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level: Level 1

Questions and Answers List

level questions: Level 1

QuestionAnswer
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 interactionsWhat are examples of non covalent interactions?
Hydrogen bondingWhat kind of non covalent interaction determines the structure and properties of biomolecules?
Attractive forces with permanent dipoleHow would you characterize hydrogen bonding?
high electronegativity and small atomsWhy are nitrogen, oxygen and fluorine used for hydrogen bonding?
DNA and proteinsWhere 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 dipoleWhat are four properties of water?
Presence of hydrogen bondingWhat makes the heat capacity different in all compounds?
IceWhat is known as the molecular lattice formed by indefinite repetition of tetrahedral?
Hydrogen Bonding- gaps increase in volumeWhat 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?
ElectrolytesWhat are compounds that ionize when dissolved in water?
Nonpolar Hydrophobic moleculesWhat kind of molecules form clathrate around them?
ClathrateWhat is the name of the structures that surround nonpolar surfaces?
cell membraneWhich of the following is an example of an amphipathic molecule?
a monolayer, a micelles, or a bilayerWhat do ampiphatic substances form?
Hydrophobic interior, hydrophilic exterior also surrounded by a shell of waterDescribe a micelle
1. Carbohydrates 2. Nucleic Acids- DNA and RNA 3. Lipids 4. ProteinsWhat 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 RNAWhat is the difference between DNA and RNA?
Cytosine Methylcytosine Uracil Thymine Single ring is also known as a pyrimadineWhich of the following have a single ring?
Adenine and Guanine Purine is a double ringWhich is a purine?
phosphate diester bond Carbon 5 and carbon 3What 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 ThymineWhich of the following go through keto-enol tautomerization?
Adenine and CytosineWhich 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 synthesisWhich of the following are functions of nucleotides?
GTPWhat drives protein synthesis?
Cyclic nucleotidesWhat serves as signal molecules and regulators for cellular metabolism and reproduction?
ATPWhat functions in energy metabolism?
UTPWhat functions in carbohydrate synthesis?
DNAWhere is the close packing of atoms found? Where can we also find major and minor grooves?
2.2nmWhat would be an example of the distance in major grooves?
The parental molecule will produce an entirely new double stranded moleculeWhat does the conservative model state?
DNA polymerase I functions in the repair of damaged DNA in prokaryotesWhat 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 basesExplain 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 subunitWhich of the following subunits form a ring around DNA?
alphaWhich of the following subunits are involved in polymerase activity?
thetaWhich of the following subunits are involved in holoenzyme assembly?
exonuclease activityWhat is the function of the epsilon subunit?
zwitterionsAt 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 hemoglobinWhat are characteristics of amino acids? Why are proteins important?
GlycineWhich amino acid does not have a chiral center?
GlycineWhich amino acid lack an asymmetrical center?
enantiomersL-alanine and D-alanine are known as
because of evolution, its fixedWhy do all living things have L-amino acids?
Alanine, valine, isoleucine, leucineWhich of the following amino acids are alipathic and hydrophobic?
the presence of CH3What makes an R group uncharged?
alanineWhich is the simplest amino acid?
phenylalanineWhich of the following amino acids contain a phenyl ring?
Tyrosine because of the presence of hydrogen bondingWhich of the following aromatic rings are hydrophilic and why?
tryptophanWhich of the following amino acids have an indole ring?
methionine (hydrophobic)which of the following amino acids are sulfur containing?
glutamate and aspartateWhich amino acids contain an electronegative atom?
Acidic side chains-aspartate and glutamate Asp and GluWhich amino acids serve as nucleophiles in enzymatic reactions? How would you characterize their side chains?
Basic side chains Lysine, arginine and histidineWhat side chains are positively charged?
both hydrophilicWhat similarity is there between basic and acidic side chains?
LysineWhich side chain has an NH3 group attached to an alipathic hydrocarbon chain?
histidinewhich amino acid contains an imidazole group
histidinewhich amino acid serve as a buffer in active sites of enzymes?
histidineWhich of the following amino acids are found in active sites of enzymes?
imidazole ringWhat kind of ring can bind and release protons in enzymatic reactions?
arginineWhich of the following amino acids contain a guanidinium group?
arginine and lysineWhich amino acids end with a group that is positively charged at neutral pH?
