Biochemistry
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| Van der waals forces also known as dispersion forces (induced dipole-induced dipole interactions) | What determines the stability of 3D structures in proteins? |
| Dipole Dipole/Van Der Waals/ Hydrogen Bonding/ ionic bonding/hydrophic interactions | What are examples of non covalent interactions? |
| Hydrogen bonding | What kind of non covalent interaction determines the structure and properties of biomolecules? |
| Attractive forces with permanent dipole | How would you characterize hydrogen bonding? |
| High electronegativity and small atoms | Why are nitrogen, oxygen and fluorine used for hydrogen bonding? |
| DNA and proteins | Where is hydrogen bonding found? |
| 1. High heat capacity 2. A density greater in liquid 3. Two H bond donor sites and an acceptor site 4. Permanent dipole | What are four properties of water? |
| Presence of hydrogen bonding | What makes the heat capacity different in all compounds? |
| Ice | What is known as the molecular lattice formed by indefinite repetition of tetrahedral? |
| Hydrogen Bonding- gaps increase in volume | What is the cause of water expanding in ice? |
| Increase in temperature (melting of ice) | What destroys/breaks the regular tetrahedral lattice? |
| Good solvent-those which dissolve in water (hydrophilic molecules) | What competes with intramolecular hydrogen bond donors and acceptors? |
| Electrolytes | What are compounds that ionize when dissolved in water? |
| Nonpolar Hydrophobic molecules | What kind of molecules form clathrate around them? |
| Clathrate | What is the name of the structures that surround nonpolar surfaces? |
| Cell membrane | Which of the following is an example of an amphipathic molecule? |
| A monolayer, a micelles, or a bilayer | What do ampiphatic substances form? |
| 1. Carbohydrates 2. Nucleic Acids- DNA and RNA 3. Lipids 4. Proteins | What are the four types of macromolecules? |
| Cytosine Methylcytosine Uracil Thymine Single ring is also known as a pyrimadine | Which of the following have a single ring? |
| Adenine and Guanine Purine is a double ring | Which is a purine? |
| Phosphate diester bond Carbon 5 and carbon 3 | What is the name of the bond formed between a sugar and phosphate? |
| Nucleotide is the whole thing-nitrogenous base, sugar and phosphate Nucleoside has no phosphate. It is just the nitrogenous base and sugar (ends in -osine) | How would you characterize the difference between nucleotide and nucleoside? |
| Guanine and Thymine | Which of the following go through keto-enol tautomerization? |
| Adenine and Cytosine | Which of the following go through amino-imino tautomerization? |
| GTP | What drives protein synthesis? |
| Cyclic nucleotides | What serves as signal molecules and regulators for cellular metabolism and reproduction? |
| ATP | What functions in energy metabolism? |
| UTP | What functions in carbohydrate synthesis? |
| DNA | Where is the close packing of atoms found? Where can we also find major and minor grooves? |
| 2.2nm | What would be an example of the distance in major grooves? |
| The parental molecule will produce an entirely new double stranded molecule | What does the conservative model state? |
| DNA polymerase I functions in the repair of damaged DNA in prokaryotes | What enzyme assists with DNA replication? |
| First three carry out DNA polymerase activity last domain functions in exonuclease activity: proofreads the product of DNA polymerase I and can remove any incorrectly matched bases | Explain the four domains associated with DNA polymerase I? |
| Replication occurs in the 5' to 3' end New strands are added in the 3' end. | What direction does replication occur? On what end are new strands added? |
| Beta subunit | Which of the following subunits form a ring around DNA? |
| Alpha | Which of the following subunits are involved in polymerase activity? |
| Theta | Which of the following subunits are involved in holoenzyme assembly? |
| Exonuclease activity | What is the function of the epsilon subunit? |
| Zwitterions | At pH 7.0, what are uncharged amino acids called? |
| Amino acids are able to polymerize, and can also act as acids and bases (amphoteric) Proteins are important for enzyme, antibodies, hormones, and hemoglobin | What are characteristics of amino acids? Why are proteins important? |
| Glycine | Which amino acid does not have a chiral center? |
| Glycine | Which amino acid lack an asymmetrical center? |
| Enantiomers | L-alanine and D-alanine are known as |
| Because of evolution, its fixed | Why do all living things have L-amino acids? |
| Alanine, valine, isoleucine, leucine | Which of the following amino acids are alipathic and hydrophobic? |
