Mod+7+Reading+Guide


 * __Mod 7 Main Idea__:** The main idea of Mod 7 is that Amines and Amides are involved in the formation of amino acids that build proteins into several different structures that are used to conduct most process within living cells.

-Summary: **Amines** are derivatives of ammonia (NH3) where one or more hydrogen atoms are replaced with alkyl or aromatic groups. Amines are classified as **primary**, **secondary**, or **tertiary** when the nitrogen atom is bonded to 1, 2, or 3 carbon atoms respectively. **Amines are named** with common or with IUPAC names. Common amine names list the alkyl groups bonded to the nitrogen in alphabetical order using di- and tri- to indicate identical substituents (ex: diethylpropylamine). IUPAC names for amines are similar to the way we named alcohols but the -e in the alkane name is replaced with -amine (ex: pentanamine or hexanamine). Also the location of the Amine group is numbered and given in front of the generic name (1-butanamine or 2-hexanamine). If the amine is secondary or tertiary, then the longest carbon chain is named a 1-alkyanamine with the other carbon chain groups named before it as N-ethyl or N-butyl, etc. If the amine is in a molecule with a higher priority functional group (the higher the oxidation level, the higher the priority), then the NH2 group is named as a substituent **amino** group (amino acid refers to a carboxylic acid with an amino substituent). An aromatic amine, **aniline**, is an aromatic ring connected to an amino group on carbon 1.
 * __18.1 Amines__**

-Struggling Topic 1: How would you name a compound that had a more oxidized functional group than the amine group such as an aldehyde group that had substituents connected to the amine group. Could you have N2-ethylbutanal if you had a 4 carbon aldehyde with an ethyl group connected to an amine group on carbon 2?

-Struggling Topic 2: Does a secondary amine cause a molecule to have a bent shape? I would think not. When you draw a molecule that looks like CH3-CH2-NH-CH2-CH3, it would appear as though the N's H atom would take up more space and cause a bend, but the N atom also has a lone pair of electrons that should take up the same amount of space as the H atom would.

-Struggling Topic 3: HW problem 18.45 A: Given: condensed molecular formula; Find the name: diethylmethylamine. Does this compound get named by alkyl groups in alphabetical order? I had assumed that it would be named with the largest alkane group closest to the amine suffix. Is it because it is a tertiary amine that the substituent groups get listed alphabetically rather than by the "main" or "longest" carbon chain?

-Summary: **Amides** are related to carboxylic acids but have an amino group instead of a hydroxyl group. An amide is amide is made by a reaction called **amidation** that is similar to esterification. A molecule of water is eliminated (OH from the carboxylic acid and H from the nitrogen), so only primary and secondary amines can be amidated. **Amides are named** by dropping the -ic acid or -oic acid from the carboxylic acid names and adding the suffix -amide. When alkyl groups are attachd to the nitrogen atom, the name of the amide is preceded by N- or N,N- depending upon how many substituents are connected to the nitrogen atom. **The properties of amides** are different from those of amines. Amines have many properties of bases, but amides do not. All amides except formamide are solids at room temperature, and primary amides can hydrogen bond which gives them higher melting points. Secondary and tertiary amides have lower melting points because they cannot form hydrogen bonds with itself as easily or at all respectively. **Some amides are water soluble** up to five carbons in their carbon chain because of their hydrogen bonding with water.
 * __18.4 Amides__**

-Struggling Topic 1: When the book says that tertiary amides cannot hydrogen bond with themselves, this is because there are no hydrogen atoms connected to the Nitrogen atom, correct? But, a tertiary amide can hydrogen bond with water because the water will supply hydrogen ions for hydrogen bonding, right?

-Struggling Topic 2: Will amides have different shapes than esters? They look similar the way they are drawn, but they should be different since oxygen atoms have two lone electron pairs and nitrogen atoms have only 1 lone electron pair.

-Summary: **Amino acids** are compounds that contain an amino group (NH2), a carboxylic acid group (COOH), and a hydrogen atom bonded to a central carbon. Most often in the body, amino acids exist as **alpha-amino acids** which are ionized to include an NH3+ group and a COO- group. Amino acids have unique characteristics that are determined by their side chains that can include alkyl, hydroxyl, thiol, amino, sulfide, aromatic, or even heterocyclic groups. **Nonpolar amino acids** are hydrophobic and have alkyl or aromatic side chains. **Polar amino acids** are hydrophilic and have polar side chains such as hydroxyl, thiol, or amide groups. **Acidic amino acids** have side chains that contain a carboxylic acid group that allows it to ionize as a weak acid. **Basic amino acids** have an amino group that can ionize as a weak base. All alpha-amino acids except glycine are chiral because the alpha carbon is attached to four different groups. The **D and L enantiomers are determined by** which side of the alpha carbon contains the amino group (D for right side, L for left side).
 * __19.1 Proteins and Amino Acids__**

-Struggling Topic 1: Since amino acids must have an amino group, a carboxylic acid group, and a hydrogen bonded to a central carbon, does this mean that NH2-COOH would not be classified as an amino acid? Yes, because it wouldn't have a side chain.

