases is unique for each gene and provides information for the cell—limitless number of possible sequences ( Ex. 5′-AGGTAACTT-3′)

• DNA

  • Two strands—double helix

  • Deoxyribose sugar

  • Antiparallel- sugar-phosphate backbones run in opposite 5’ → 3’ (leading strand) and 3’ → 5’ (lagging strand) directions

  • Strands held together by hydrogen bonds between the paired nitrogen bases

    • Adenine—Thymine base pairs have TWO hydrogen bonds; Guanine—Cytosine held together by THREE hydrogen bonds

      • More hydrogen bonds = more stable the molecule’s structure is

    • Strands are complementary → able to generate two identical copies of each DNA in a cell preparing to divide

• RNA

  • Ribose sugar

  • Usually exists as a single strand

    • Complementary base pairing can occur between regions of 2 RNA molecules/stretches of nucleotides in the same RNA → allows it to take a 3D shape needed for its function

    • Adenine—Uracil and Guanine—Cytosine base pairs

1.6 Nucleic Acids

• DNA vs RNA

  • Similarities:

    • Both made from nucleotide monomers/subunits comprise of: 5-carbon sugar, phosphate group, nitrogen group

    • Each nucleotide connected by covalent bonds forming sugar-phosphate backbone

    • Each linear srand of nucleotides has a 5’ and 3’ end

    • Nitrogenous bases perpendicular to sugar-phosphate backbone

      

  • Differences:

    Deoxyribose (sugar)	Ribose (sugar)
    Nitrogen bases: Thymine, Adenine, Guanine, Cytosine	Nitrogen bases: Uracil, Adenine, Guanine, Cytosine
    Double-stranded + antiparallel	Single-stranded

• Nucleus Acids

  • The information storage molecules biological systems

  • Made of C, H, O, N & P

  • DNA vs RNA

  • Deoxyribose

  • DNA = Adenine, Thymine, Guanine Cytosine

  • 2 Strands

  • Ribose

  • RNA = Adenine, Uracil, Guanine, Cytosine

  • 1 Strand

• Ribonucleic Acid

  • Transmits and translates DNA information into protein

  • Many enzymatic and regulatory functions

  • 1 kind of DNA, -15 types of known RNA at current (3 main types)