| The presence of CH3 | What makes an R group uncharged? |
| Alanine | Which is the simplest amino acid? |
| Phenylalanine | Which of the following amino acids contain a phenyl ring? |
| Tyrosine because of the presence of hydrogen bonding | Which of the following aromatic rings are hydrophilic and why? |
| Tryptophan | Which of the following amino acids have an indole ring? |
| Methionine (hydrophobic) | Which of the following amino acids are sulfur containing? |
| Glutamate and aspartate | Which amino acids contain an electronegative atom? |
| Acidic side chains-aspartate and glutamate Asp and Glu | Which amino acids serve as nucleophiles in enzymatic reactions? How would you characterize their side chains? |
| Basic side chains Lysine, arginine and histidine | What side chains are positively charged? |
| Both hydrophilic | What similarity is there between basic and acidic side chains? |
| Lysine | Which side chain has an NH3 group attached to an alipathic hydrocarbon chain? |
| Histidine | Which amino acid contains an imidazole group |
| Histidine | Which amino acid serve as a buffer in active sites of enzymes? |
| Histidine | Which of the following amino acids are found in active sites of enzymes? |
| Imidazole ring | What kind of ring can bind and release protons in enzymatic reactions? |
| Arginine | Which of the following amino acids contain a guanidinium group? |
| Arginine and lysine | Which amino acids end with a group that is positively charged at neutral pH? |
| GABA-chief inhibitory neurotransmitter in CNS | Which amino acid reduces neuronal excitability? |
| Methionine | Which of the following amino acids contain a thio-ether group? |
| Glycine, glutamate, serotonin, and melatonin | Examples of neurotransmitters include |
| Arginine | Which of the following amino acids is a metabolic intermediate in the urea cycle? |
| Proline | Which of the following amino acids influence protein architecture? In other words, which amino acid is conformationally restricted? |
| 9 Valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, threonine, lysine, histidine | How many essential amino acids are there? What are they? |
| Threonine | Which polar amino acid is essential? |
| Pepsin | What is important for enzymatic digestion? |
| Histidine | Which amino acid produces histamine? |
| Lysine | Which amino acid is important in protein synthesis? |
| Methionine in smooth ER | Which amino acid is important in metabolism and detoxification? |
| Phenylalanine | Which amino acid is the precursor for neurotransmitters? |
| Leucine | Which amino acid regulates blood sugar levels? |
| Threonine | Which amino acid is the principal part of structural proteins, such as collagen and clastin? |
| Kwashiorkor disease swell with fluid in belly, for example | What disease is the result of a lack of protein in diet? |
| Amino acid sequence | How do you differentiate all primary proteins from one another? |
| Primary structures are linear chains of amino acids connected by peptide bonds | Describe primary structures |
| Because its ends are different | Why do polypeptides chains have directionality? |
| Hydrogen bonds | How are secondary structures stabilized? |
| Carbonyl and N-H groups | What kind of functional groups form hydrogen bonding in secondary structures? |
| Alpha Helix Beta Sheets U-Turn | What are three repeating structures in secondary structures? |
| Regular combinations of protein structures | What best describes motifs? |
| Motif | What is the name of the part of a protein's sequence that is associated with specific biological information? |
| Because of steric hindrance | Why are all alpha helices found in proteins right-handed? |
| Nature of side chains (R groups) | What can affect overall stability of alpha helices? |
| Proline because it creates bends -lacks N-H group -restricted rotation due to its cyclic structure (can't fit in alpha helix) | What kind of amino acid is a helix breaker? |
| Steric clashes | Unnatural overall of any two non-bonding atoms in a protein structure result in |
| Valine, isoleucine, threonine Because of the branching at the beta carbon which destabilize alpha helices | Which of the following amino acids have steric clashes? (considered bulky amino acids) Which amino acids destabilize alpha helices? |
| Cis conformation | Which kind of conformation is steric clashes found in? |
| Glycine because of two mobile hydrogens | Which amino acid is unfavorable for alpha helix? |
| Collagen and keratin | Alpha helix has which two proteins? |
| Triple helix fibrous protein rich in proline | Describe collagen |
| Proline | Which amino acid is found in collagen |
| Disulfide bond forms rigidity | Which bonds are formed with cysteine? |