-Struggling Topic 2: The objectives appear to say that we should be able to draw amino acids from their names or from their 3 letter abbreviations. Will we need to do this without reference materials? It seems unreasonable to memorize these, but it seems reasonable that we should be expected to identify (given their structure) whether the amino acid is polar, nonpolar, acidic, or basic.

-Summary: A **zwitterion** is the dipolar form of an amino acid that has a net charge of zero because the amino group is ionized to +1 charge and the carboxylic acid group is ionized to -1 charge. The **isoelectric point (pI)** is the pH where the positive and negative charges are equal. When the pH is different from the pI, the sqitterion accepts or donates H+ ions. Most amino acids have a pI value around 5 or 6, acidic amino acids have pI values around 3, and basic amino acids have pI values between 7 and 11. **Electrophoresis** is a method for separating mixtures of amino acids in a lab. In this process, a positively charged amino acid (when the amino acid's pI is greater than the pH of the solution) moves towards the negative electrode while a negatively charged amino acid (when the amino acid's pI is less than the pH of the solution) moves towards the positive electrode.
 * __19.2 Amino Acids as Acids and Bases__**

-Struggling Topic 1: There were no required HW problems having us write an acidic or basic amino acid that has been ionized. Say a solution had a pH of 1 and we put an acidic amino acid such as glutamic acid in this solution. Would this glutamic acid accept a H+ at both COO- groups? I would assume that it would. Likewise with a basic amino acid in a basic solution, would lysine lose an H+ from both NH3 groups in a solution that had a high enough pH?

-Struggling Topic 2: Sort of the opposite of the above scenario, would an acidic amino acid remain ionized with its COO- groups in an acidic solution? I would assume it would. I would also assume that a basic amino acid would remain ionized with its NH3+ groups in a basic solution.

-Summary: A **peptide** is a linking of two or more amino acids, and a **peptide bond** is an amide bond that forms from the COO- group of one amino acid and the NH3+ group of the next amino acid. The **N-terminal** of a peptide bond is the side with an unreacted amino group, and the **C-terminal** is the side with an unreacted COO- group. **Peptides are named** beginning with amino acid that has the N-terminal. Then each amino acid is listed with its -ine suffix replaced with a -yl suffix until the final amino acid is listed normally.
 * __19.3 Formation of Peptides__**

-Struggling Topic 1: It seems reasonable that there should be common names for proteins rather than these IUPAC names. Is this the case?

-Struggling Topic 2: Are peptide bonds linear? It seems like peptide bonds will always be linear because they always bond from the amino group to the carboxylic acid group, and these groups are on opposite sides of the amino acids.

-Summary: **Proteins** are molecules that are made of more than 50 amino acids in a polypeptide chain. Each protein has a unique amino acid sequence. The **primary structure** of a protein is the sequence of amino acids. The order of the amino acids DOES matter in determining the function of the protein. **Disulfide bonds**, bonds between sulfur atoms in cysteine, hold some primary structure proteins close to other proteins. The **secondary structure** of a protein describes how the amino acids are arranged in space relative to the neighboring amino acids. An **alpha helix** is one secondary structure where the hydrogen bonds between N-H groups and C=O groups bend the amino acids into a corkscrew shape with all the side chains located outside the helix. A **beta-pleated sheet** is another secondary structure where the peptide chains are held together (in parallel) by hydrogen bonding between the C=O group of one and the N-H group of the other chain. The **alpha-helix** is more likely to occur with amino acids such as alanine, histidine, leucine, and methionine while the **beta-pleated sheet** is more likely to occur with amino acids such as valine, proline, serine, and aspartic acid. **Collagen** is the most abundant protein, and it is found in connective tissue, blood vessels, skin, tendons, ligaments, cornea, and cartilage. Collagen forms a secondary structure in a **triple helix** form that is the result of three polypeptides woven together like a braid.
 * __19.4 Protein Structure: Primary and Secondary Levels (MAKE QUIZ QUESTIONS ON THIS ONE)__**

-Struggling Topic 1: Does the R group of the amino acids that make up a protein in the secondary structure make the biggest difference as to which secondary structure, helix or pleated sheet, will form? It would seem reasonable that the larger R groups would have more space in an alpha-helix form than in a beta-pleated sheet form because of the spatial arrangement of the molecules. If this is not the case, what does cause the protein to be more likely to form one structure rather than the other?

