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Biochemistry


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[Front]


van der waals forces also known as dispersion forces (induced dipole-induced dipole interactions)
[Back]


What determines the stability of 3D structures in proteins?

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Biochemistry - Details

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209 questions
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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?
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?
Phosphate diester bond Carbon 5 and carbon 3
What is the name of the bond formed between a sugar and phosphate?
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?
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?
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?
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?
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?
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?
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?
Proline
Which amino acid is found in collagen
Disulfide bond forms rigidity
Which bonds are formed with cysteine?