1. (5) Draw a diagram of an isomeric molecule to demonstrate a structural, geometric, and an enantiomer organization.

Size: px

Start display at page:

Download "1. (5) Draw a diagram of an isomeric molecule to demonstrate a structural, geometric, and an enantiomer organization."

Osborne Henderson
5 years ago
Views:

1 Organic Chemistry Assignment Score. Name Sec.. Date. Working by yourself or in a group, answer the following questions about the Organic Chemistry material. This assignment is worth 35 points with the possible points for each question in parenthesis. This web site may be of assistance: (5) Draw a diagram of an isomeric molecule to demonstrate a structural, geometric, and an enantiomer organization. Structural isomers have the same molecular make up but they differ in the way that the atoms are bonded together like the two molecules in a in the picture above. Geometric isomers have the same atomic structure but the organization is different across a double bond. In the case of b above if the hydrogen atoms across the double bond are on the same side it called the cis configuration and if the hydrogens are on the opposite sides of the double bond it is in the trans configuration. Enantiomeric isomers are molecules which are built to be mirror images of each other around what is called a chiral carbon atom as in c above to which four different atoms or molecules are bonded. 2. (5) Draw a diagram of each of the functional groups (outlined in lecture or Table 4.1) to show how the properties of a molecule of ethane would change when each of the functional groups is added to the ethane? Functional groups, as in the table below, are a group of atoms bonded together and when added to a carbon backbone molecule will give different properties to the backbone due to the reactivity of each functional group. Not shown is a Methyl group (CH3) that when added to a 1

carbon in the chain makes that carbon inactive at this position or unable to bind to other molecules and an Acetyl group ( ) that when added opens a carbon for binding to other molecules.

2 carbon in the chain makes that carbon inactive at this position or unable to bind to other molecules and an Acetyl group ( ) that when added opens a carbon for binding to other molecules. Can you figure out what each functional group does to the resulting carbon chain when added to the carbon chain or in this case an ethane? Look at the charge of each functional group (polarity), or the ability of the functional group to change the ph of a solution, is the functional group reactive or not, or is the functional group neutral. 3. (5) Draw a diagram to show the atomic relationship of the atoms found within a C6H12O6 carbohydrate? 2

3 Notice how a linear chain is established first when building a Carbohydrate. Once the backbone chain is established the molecules will fold over or bend to form a ring structure with the ultimate shape of the ring dependent on where the carbonyl functional group highlighted in red above (the C is bonded to the O highlighted in blue above)) is found within the linear chain. If the carbonyl is attached to the #1 carbon we get a six sided figure (like glucose or galactose) but if the carbonyl if attached to the #2 carbon we get a five sided figure (like fructose or ribose). 4. (7) Explain in words and a diagram how neutral fats differ from a carbohydrate and from a steroid. Neutral Fats have a linear structure with at most three fatty acids (outlined in yellow above) attached to a backbone of a glycerol molecule. Notice along the chains that each carbon is bound to at least two hydrogen s (saturated fatty acid versus unsaturated fatty acid) and therefore cannot interact with other molecules (mainly water because water is polar). The carbohydrate molecule (see figure with question #2 above) on the other hand has multiple sites where interactions with other molecules are possible (the OH groups). Each of the alcohol side groups of the carbohydrate could be sites of interaction with the base carbohydrate. This characteristic allows carbohydrates to form long chains (polymers) that can be straight, coiled, form side chains with other carbohydrates or other molecules. It is this characteristic in their structure that make carbohydrates miscible in water (hydrophilic) and neutral fats not miscible (hydrophobic). 3

Cholesterol Steroids unlike their cousins the neutral fats or phospholipids (a phosphate group would replace

4 Cholesterol Steroids unlike their cousins the neutral fats or phospholipids (a phosphate group would replace one of the end fatty acids in the molecule above) have a backbone of four ringed molecules that form the base molecule known as cholesterol. Changing the various side functional groups of the cholesterol will make the steroid take on different forms and therefore various functions. Comparing the structure of estradiol with testosterone very readily reveals this idea giving each a different function in the organism. 5. (7) Explain in words and a diagram how the primary, secondary, tertiary, and quaternary structure of a protein varies? 4

