Biochem Final - Exam Questions

Glycolysis uses ___

1 glucose 2 ATP 2 NAD+

Which of the following amino acids have polar, uncharged R groups?

1. Lysine and cysteine 2. Serine and asparagine 3. Methionine and glutamine 4. Tryptophan and tyrosine

In the following LDH reaction what is 1 and what is 2? (2 is on top)

1. NADH 2. NAD+

Formation of open complex involves unwinding of DNA, how many bases are unwound in that complex?

14

Eukaryotic ribosomes have all of the following RNAs except:

16s

Epimers

2 sugars that differ in stereochemistry at only one carbon

Alpha helix with the length of 40 A will have __ amino acids

26

DNA polymerase have all of the following enzymatic activities EXCEPT:

3'-5' Endonuclease

EXCEPT:

3'-5' endonuclease activity

When glucose completely oxidizes to CO2 through glycolysis and then CAC then the direct and indirect ATP yield is ___

32 ATP

How many ATPs are generated during the pay off phase of glycolysis?

4

In ice, water molecule makes hydrogen bonds with ____ total surrounding molecules

4

DNA sequence is read from ..

5' to 3'

DNA polymerases enzymatic activities are:

5'-3' exonuclease 5'-3' polymerase 3'-5' exonuclease

Which of the following process is used in the production of foods like yogurt and soy sauce?

Fermentation & Anaerobic glycolysis

Stop codons are also called..

Nonsense codons

Compounds that inhibit key steps in glycolysis can kill cancer cells by

limiting energy production

What will be the net charge on the following peptide in pH 3 solution? Ala-Ser-Asp-Pro-Lys-Val-Glu-Leu-His-Gly

+2

Which of the following forms of Lysine will exist at pH 5?

+H3N - CH - COO- (NH3+ at the end of chain)

TTGACA sequence after trp..... before sequence

-35

Determine the fraction of Vmax that would be obtained at substrate concentration that is equal to 3.75 km.

0.8

Eukaryotic translation initiation is different from prokaryotes by:

1. Eukaryotic initiation requires more initiation factors. 2. Eukaryotic translational initiation is mechanistically different. 3. There is a step that circularizes mRNA during eukaryotic intiation.

White type of enzymes facilitate lateral diffusion of lipids in a bilayer?

1. Flippase 2. Floppase 3. Scramblase 4. None of the above Answer: ?

Which of the following is true for membranes?

1. Two leaflets of lipid bilayer have different lipid compositions. 2. Ratio of lipid to protein does not change from one membrane to the other. 3. Membranes retain metabolites and ions within the cell.

Which of the following is not a covalent bond?

1. peptide bond 2. Disulfide bond 3. Glycosidic bond 4. Hydrogen Bond

If a pKa of a carboxylic group A is 7 and for carboxylic group B is 2, then group A is ____ times less acidic than group B.

100,000

If a velocity of a reaction (vo) is 30 microMS-1, K2 is 800, s is 0.04 mM and Et is 50 nM. Calculate Km for substrate S.

13

Which fatty acid has the highest melting temperature?

20:0

If carbon 1 is the carbonyl group of an aldohexose, which carbon determines if the sugar is regarded as a D or L stereoisomer?

5

Calculate the pH of a solution that contains a molar ratio of conjugate base to acid (pKa = 4.76) of 5:1 and 1:10

5.46 and 3.76

If there are 50 purines in a DNA molecule, how many pyrimidines will be present in the same molecule?

50

If an uncatalyzed reaction occurs at a rate of 5x10^2 and if an enzyme accelerates this reaction 500 times then the rate of the reaction will be?

500x500 = 250,000 = 2.5x10^5

Eukaryotic ribosomes have which RNAs:

5s 28s 5.8s

If the best buffering range for a buffer is ph 6 to ph 8 then what would be the pKa for this buffer?

7

What will be the pH of 0.0000001 M NaOH solution?

7

An activator is..

