MCB Final Exam

Ionic attraction

attraction of opposite charges

covalent bond

sharing of electron pairs

hydrogen bond

attraction between H and a strongly electronegative atom

hydrophobic interaction

interaction of non polar substances in the presence of polar substances (especially water)

van der Waals interaction

interaction of electrons of non polar substances

The hydrophobic effect plays a very important role in protein folding. What distinguishes the hydrophobic effect from other non-covalent interactions such as hydrogen-bonds and ionic interactions?

hydrophobic effect is driven by entropy and is not electrostatic in nature

hydrophobic interactions play an important role in _____.

protein folding reactions

______ occur between non polar amino acids.

Hydrophobic interactions

The two hydrophobic amino acids are ________ and ___.

leucine and isoleucine

Which of the following statements about hydrophobic interaction is __correct__?

A. Hydrophobic interaction is very important for membrane formation.

B. During protein folding, polar side chains of amino acids are buried inside via hydrophobic interaction.

C. Hydrophobic effect occurs because the hydrophobic molecules attract each other.

D. Hydrophobic interaction is a type of electrostatic interaction.

Hydrophobic interaction is very important for membrane formation.

Which of the following does not form a biological polymer?

A) Amino acid

B) Carbohydrate

C) Lipid

D) Nucleotide

Lipids

Membrane formation is driven by ______.

the hydrophobic effect

Common biological buffer systems

\-Phosphate buffer

\-bicarbonate buffer

\-cellular proteins

Nonpolar (hydrophobic) amino acids

Gly, Ala, Pro, Val, Leu, Ile, Met

Polar (hydrophilic) amino acids

Ser, Thr, Cls, Así, Gln

Positively charged amino acids

Lys, Arg, His

Negatively charged amino acids

Asp, Glu

What types of bonds are present in proteins?

peptide bonds

The covalent bond that joins carbohydrate molecules to another carbohydrate or other group.

Glycosidic bond

Chemical bond that joins the sugar molecule

phosphodiester

What does a positive Δ*G* indicate?

endergonic reaction

Which atoms are the strongest H-bond acceptors?

more electronegative atoms (approaching F)

Under what conditions would a carboxyl group be mostly charged?

pH > pKa ; more protons so positively charged

If an amino acid does not contain an ionizable side chain, it’s net charge at physiological pH will be what?

0

Which amino acid would most likely be found in the internal core of a globular protein?

Leucine

Amino acids on the internal core of a protein should be _____.

Charged

(-) Glutamic Acid (Glu, E) and Aspartic Acid (Asp, D)

(+) Arginine (Arg, R), Histidine (His, H), and Lysine (Lys, K)

Amino acids on the outside of a protein should be ____.

Nonpolar (hydrophobic) to create the membrane.

What type of chromatography separates protein based on net charge?

ion exchange chromatography

______ allows a biochemist to estimate the molecular mass of a protein in its native state.

gel filtration chromatography

______ allows a biochemist to estimate the molecular weight of a protein in its denatured state.

SDS-PAGE

A protein that consists of a single polypeptide chain will lack which level of protein structure?

Quaternary; has multiple chains

What type of covalent bonds are responsible for holding together the secondary structure of proteins?

Hydrogen bonds

People who live at moderately high altitudes experience a change in 2,3-BPG concentration order to prevent hypoxia. Would you expect the concentration of BPG to increase or decrease in these individuals?

increase; a an increase in BPG makes it easier for oxygen (O2) to be released - higher altitudes means we need more O2

The minimum amount of energy required to bring about a chemical reaction.

activation energy

enzymes bind more tightly to ____.

the transition state

The model that describes a conformational change in enzyme structure upon binding substrate is referred to as…

the induced-fit model

Type of enzyme that transfers electrons and results in a change in oxidation state.

oxidoreductase

Type of enzyme that transfers a functional group from one molecule to another.

transferase

Dehydrogenases are an example of what type of enzyme?

oxidoreductase

Phosphorylases and kinases are examples of what type of enzyme?

transferase

Proteases and phophatases are examples of what type of enzyme?

hydrolase

This type of enzyme breaks down a covalent bond using water.

hydrolase

this type of enzyme breaks down a covalent bond without water or oxidation.

Lyase

Examples of lyase

decarboxylase

this enzyme catalyzes a rearrangement of bonds within a molecule.

isomerase

Mutates are examples of what type of enzyme?

isomerase

This enzyme catalyzes a formation of a covalent bond between two large molecules.

Ligase

What type of curve is yielded for a Michaelis-Menten enzyme?

hyperbolic

Competitive inhibitor

any molecule that can bind to the active site of an enzyme with sufficient affinity such that it can compete with the enzyme’s natural substrate and reduce enzyme activity as a result

Non-competitive inhibitor

binds equally well to the enzyme and the enzyme-substrate complex

Uncompetitive inhibitors

only bind to the enzyme-substrate complex

In what type of reversible inhibition is binding of the inhibitor and substrate mutually exclusive?

competitive

Competitive inhibition ____ __Km and__ ____Vmax.

increases, does not affect

Uncompetitive inhibition ___ Km and ____ Vmax.

reduces, reduces

Noncompetitive inhibition ___ Km and ____ Vmax.

does not affect, reduces

Which are the purine bases?

