| 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? |
| Hydrophobic interior, hydrophilic exterior
also surrounded by a shell of water | Describe a micelle |
| 1. Carbohydrates
2. Nucleic Acids- DNA and RNA
3. Lipids
4. Proteins | What are the four types of macromolecules? |
| The sugars- RNA has ribose sugar, while DNA has deoxyribose sugar.
Bases- RNA has Uracil, while DNA has thymine.
Hydrogen- DNA has a hydrogen on carbon #2 rather than an alcohol like RNA | What is the difference between DNA and RNA? |
| 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? |
| 1. Nucleoside 5-triphosphate are carriers of energy
2. Bases serve as recognition unit
3. Cyclic nucleotides are signal molecules and regulators for cellular metabolism and reproduction
4. ATP is central to energy metabolism
5. GTP drives protein synthesis
6.CTP drives lipid synthesis
7. UTP drives carbohydrate synthesis | Which of the following are functions of nucleotides? |
| 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? |
| serine, aspartate and asparagine
side chains contain hydrogen bonding or acceptors in close proximity to the main chain, where they compete for main chain NH and CO groups. | Which amino acids disrupt alpha helices? |
| 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? |
| hydrogen bonding | What stabilizes beta sheets |
| typically 4 or 5, but as many as 10 or more can come together | How many strands come together in beta sheets? |
| perpendicular to the axis | In beta sheets, CO and NH groups are |
| true | True or false: Antiparallel sheets are much more stable than parallel sheets in beta sheets |
| silk | What is an example of something made of beta sheets? |
| Lactate dehydrogenase
beta-alpha-beta | What is an example of a super secondary structure? What is the composition |
| lysosome | What connects two antiparallel alpha helices? |
| in cell membrane | Where are beta barrels found? |
| parallel to the axis | In alpha helix, hydrogen bond is |
| alpha keratin | What is the primary component of wool and hair? |
| coiled-coil proteins | what is the superfamily of proteins referred as |
| van der Waals forces and ionic interactions | what are the two helices in alpha keratin cross linked by? |
| disulfide bonds formed by neighboring cysteine residues | Two helices in alpha keratin may be linked by |
| cysteine | which of the following amino acids form disulfide bonds? |
| Two | How many coils are in keratin? |
| three | how many coils are in collagen |
| collagen | What is the fibrous component of skin, tendon, cartilage and teeth? |
| glycine | Which amino acid in collagen is present every third residue? |
| glycine-proline-hydroxyproline | which amino acid sequence reoccurs frequently in collagen? |
| glycine
amino acid on either side of glycine is located on outside because on the outside is where there is room for bulky amino acids, such as proline | What amino acid fits in the crowded interior of the triple helix of collagen? |
| 4-hydroxyproline | Which element is common in collagen? |
| prolyhydroxyproline | Which element requires Vitamin C as a cofactor to keep iron in the reduced state? |
| By prosthetic groups | How is tertiary structures best identified? |
| globular proteins-water soluble and spherical | Describe the kind of proteins are associated with tertiary structures |
| Hydrophobic interactions with nonpolar side chains
covalent interactions (disulfide bonds)
attractive forces with opposite charges | Tertiary structures have what kind of interactions |
| Myoglobin-oxygen carrier binding protein | Water soluble proteins fold into compact structures called |
| myoglobin
globular proteins
tertiary structures | Which facilitate the diffusion of oxygen from the blood to mitochondria? |
| tertiary structures
globular proteins | Myoglobins are associated with what structure of proteins? What kind of proteins are they called? |
| Globular proteins have a compact three dimensional structure and are water soluble | What differentiates globular from fibrous proteins? |
| skeletal muscle and heart | where are globular proteins found |
| prosthetic groups | What are small organic molecules or metal ions associated with a protein called? |
| Enzymes, myoglobin, porins | What are examples of tertiary structures? |
| Porins are formed in the cell membrane, and they are pores allow the diffusion of molecules
beta barrel proteins | What are porins and where are they formed? |
| When an alpha helix is separated from another alpha helix by turn | What best describes helix turn helix units? |
| a compact globular unit
Example: CD4-contains four similar domains
ranges from about 30 to 400 amino acids | What is a domain? What is an example of a domain? |
| arrangement of multiple protein molecules into complexes | How are quaternary structures identified? |
| oligomers | Many protein monomers are called |
| many different protein monomers
hemoglobin (4 subunits-2 alpha and 2 beta) | What are heterooligomers? What is an example of a heterooligomer? |
| homooligomer | What is formed with identical protein monomer? What is an example? |
| hemoglobin-2 alpha 2 beta | Which of the following have 4 subunits?
Which of the following is a heterotetramer? |
| non covalent interactions | protein subunits of oligomers interact through |
| Dimer consisting of two identical subunits | What is the simplest quaternary structure? |
| liver alcohol dehydrogenase | Which is a quaternary structure with two subunits? |
| subunit | Each polypeptide chain in a protein is called a |
| human hemoglobin
changes in conformation or shape | What does allosteric mean?