-Struggling Topic 2: It sounds like the primary structure of a protein often includes more than 1 peptide chain. Is this the case? And can these peptide chains be connected by bonding other than disulfide bonding? Could there be hydrogen bonding between two peptide chains in a primary structure of a protein?

-Summary: The **tertiary structure** of a protein involves the repulsions and attractions between side group chains of amino acids that give a protein a unique 3D shape. **Hydrophobic interactions** within a tertiary protein structure cause side chains that are nonpolar to push as far away from the aqueous environment as possible and form a nonpolar center to the molecule. **Hydrophillic interactions** within a tertiary protein structure are attractions between polar or ionized side chains and an external aqueous environment. **Salt bridges** are ionic bonds between side groups of basic and acidic amino acids. **Hydrogen bonds** form betwen polar amino cids such as OH and NH3 groups. **Disulfide bonds** are covalent bonds that form between SH groups of two amino acids in a polypeptide chain (cysteine is the amino acid with SH groups in it). **Globular proteins** have compact spherical shapes and carry out the work of the cells (synthesis, transport, and metabolism). This spherical shape forms because of the secondary structures of the polypeptide chain and the way they fold over on top of each other. **Fibrous proteins** are proteins that are long, thin, and fiber-like in shape. These are typically involved in the structure of cells and tissues. **Alpha-keratins** are fibrous proteins formed from three alpha helixes that coil together like a braid to make up structures like hair, wool, skin, and nails. **Beta-keratins** are formed from many beta pleated sheets and are often found in bird feathers and reptile scales. The **quaternary structure** of proteins consist of two or more polypeptide subunits that are held together by the same interactions that stabilized the tertiary structure (above).
 * __19.5 Protein Structure: Tertiary and Quaternary Levels__**

-Struggling Topic 1: Is the difference between hydrophilic interactions and hydrogen bonds forming in tertiary proteins that hydrophilic interactions must happen between an amino acid's side chain and the __external__ aqueous environment while the hydrogen bonding is what would happen between -OH or -NH3 groups within the protein structure?

-Struggling Topic 2: Is the main difference between quaternary structures of proteins and tertiary structures of proteins that quaternary structures are made from more than 1 functioning tertiary structure? Both are made of the same amino acids and peptide chains connected in similar ways, but it seems like the function of the __parts__ of quaternary structures is not present in tertiary structures.

-Summary: The **hydrolysis** of a protein breaks the bonds between amino acids and causes the primary structure of the protein to break apart into its amino acid subunits. The **denaturation** of a protein happens when the bonds that stabilize the secondary, tertiary, or quaternary structures are disrupted but the primary peptide bonds are not affected. Denaturation can happen because of heat (breaks apart hydrogen bonds and hydrophilic attractions), acids/bases (affects hydrogen bonding and disrupts ionic bonds), organic compounds (disrupt hydrophobic interactions by forming their own hydrogen bonds with a protein), heavy metal ions (react with disulfide bonds and cause them to solidify), or by agitation (stretching and moving polypeptide chains until the stabilizing interactions are disrupted).
 * __19.6 Protein Hydrolysis and Denaturation__**

-Struggling Topic 1: What effect does the denaturation of protein have on an organism? Does this always result in cell death, or are there some enyzems that can be denatured and the body can respond to this in an effective manner?

-Struggling Topic 2: If it is helpful to denature proteins to make them easier to digest, does this suggest that we shouldn't eat our food raw? Or, is it that cooking food can remove some valuable nutrients that our bodies need that means that we shouldn't always cook or overcook our food?

A. specifics about how clearly the author communicated individual topics ->18.1 - step by step directions for naming amines with IUPAC names were clear and easy to follow.
 * Critique of this chapter**

B. specifics about the amount of content and whether it was sufficient to help learn the material (did you need more examples?) ->19.5 - the pictures and diagrams/charts that summarized the four protein structures did a good job of helping to put all the information in one place. This helped make it clear to me.

C. why did the author place this chapter where she did in the overall text? not later or earlier, transitions with previous chapter, with subsequent chapter(s), did this chapter seem out of place? ->18.1 - it was clear that classifying primary, secondary, and tertiary alcohols was a good prerequisite for classifying amines as primary, secondary, and tertiary. ->18.1 - the author was also able to relate the naming of amines to the naming of alcohols using IUPAC names.