GABA-chief inhibitory neurotransmitter in CNSWhich amino acid reduces neuronal excitability?
methionineWhich of the following amino acids contain a thio-ether group?
glycine, glutamate, serotonin, and melatoninExamples of neurotransmitters include
arginineWhich of the following amino acids is a metabolic intermediate in the urea cycle?
ProlineWhich 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, histidineHow many essential amino acids are there? What are they?
ThreonineWhich polar amino acid is essential?
pepsinWhat is important for enzymatic digestion?
histidineWhich amino acid produces histamine?
LysineWhich amino acid is important in protein synthesis?
methionine in smooth ERWhich amino acid is important in metabolism and detoxification?
phenylalanineWhich amino acid is the precursor for neurotransmitters?
leucineWhich amino acid regulates blood sugar levels?
threonineWhich amino acid is the principal part of structural proteins, such as collagen and clastin?
kwashiorkor disease swell with fluid in belly, for exampleWhat disease is the result of a lack of protein in diet?
amino acid sequenceHow do you differentiate all primary proteins from one another?
Primary structures are linear chains of amino acids connected by peptide bondsDescribe primary structures
Because its ends are differentWhy do polypeptides chains have directionality?
hydrogen bondsHow are secondary structures stabilized?
carbonyl and N-H groupsWhat kind of functional groups form hydrogen bonding in secondary structures?
Alpha Helix Beta Sheets U-TurnWhat are three repeating structures in secondary structures?
Regular combinations of protein structuresWhat best describes motifs?
motifWhat is the name of the part of a protein's sequence that is associated with specific biological information?
because of steric hindranceWhy 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 clashesUnnatural 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 helicesWhich of the following amino acids have steric clashes? (considered bulky amino acids) Which amino acids destabilize alpha helices?
cis conformationWhich 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 hydrogensWhich amino acid is unfavorable for alpha helix?
collagen and keratinAlpha helix has which two proteins?
triple helix fibrous protein rich in prolineDescribe collagen
prolineWhich amino acid is found in collagen
disulfide bond forms rigidityWhich bonds are formed with cysteine?
hydrogen bondingWhat stabilizes beta sheets
typically 4 or 5, but as many as 10 or more can come togetherHow many strands come together in beta sheets?
perpendicular to the axisIn beta sheets, CO and NH groups are
trueTrue or false: Antiparallel sheets are much more stable than parallel sheets in beta sheets
silkWhat is an example of something made of beta sheets?
Lactate dehydrogenase beta-alpha-betaWhat is an example of a super secondary structure? What is the composition
lysosomeWhat connects two antiparallel alpha helices?
in cell membraneWhere are beta barrels found?
parallel to the axisIn alpha helix, hydrogen bond is
alpha keratinWhat is the primary component of wool and hair?
coiled-coil proteinswhat is the superfamily of proteins referred as
van der Waals forces and ionic interactionswhat are the two helices in alpha keratin cross linked by?
disulfide bonds formed by neighboring cysteine residuesTwo helices in alpha keratin may be linked by
cysteinewhich of the following amino acids form disulfide bonds?
TwoHow many coils are in keratin?
threehow many coils are in collagen
collagenWhat is the fibrous component of skin, tendon, cartilage and teeth?
glycineWhich amino acid in collagen is present every third residue?
glycine-proline-hydroxyprolinewhich 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 prolineWhat amino acid fits in the crowded interior of the triple helix of collagen?
4-hydroxyprolineWhich element is common in collagen?
prolyhydroxyprolineWhich element requires Vitamin C as a cofactor to keep iron in the reduced state?
By prosthetic groupsHow is tertiary structures best identified?
globular proteins-water soluble and sphericalDescribe the kind of proteins are associated with tertiary structures
Hydrophobic interactions with nonpolar side chains covalent interactions (disulfide bonds) attractive forces with opposite chargesTertiary structures have what kind of interactions
Myoglobin-oxygen carrier binding proteinWater soluble proteins fold into compact structures called
myoglobin globular proteins tertiary structuresWhich facilitate the diffusion of oxygen from the blood to mitochondria?
tertiary structures globular proteinsMyoglobins 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 solubleWhat differentiates globular from fibrous proteins?
skeletal muscle and heartwhere are globular proteins found
prosthetic groupsWhat are small organic molecules or metal ions associated with a protein called?