Adenine and Guanine (Pur(e)ines Are Good)

Pyramidines

Cytosine, uracil, thymine

(pyramids CUT)

What is the distinction between a nucleoside and a nucleotide?

A nucleoside contains no phosphate groups but a nucleotide does.

Which size of DNA fragments will be at the bottom of an agarose gel?

smaller fragments

Would DNA-binding proteins be more likely to associate with the major or the minor groove?

Major groove

Which of the following organisms would likely have a higher GC content?

A)*Thermus aquaticus* (a thermophile)

B)*Escherichia coli*

*Thermus aquaticus*

GC has three H bonds so higher melting temp (less likely to degrade at higher temperatures)

Which of the following will hybridize with a DNA molecule with the sequence: 5’-AGACTGGTC-3’

5’-GACCAGTCT-3’

Type ___ topoisomerase make double-strand breaks in DNA.

II

Which DNA strand would carry multiple RNA primers?

lagging strand

Repetitive sequences of chromosomes that allow the ends to be replicated are ____.

telomeres

What keeps DNA dissociated during replication and protects it?

SSB (single-strand binding protein)

What type of DNA damage occurs due to reactive oxygen species?

Oxidation of nucleotide bases

Which of the following are involved in mismatch repair of DNA?

A) AP endonuclease

B) DNA glycosylase

C) MutS

D) Ku protein

E) RecAprotein

MutS

In eukaryotes, mRNAs are synthesized in the cell ____, whereas most translation occurs in the _____.

nucleus; cytosol

The RNA polymerase subunit that recognizes the bacterial promoter is…

σ (sigma)

Which of the following is the cap nucleotide on a eukaryotic mRNA?

A) G

B) T

C) C

D) U

E) A

Guanosine cap (G)

In _____ transcription termination in prokaryotes, the signal for termination is in the message itself.

rho-independent

How does the transcriptional machinery gain access to the nucleosome-bound DNA?

Chromatin-remodeling complexes allow sections of DNA to be transiently exposed to transcription factors.

Would the human genome most likely carry more genes for rRNA or for mRNA?

rRNA; because rRNA isn’t dissociated as fast as mRNA because it is necessary for ribosomes

Which types of interactions predominate for sequence-specific DNA-binding proteins?

hydrogen bonding

Transcriptionally active DNA in eukaryotes is contained in

euchromatin

What polymers are formed by amino acids?

proteins

What polymers are formed by carbohydrates?

polysaccharides

What polymers are formed by nucleotides?

DNA

The correct amino acid is covalently attached to a tRNA by the corresponding …

aminoacyl-tRNA synthetase

The incoming aminoacyl-tRNA enters the ribosome at the ___ site.

A

Which chaperone contains 2 heptameric rings?

GroEL

In E. coli, base-pairing between an mRNA’s ___ and the 3’ end of the 16S rRNA persists the ribosome to select the proper initiation codon.

Shine-Dalgarno sequence

Hydrolysis of GTP by EF-Tu is thermodynamically required for…

formation of the peptide bond

Ile amino acyl tRNA synthetase uses a double-sieve mechanism to accurately produce Ile-tRNAIle and prevent synthesis of Val-tRNAIle.  Which of the amino acid pairs might have amino acyl tRNA synthetases that have a similar proofreading mechanism?

Gly/Val (both non-polar)

Ser/Thr (both polar)

Which mechanism for degrading cellular proteins involves a barrel-shaped protein complex?

proteasome

What is the primary storage form of fatty acids?

triglycerols (triglycerides)

Rank the melting points of the following fatty acids:

(1)*cis*-oleate (18:1)

(2)*trans*-oleate (18:1)

(3)Linoleate (18:2)

2 > 1 > 3

The simplest sugars have a minimum of ___ carbon atoms.

3

The molecules D-glucose and L-glucose are examples of

enantiomers

Catabolic reactions are chiefly __*___*__ whereas anabolic reactions are _____.__

degradative; synthetic

Glycogen is primarily stored in

muscle and liver

Which of the following represents the preferred order of fuel mobilization in humans?

A) Amino acids > fatty acids > carbohydrates

B) Carbohydrates > amino acids > fatty acids

C) Carbohydrates > fatty acids > amino acids

D) Fatty acids > carbohydrates > amino acids

Carbohydrates > fatty acids > amino acids

Cells control or regulate flux through metabolic pathways by:

allosteric control of enzymes, covalent modification of enzymes, and genetic control of enzyme concentrations

What cofactor would be needed to carry out the reaction catalyzed by the Krebs cycle enzyme isocitrate dehydrogenase?

NAD+

What are the potential control points in glycolysis?  What is the actual control point?

Possible: Steps 1, 3, 10

Actual: Step 3

The enzyme ____ participates in a regulatory substrate cycle with phosphofructokinase

Fructose-1,6-bisphosphatase

In circulation, free fatty acids are bound to …

chylomicrons

Fatty acid activation occurs in the …

cytosol

Fatty acids are activated for β-oxidation by the transfer of

AMP from ATP