Which of the following is allosteric? |
| Heme in hemoglobin
heme is responsible for the red color of blood and binding of oxygen | What is an example of a prosthetic group? |
| Heme | _______ consists of an organic component and a central iron atom |
| 6th | Which position does hemoglobin carry oxygen? |
| imidazole | What is the name of the compound attached to the 5th position? |
| 5th coordination site | Where is histidine attached? |
| planar | When oxygenated, heme is ____ |
| nonplanar | When deoxygenated, heme is ____ |
| histidine
6th
planar | What is the name of the amino acid attached to the heme?
Which position is oxygen carried?
If oxygenated, is the heme planar or nonplanar? |
| T state conformation | Oxygen is not present
iron is larger and outside of the hole
Both of these describe which conformation? |
| R state conformation | Oxygen is present
Iron is smaller and inside of the hole
This describes which conformation? |
| binds oxygen and responsible for red color of blood | What is the function of heme? |
| protoporphyrin | What is the organic component made up of four pyrrole rings linked by methene bridges? |
| Innate and adaptive | Describe the two types of immune responses |
| two (T and R states) | How many conformational states does Hb have? |
| Binding of the oxygen at the iron ion rearranges the electrons within the iron so that the ion becomes effectively smaller | What makes an ion become effectively smaller? |
| Movement of Fe(II) into the heme plane | What triggers the shift between T and R conformational shift? |
| porins | Which is an example of a trans-membrane protein? |
| EcoRI bound to DNA | Which is a restriction enzyme? |
| 20S Proteasome | Which is a multisubunit complex? |
| MHC with viral peptide | Which is an immunological complex? |
| body's primary defense against invaders (pathogens causing infection) and cancer
Immune response is able to distinguish between foreign and self | Describe immune response |
| Part of the adaptive immune response, humoral has B lymphocytes that produce an antibody/immunoglobin called IgG | Which immune response synthesizes IgG? |
| kills infected or cancerous cells
part of the cellular adaptive immune response | What is the function of T lymphocytes?
What is the origin of T lymphocytes? |
| nonspecific mechanisms that come into play immediately or within hours of an antigen's appearance in the body | Describe innate immune response. |
| Antibody molecule
Precipitation occurs when the antigen is crosslinked with the collection of antibodies | Produced by white blood cells, what molecule has two binding sites for its antigenic determinant?
When does precipitation occur? |
| B lymphocyte cells
effector cells
memory | Initial exposure to an antigen stimulates the _______ to proliferate and create ____cells, which secrete a soluble form of the antibody and _____cells. |
| igG attached on the surface of B-cell surface | Which immunoglobulin is the most abundant circulating the antibody? |
| V domains | _____domains confer specificity to antigenic determinants |
| IgA (monomer or dimer) | Which immunoglobulin prevents antigens (foreign substances) from directly attaching to the body cell? |
| IgM (pentamer) | Which immunoglobulin is a pentamer?
Which immunoglobulin is effective in foreign cell destruction? |
| IgE | Which antibody is associated with allergic reactions? |
| IgD and IgG | Which immunoglobulins are found on the surface of B-cells? |
| Antigen-binding site | What comprises the complementarity-determining regions of the antibody amino acid sequence?
_____ is hypervariable? |
| metabolism | What is the name of all chemical reactions inside the body? |
| IgG | Which immunoglobulin has disulfide bonding? |
| oxidoreductase | Which enzyme catalyzes redox reactions? |
| transferase | Which enzyme catalyzes group transfer reactions, often needing a coenzyme? |
| Hydrolase is an enzyme that catalyzes hydrolysis reactions | What is the function of hydrolase? |
| lyase
lysis of substrate | Which enzyme has a produce that contains a double bond? |
| isomerase
isomerization | Which enzyme catalyzes structural changes? |
| ligase | Which enzyme joins two substrates with input of energy?
Which enzyme is often called synthetase or synthase? |
| They accelerate and control the rate of vitally important biochemical reactions
Enzymes decrease the activation energy of a reaction | Why are enzymes important? |
| Binding energy is used to lower the activation energy barrier | Why is binding energy important? |
| A reaction is thermodynamically favorable or spontaneous when delta g is negative. | When is a reaction thermodynamically favorable? |
| Delta G, standard free energy change
Enzymes do not change thermodynamics! They do not alter standard free energy change, delta g of a reaction | The amount of energy consumed or liberated in a reaction is known as |
| binding energy | What ensures the favorable formation of the ES complex? |
| transition state | if a substance is neither a product or reactant, it is in the |
| binding site | What is the area that holds a substrate in place via non covalent interactions? |
| catalytic | The reaction occurs at the _____site. It reduces activation energy. |
| first step | The formation of the enzyme-substrate complex is which step?
What comes next? |
| fourth step is the release of the product. Before that. the transition state complex form the enzyme-product complex. | Which step is the release of the product? What comes before that? |
| enzymes | ____are proteins that provide a 3D surface for catalysis |
| Lock and Key Model | Which model explains how an unbound enzyme is complementary to the shape of the substrate? |
| Induced fit model | _________explains how the shapes of the active site can be markedly modified by the binding of the substrate |
| By the disappearance of the substrate (negative) and appearance of the product (positive) | How can the rate of enzyme activity be determined? |