5 Proteins are huge macromolecules that have a wide range in shapes and functions but they all begin as a simple polymer of linked amino acids (AA). The amino acids (twenty or so different types of AA s that are divided how?) are lined up with the amino end of one amino acid bonded to the carboxylic acid end of the next amino acid forming a special non-polar covalent bond called a dipeptide bond. The amino acid sequence is defined as the primary (1 o ) level structure of a protein and the sequence of AA s will dictate the final shape of the protein. As the AA s are laid down their variable side groups (due to their size and polar properties) can force the chain to begin to coil into a helical shape called alpha ( ) helical (where one amino acid can form a hydrogen bond with another amino acid down the chain somewhere) or on the other hand the position of the amino acids in the 1 o structure can cause the chain to remain straight yet sort of kinky or fold back on themselves which brings amino acids close enough to form hydrogen bonds in what is termed a beta ( ) pleated sheet. This hydrogen bonding between different AA s in the chains forms the next level of organization or the secondary (2 o ) level of structure. The 2 o level of organization also brings other amino acids close enough together where their variable (or side) groups can interact and form hydrogen bonds, ionic interactions, or covalent interactions. This causes the protein to take on an even more defined shape (conformation) called the tertiary (3 o ) level structure (R group to R group interaction). This structure (3 o ) defines the functional conformation for most proteins such as enzymes. Some proteins only become functional after they have been bonded to other proteins in a mega protein arrangement. When individual proteins (each with their own 1 o, 2 o, and 3 o shapes) come together to ultimately make a functional protein we call this the quaternary structure (4 o ) conformation. So the take home lesson concerning protein function is get the correct amino acid into the proper position during the primary construction OR risk conformational (shape) functional problems. This could result in a decrease in hooooomeooooostatic function for the organism. 6. (6) Explain and draw how DNA can be differentiated from RNA in terms of structure, function and location in eukaryotic cells. The atoms found in nucleic acids are Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus. These atoms are arranged into a monomer called a nucleotide (see below) that has different molecules in its structure. All nucleotides have a ribose sugar as the basis with a phosphate group bonded to its #5 carbon (at the corners or hanging to the side of the 4 th carbon position of the ring) of the sugar and a nitrogenous base bonded to its #1 carbon. 5

The sugar can be either a Ribose (RNA) or a Deoxyribose (DNA) (see figure below for the difference in structure)and the bases can be guanine (G), cytosine (C), thymine (T), Adenine (A), or Uracil (U).

6 The sugar can be either a Ribose (RNA) or a Deoxyribose (DNA) (see figure below for the difference in structure)and the bases can be guanine (G), cytosine (C), thymine (T), Adenine (A), or Uracil (U). Nucleic acids come in two forms Deoxyribose Nucleic Acid (DNA) or Ribose Nucleic Acid (RNA). To build either DNA or RNA the nucleotide monomers are linked together to form the polymeric DNA or RNA which vary from each other based on the sequence of bases DNA RNA Strand double singular Bases A, T, G, & C A, U, G, & C Sugars Deoxyribose Ribose Size Huge Portion copied from DNA Location Eukaryotes have in nucleus Both in the nucleus and the cytoplasm Types One Three (mrna, rrna, & trna These molecules function as information storage (DNA) and retrieval molecules (RNA). The DNA (storage) houses the original plans or directions to build the products which make-up the organism, while the RNA (retrieval) is a copy of those plans which are read to actually build the products for the organism. In eukaryotes this strategy of keeping the DNA inside a double membrane bound nucleus allows for maximum protection against having the original plans (DNA) being altered when building product or the cell replicating its DNA during cellular division, because if the RNA is built correctly but later damaged the original directions remain intact inside the eukaryotic nucleus. Cool. Why don t we consider prokaryotes in terms of location in terms of their DNA and RNA? 6

1/23/2012. Atoms. Atoms Atoms - Electron Shells. Chapter 2 Outline. Planetary Models of Elements Chemical Bonds

1/23/2012. Atoms. Atoms Atoms - Electron Shells. Chapter 2 Outline. Planetary Models of Elements Chemical Bonds Chapter 2 Outline Atoms Chemical Bonds Acids, Bases and the p Scale Organic Molecules Carbohydrates Lipids Proteins Nucleic Acids Are smallest units of the chemical elements Composed of protons, neutrons