A positive heterotropic effector

During rho-factor independent termination,

A's in DNA spontaneously attaches to T's in DNA and weakens RNA-DNA hybrid

During prokaryotic translation elongation, the incoming aminoacyl tRNA binds to ____ site of the 70s initiation complex

A.

All of the following are coenzymes for pyruvate dehydrogenase complex EXCEPT:

AMP

The currency of energy in the cell is in the form of

ATP and NAD(P)H

What are the products of pyruvate decarboxylase reaction during ethanol fermentation?

Acetaldehyde and CO2

Cellular respiration involves all of these stages:

Acetyl CoA production Acetyl CoA oxidation Electron transfer and oxidative phosphorylation

EXCEPTT:

Acetyl coA reduction

Which enzyme catalyzes a conversion of a tertiary alcohol to a secondary alcohol in a CAC?

Aconitase

Which of the following CAC reaction is reversible?

Aconitase

Phosphorylation of glucose does:

Activates glucose Traps glucose inside the cell Lowers intracellular glucose concentration

EXCEPT :

Addition of large peptide to the protein.

Which step utilizes CoASH in CAC?

Alpha Ketoglutarate dehydrogenase

tRNA molecules have amino acid attached at 3' end via ____

Amino acyl ester bond

In an alpha helix, the R groups on the amino acid residues:

Are found on the outside of the helix spiral

Beta sheets are either parallel or anti-parallel, because of ___.

Arrangement of N and C terminal

Ionic Bonds & forces

Attraction between 2 opposite charges - 20 kj/mol individually weak, together strong

Phosphofructokinase-1 is regulated by:

Both ATP and Fructose-2,6-biphosphate

DNA denaturation does NOT cause

Breakage of covalent bonds

Protein X has a bound small molecule compound A. Compound A has unique absorbance at 450 nm. For this reason, you wish to separate a population of protein that has bound compound A from free compound A in solution. This will help in characterizing protein by using 450 nm as a unique wavelength. How would you do that?

By size exclusion chromatography

If an anticodon 1st position is G then it can make H bond interaction with this base in the third position of the codon

C, A

What is an ampholyte and zwitterion?

Can both act as an acid or a base Has R groups with one - charge and one + charge

Posttranslational modifications of protein all of the following:

Carbohydrate attachment Removing sequence to activate enzyme Removal of signal sequences

Nucleotides play functions other than being a part of DNA/RNA, which of the following functions CANT be performed by nucleotides?

Catalysts

Eukaryotes are largely

Chemoheterotrophs

What is the product of the rate limiting step of the CAC?

Citrate

The following figure shows attachment of aminoacyl ACP to a sugar of the adenin base during a catalysis by aminoacyl tRNA synthetases. Which class is this for?

Class 2

Allosteric modulator does everything that is listed below except:

Competes with a substrate for the same binding site.

Which of the following is the first committed step of glycolysis?

Conversion of fructose-6-P to fructose-1,6-biphosphate

Which step of the citric acid cycle is a hydration step?

Conversion of fumarate to malate

Inosine can be made by ___ of ___.

Deamination, adenosine

Acetylation modifies enzymatic activity by

Decreasing and Increasing it

Below is a structure of L-Fucose, this is a type of _____

Deoxy sugar (oxygen missing on the 6 carbon)

Which of the following component is NOT required for prokaryotic translation initiation?

EF-G

2-phosphoglycerate is converted to phosphoenolpyruvate by

Enolase

Flippases

Enzyme that catalyzes lipid movement in a bilayered membrane. Moves from outer to cytosolic leaflet

Eukaryotic translation initiation is different from prokaryotic by the following EXCEPT:

Eukaryotic initiation requires both ribosomal subunits.

Exam 2

Exam 2

Exam 3

Exam 3

What form is this structure of alanine?

