Lecture 3: Macromolcules Flashcards
Explain the role of hydrogen bonding in the formation of all of the biological macromolecules.
In proteins, hydrogen bonding holds beta-sheeting together in peptide formations. And there are hydrogen bondings happening between R-groups in tertiary structures.
In carbohydrates, hydrogen bonds make cellulose rigid enough to become a cell wall. Cellulose is unbranched and therefore can hydrogen bond. Hydrogen is partially positive and is polar covalent. Unbranched means hydrogen can get close to the electronegative atom to form an attraction.
In nucleic acids, hydrogen bonds are needed to make a double helix.
In lipids, there are hydrogen bonds that form between water and water as well as water and phosphates. The hydrophobic effect is when water hydrogen bonds with other water molecules and excludes the phosphates which may form a lipid bilayer. The lower the pH the more hydrogens.
Be able to sketch generic dehydration synthesis and hydrolysis reactions.
see lecture 3
Be able to sketch a generic amino acid, identify the amino and carboxyl groups, and sketch how they are involved in peptide formation.
H
|
NH3 -- C -- COO
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RBe able to place a given amino acid structure in one of the groups on slide 7, and know why it matters which group a particular amino acid belongs to.
Check slide 7 lecture 3
Recognize when a molecule has stereoisomers.
You know a molecule is a stereoisomer if you switch around a carbon atom, you will have a new molecule. A carbon atom with 4 different groups attached,
Define what we mean by protein primary, secondary, and tertiary structure.
Primary structures have amino acids with peptide bonds.
Secondary structures are alpha helices and beta sheets.
Tertiary structures contain hydrogen bonding, ionic bonding, can der waals interaction, and disulfide bonds forms into proteins. Contains a single polypeptide chain backbone with one or more protein secondary structures.
Know what types of interactions are involved in protein tertiary structure formation.
Disulfide bonds (Cysteine) and weak bonds such as hydrogen bonds, van der waals interactions (non-polar amino acids), and ionic bonds.
Recognize the difference between an alpha helix and a beta sheet.
Alpha helix structures of proteins forms due to hydrogen bonding between its backbone amide and carbonyl groups. It is a right-handed coil with an n+4 structure. Hydrogen bonds form between an N-H group of one amino residue with a C=O group of another amino acid. Proline destablizes alpha helices due to its irregular geometry (steric hindrance). R groups are facing outwards.
Beta pleated sheets are connected laterally by at least 2 or 3 backbone hydrogen bonds, forming a generally twisted, pleated sheets. N-H groups in the backbone or one strand create hydrogen bonds with the C=O groups in the backbone of the adjacent strands. N-terminus and C-terminus illustrate the direction. R-groups are facing both inside and outside of the beta-sheet.
Understand how a protein’s structure determines its function.
The function of a protein is directly dependent on it’s 3D structure. Remarkably, proteins spontaneously fold up into 3D structures that are determined by the sequence of amino acids in the protein polymer. Protein structure plays a key role in its function; if a protein loses its shape at any structural level, it may no longer be functional.
Recognize the difference between alpha and beta glycosidic bonds, and know why it’s important.
Alpha glycosidic bonds have anomeric carbon that points downward. They are easily hydrolyzed and cannot be digested by humans (glycogen).
Beta-glycosidic bonds have anomeric carbon that points upward. Can only be broken down by bacteria and fungi (cellulose).
Assemble structures of ribose, phosphate, and nucleotides to form a nucleoside triphosphate.
Nucleoside has a nitrogenous base and a sugar. A nucleotide has a nitrogenous base, sugar, and a phosphate.
Know the hydrogen bond base pairing rules.
Pyrimidines: Cysteine, Thymine, and Uracil
Purines: Adenine and Guanine
A with U or T
C with G
Recognize the difference between the 5’ and 3’ ends of a nucleic acid polymer.
In a phosphodiester bond, the 5’ end is the phosphate and the 3’ end is the -OH.
Assemble structures of glycerol, fatty acids, and phosphate to form a phospholipid.
Contains an ester bond.
Explain the relationship between saturated, cis-unsaturated, and trans-unsaturated fatty acids.
Saturated: Most rigid and has all the hydrogens it can take; no double bonds. Packs tightly, is solid, and found in animals and bacteria.
Cis-unsaturated: Least unsaturated; Hydrogens on the same side of the double bond and more liquid at room temperature. Very bent, packs loosely, found in plants and bacteria.
Trans-unsaturated: Hydrogens on the opposite side of the double bond. Slightly bent, packs tightly, solid, found in bacteria.
Hydrogenation makes unsaturated into saturated