Enzymes, myoglobin, porinsWhat are examples of tertiary structures?
Porins are formed in the cell membrane, and they are pores allow the diffusion of molecules beta barrel proteinsWhat are porins and where are they formed?
When an alpha helix is separated from another alpha helix by turnWhat best describes helix turn helix units?
a compact globular unit Example: CD4-contains four similar domains ranges from about 30 to 400 amino acidsWhat is a domain? What is an example of a domain?
arrangement of multiple protein molecules into complexesHow are quaternary structures identified?
oligomersMany 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?
homooligomerWhat is formed with identical protein monomer? What is an example?
hemoglobin-2 alpha 2 betaWhich of the following have 4 subunits? Which of the following is a heterotetramer?
non covalent interactionsprotein subunits of oligomers interact through
Dimer consisting of two identical subunitsWhat is the simplest quaternary structure?
liver alcohol dehydrogenaseWhich is a quaternary structure with two subunits?
subunitEach polypeptide chain in a protein is called a
human hemoglobin changes in conformation or shapeWhat does allosteric mean? Which of the following is allosteric?
Heme in hemoglobin heme is responsible for the red color of blood and binding of oxygenWhat is an example of a prosthetic group?
Heme_______ consists of an organic component and a central iron atom
6thWhich position does hemoglobin carry oxygen?
imidazoleWhat is the name of the compound attached to the 5th position?
5th coordination siteWhere is histidine attached?
planarWhen oxygenated, heme is ____
nonplanarWhen deoxygenated, heme is ____
histidine 6th planarWhat 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 conformationOxygen is not present iron is larger and outside of the hole Both of these describe which conformation?
R state conformationOxygen is present Iron is smaller and inside of the hole This describes which conformation?
binds oxygen and responsible for red color of bloodWhat is the function of heme?
protoporphyrinWhat is the organic component made up of four pyrrole rings linked by methene bridges?
Innate and adaptiveDescribe 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 smallerWhat makes an ion become effectively smaller?
Movement of Fe(II) into the heme planeWhat triggers the shift between T and R conformational shift?
porinsWhich is an example of a trans-membrane protein?
EcoRI bound to DNAWhich is a restriction enzyme?
20S ProteasomeWhich is a multisubunit complex?
MHC with viral peptideWhich is an immunological complex?
body's primary defense against invaders (pathogens causing infection) and cancer Immune response is able to distinguish between foreign and selfDescribe immune response
Part of the adaptive immune response, humoral has B lymphocytes that produce an antibody/immunoglobin called IgGWhich immune response synthesizes IgG?
kills infected or cancerous cells part of the cellular adaptive immune responseWhat 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 bodyDescribe innate immune response.
Antibody molecule Precipitation occurs when the antigen is crosslinked with the collection of antibodiesProduced by white blood cells, what molecule has two binding sites for its antigenic determinant? When does precipitation occur?
B lymphocyte cells effector cells memoryInitial 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 surfaceWhich 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?
IgEWhich antibody is associated with allergic reactions?
IgD and IgGWhich immunoglobulins are found on the surface of B-cells?
Antigen-binding siteWhat comprises the complementarity-determining regions of the antibody amino acid sequence? _____ is hypervariable?
metabolismWhat is the name of all chemical reactions inside the body?
IgGWhich immunoglobulin has disulfide bonding?
oxidoreductaseWhich enzyme catalyzes redox reactions?
transferaseWhich enzyme catalyzes group transfer reactions, often needing a coenzyme?
Hydrolase is an enzyme that catalyzes hydrolysis reactionsWhat is the function of hydrolase?
lyase lysis of substrateWhich enzyme has a produce that contains a double bond?
isomerase isomerizationWhich enzyme catalyzes structural changes?
ligaseWhich 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 reactionWhy are enzymes important?
Binding energy is used to lower the activation energy barrierWhy 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 reactionThe amount of energy consumed or liberated in a reaction is known as
binding energyWhat ensures the favorable formation of the ES complex?
transition stateif a substance is neither a product or reactant, it is in the
binding siteWhat is the area that holds a substrate in place via non covalent interactions?
catalyticThe reaction occurs at the _____site. It reduces activation energy.
first stepThe 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 ModelWhich 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?