Fully protonated

All of the following is true about fermentation-

Generation of ATP without consuming O or NAD+ No net change in oxidation state of sugars Regenerates NAD+ for further glycolysis Reduction of pyruvate to another product

Glucose molecules are cleaved from glycogen and starch by glycogen phosphorylase yielding ___

Glucose 1-phosphate

Maximum gene expression for lac operon will occur by

Glucose low, cAMP high, Lactose present

What amino acids DO take part of acid base catalysis?

Glutamate Cystine Lysine

Amino acid below is a derivative of a common amino acid ____, which is ____ amino acid.

Glutamate & uncharged

Of the 20 standard amino acids, only _________ is not chiral. The reason is that its side chain _______.

Glycine; is a hydrogen atom.

Succinate dehydrogenase reaction

Has a covalently linked FAD Not regulated Does not produce NADH

What is NOT true about transition state?

Has a defined chemical structure.

A glycosidic bond is the result of a..

Hemiketal or hemi acetal reacting with an alcohol.

What determines a high Tm in a DNA sequence?

High amounts of G and C

How to determine if a structure of a sugar is D or L?

If the OH is on the right (D) or the left (L) of the chiral center farthest from the carbonyl carbon (C=O)

DNA proofreading activity is all of the following:

Increases fidelity of replicaiton Removes mispaired nucleotide Double checks each nucleotide after adding it

Lac operon is an example of ___

Induction

EXCCEPT:

Is also called aerobic glycolysis

DNA POL 1 functions:

Is not ideal for DNA replication Polymerization rate is slower than the fork movement Main function is clean up in various processes

Which of the following enzyme catalyzes oxidative decarboxylation step in CAC?

Isocitrate dehydrogenase & Alpha ketoglutarate dehydrogenase

DNA POL 1 is not a primary replication polymerase because:

It has low processivity and polymerization rate.

When phosphatidylserine is present outside of the cell,

It is a marker for cell destruction.

Which of the following is NOT true about the nature of the genetic code?

It is generally overlapping

Lactate produced by lactic acid fermentation gets transported to ___ for gluconeogenesis.

Liver

Van Der Waals forces are ______ in strength compared to H bonds.

Lower

Which of the following is NOT true for membranes?

Membranes are asymmetric

What type of catalytic mechanism is used by enzymes to participate in oxidation reactions?

Metal ion catalysis

These are the only two amino acids with single codons.

Methionine and tryptophan

RNA polymerases have which of the following metal ion to aid in the catalytic reaction?

Mg2+

Enzymes involved in the production of ethanol in yeast use all of the following cofactors EXCEPT:

Mn2+

Multienzyme complexes provide all of the following advantages EXCEPT:

Mostly involved in oxidation/reduction reactions

Protein has a characteristic 280 nm absorbance because of ___

Mostly tryptophan and tyrosine

Tautomerization

Moves a hydrogen changing enol to keto form

Scramblase

Moves lipieds in either direction toward equilibrium

The messelson-Stahl experiment used a heavy isotope of which atom?

N

Which of the following is not a substarte for the reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenase?

NADH

These molecules are general inhibitors of CAC

NADH and ATP

Which of the following organism require presence of oxygen for growth?

Obligate aerobe

Anaplerotic reactions fill up which of these intermediates in CAC?

Oxaloacetate and Malate

Which of the following enzymes is NOT a part of gluconeogenesis path way?

PEP carboxylase

Hydrophobic interactions most likely occur between which of the following R groups in amino acids?

Phenylalanine and tryptophan

Formation of 3-phosphoglycerate from 1,3-biphosphoglycerate is catalyzed by

Phosphoglycerate kinase

The lifetime of H bond in water molecules is in

Picoseconds (ps)

What IS true about transition state?

Present in enzyme catalyzed reactions Very short lived Is complementary to the enzyme

Phosphoylation of glucose does all of the following EXCEPT:

Promotes glucose transport from inside to outside of a cell

If three proteins X, Y, and Z with MW of 10, 15, 70 kDa are being separated by gel filtration chromatography then which of the following is correct?

Protein Z with MW will elute first (because it's a column)

TuC arm of tRNA contains which of the following uncommon nucleoside?

Pseudouridine

Anaplerotic reactions are catalyzed by all of the following enzymes EXCEPT:

Pyruvate carboxykinase

Ethanol fermentation in yeast involves these 2 enzymes.

Pyruvate decarboxylase & alcohol dehydrogenase

During lactate dehydrogenase catalyzed reaction

Pyruvate is reduce to give lactate

Which of the following steps of glycolysis neither use nor make ATP:

Reaction catalyzed by phosphoglycerate mutase

Fermentation involves all of the following EXCEPT:

Reduction of pyruvate to acetyl-CoA

What CAN nucleotides do?

Regulatory molecules Coenzymes Energy source

What is the bond between the following disaccharide:

Ribose-beta-1,4-glucose

The initiating 5' AUG codon of mRNA is guided to its correct position by the ___ sequence.

Shine delgarno

What is the shape of the curve of initial velocity vs substrate concentration for allosteric enzymes?

Sigmoidal

Which step of glycolysis called phosphohexose isomerization?

Step 2

DNA denaturation DOES cause:

Strand separation Increase in UV absorbance Breakage of H bonds

All of the following reactions produce NADH in the CAC EXCEPT:

Succinate dehydrogenase

All of the following steps of CAC are regulated EXCEPT:

Succinate dehydrogenase reaction

Which CAC enzyme has a covalently linked FAD, which is very unusual.

Succinate dehydrogenase.

Substrate level phosphorylation is catalyzed by ___ enzyme in CAC

Succinyl CoA Synthetase

Which of the following toxin blocks A site on the ribosome?

Tetracyclines

A glycosidic bond is the covalent linkage between

The anomeric carbon of a saccharide and an alcohol

Which of the following is NOT true for integral membrane proteins?

They are removed by disrupting ionic interactions either with high salt/pH change

Which of the following is true for integral membrane proteins

They can span both leaflets. Purified int. membrane proteins are generally associated with some lipids Integral proteins can be monotopic or polytopic

How to draw a fisher projection from a howarth projection

Top goes on the right

Mutase is an enzyme that __

Transfers a group from one carbon to another

Enzyme complementary to the ____ would be the best enzyme.

Transition state

What kind of enzyme is EF-G?

Translocase

Hydropathy plots can predict..

Transmembrane domains

Which of the following amino acid does NOT participate in acid base catalysis?

Tryptophan

Non-Covalent bonds and their forces

Van der Waals - electrical interaction - 0.4-4.0 kj/mol Hydrogen bonds - shared protons - 12-30 kj/mol

Which is NOT true about DNA POL 1?

With all its domains in tact, its also called Klenow fragment

For an acid AH, pH = pK when:

[A] = [HA]

Which of the following functional groups containing compounds participate in H-bond formation?

alcohol, ketone, aldehyde (all of the above)

Humans do not have an enzyme to synthesize this essential fatty acid

alpha-linolenic acd

Example of substrate level phosphorylation in glycolysis:

both A and B (kinase options) a. pyruvate kinase reaction b. phosphoglycerate kinase reaction

Amphitrophic proteins are __

conditionally attached to membranes and can be reversibly removed.

Conversion of Glucose-6-P to Fructose-6-P is ___ type of reaction

isomerization

Floppase

moves from cytosolic to outer leaflet

During strenuous exercise lactate builds up in

muscle

What is this structure?

n-Tetracosanoic acid

Which of the folllowing are important for human nutrition?

omega 3

Replication begins at the ___

origin

Ramachandran plot is base on..

phi and psi angles

Cation exchangers are

polymers with bound negatively charged groups

Which ribosomal component catalyzes peptide bond formation?

r-RNA

Rhodopsin is a membrane protein that acts as a..

receptor

Proteins can be eluted form ion-exchange column by using gradients of

salt & pH

The only form of DNA that is left-handed in nature is

the Z form

The isoelectric point is

the pH at which a substance has no net charge

They do use:

TPP Mg2+ Zn2+

Role of mRNA is to

code for protein