Biochemistry Exam 2

Front 1

A good transition state analog binds to the enzyme ______.

Back 1

more tightly than the substrate

Front 2

The benefit of measuring the initial rate of a reaction (Vo) is that ___.

Back 2

at the beginning of the reaction changes in [S] are negligible, so [S] can be treated as a constant

Front 3

The role of an enzyme in an enzyme-catalyzed reaction is to ____.

Back 3

increase the rate at which substrate is converted into product

Front 4

How is trypsinogen converted to trypsin?

Back 4

Proteolysis of trypsinogen forms trypsin

Front 5

To calculate the turnover number of an enzyme, you need to know____.

Back 5

the enzyme concentration and the initial velocity of the catalyzed reaction at S >> Km

Front 6

Enzymes are potent catalysts because they _____.

Back 6

lower the activation energy for the reactions they catalyze

Front 7

Penicillin related durgs inhibit the enzyme ______; this enzyme is produced by _____.

Back 7

transpeptidase; bacteria

Front 8

Can increase the reaction rate for a given reaction by a thousand-fold or more

Back 8

enzyme catalyst

Front 9

Used to solve graphically for the rate of an enzymatic reaction at infinite substrate concentration

Back 9

Lineweaver-Burk

Front 10

A small molecule that decreases the activity of an enzyme by binding to a site other than the catalytic site is termed an _______.

Back 10

allosteric inhibitor

Front 11

The concept of ____________ refers to the fact that substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation.

Back 11

induced fit

Front 12

Name the six internationally accepted classes of enzymes

Back 12

Oxidoreductases, Lyases, Transferases, Hydrolases, Isomerases, Ligases

Front 13

One of the enzymes involved in glycolysis, aldolase, requires Zn for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the _____.

Back 13

apoenzyme

Front 14

In a plot of 1/V against 1/[S] for an enzyme catalysed reaction, the presence of a competitive inhibitor will ______.

Back 14

alter the intercept on the 1/S axis.

Front 15

Enzymes differ from other catalyst in that _____.

Back 15

Only enzymes display specificity toward a single reactant

Front 16

Carbon Monoxide (CO) is toxic to humans because _____

Back 16

it binds to the Fe in hemoglobin and prevents the binding of oxygen.

Front 17

In hemoglobin the transition from T to R state (low to high affinity) is triggered by _____.

Back 17

oxygen binding

Front 18

A non correct fact about 2,3 bisphosphoglycerate is that ___

Back 18

it increases the affinity of hemoglobin for oxygen

Front 19

The amino acid substitution of Val for Glu in hemoglobin S results in aggregation of the protein because of ______.

Back 19

hydrophobic interactions between molecules.

Front 20

The interactions of ligands with proteins are usually ____.

Back 20

transient

Front 21

Myoglobin and the subunits of hemoglobin have very similar ______ but very different ______.

Back 21

tertiary structures; primary structures

Front 22

An allosteric interaction between a ligand and a protein is one in which ______.

Back 22

binding of a molecule to a binding site affects binding properties of another site on the protein.

Front 23

In the binding of oxygen to myoglobin the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as ______.

Back 23

hyperbolic

Front 24

The predominant structural feature in myosin molecules is an ____.

Back 24

alpha helix

Front 25

A monoclonal antibody differs from a polyclonal antibody in that _____.

Back 25

monoclonal antibodies are synthesized by a population of identical or cloned cells.

Front 26

Amino acid residues commonly found in the middle of Beta turn are _____.

Back 26

Pro and Gly.

Front 27

Which of the following is least likely to result in protein denaturing?

Back 27

changing salt concentration

Front 28

To alter Alpha keratin chains shape you first reduce, then you _______.

Back 28

shape remodeling and then chemical oxidation

Front 29

In an aqueous solution, protein conformation is determined by two major factors: _______.

Back 29

maximum number of hydrogen bonds and placement of hydrophobic amino acid residues within the interior of the protein.

Front 30

Proteins often have regions that show specific, coherent patterns of folding or function. These regions are called:

Back 30

domains

Front 31

Determining the precise arrangement of atoms within a large protein is possible only through the use of _____.

Back 31

xray diffraction

Front 32

In an alpha helix, the R groups on the amino acid residues are found_____.

Back 32

on the outside of the helix spiral

Front 33

Roughly how many amino acids are there in one turn of an alpha helix?

Back 33

3.6

Front 34

A non weak interaction in proteins is _____.

Back 34

peptide bonds

Front 35

Protein S will fold into its native conformation only when protein Q is also present. However Q can fold into its native conformation without protein S. Protein Q therefore may function as a _____ for protein S.

Back 35

molecular chaperone

Front 36

The information carrying intermediates of translation

Back 36

mRNA

Front 37

Scientist who noted the A:T and G:C ratios in DNA are pproximately 1:1.

Back 37

Erwin Chargroff

Front 38

the temperature at which double stranded DNA separates into separate strands

Back 38

the melting temperature

Front 39

DNA renaturation after melting is called

Back 39

annealing

Front 40

Organisms in which the flow of genetic information can be RNA > DNA

Back 40

retroviruses

Front 41

Codons that specify the same amino acids are termed

Back 41

synonyms

Front 42

a three-base codon defines a specific

Back 42

amino acid

Front 43

stop codons are read by

Back 43

release factors

Front 44

DNA is more resistant to base-catalyzed hyrdolysis than RNA. What feature of DNA is responsible for this characteristic?

Back 44

The absence of a 2'-hydroxyl group in deoxyribose

Front 45

How does a nucleotide differ from a nucleoside?

Back 45

A nucleotide is a nucleoside with a phosphate ester linked to the sugar

Front 46

What is the nucleotide sequence (5'>3') on the DNA template strand that yields the 5' > 3' CUA codon for leucine?

Back 46

TAG

Front 47

The technique used by Franklin and Wilkins to deduce the structure of DNA was

Back 47

Xray diffraction

Front 48

The feature of DNA deduced by Watson and Crick included:

Back 48

two antiparalled polynucleotide chains coiled in a helix around a common axis, the pyrimidine and purine bases lie on the inside of the helix, the bases are nearly perpendicular to the axis

Front 49

What are the common promoter regions found in bacterial genes?

Back 49

A Pribnow box about -10 and a -35 region

Front 50

Features of the genetic code include

Back 50

the code is degenerate and a codon is defined by three bases

Front 51

The first amino acid in bacterial proteins is

Back 51

fMet

Front 52

In which codon position do most synonyms differ?

Back 52

third position

Front 53

Arber, Smith, and Nathans discovered and pioneered the use of

Back 53

restriction enzymes

Front 54

A pattern of DNA fragments can serve as a _____ of a particular DNA molecule.

Back 54

genetic fingerprint

Front 55

the most common type of DNA sequencing is

Back 55

Sanger dideoxy nucleotide method

Front 56

Instead of radioactivity, current DNA sequencing commonly uses ____ base analogues.

Back 56

fluorescent

Front 57

The first genome to be sequenced of a free-living organism

Back 57

Haemophilus influenza

Front 58

Won the Nobel prize for discovery of the polymerase chain reaction.

Back 58

Kary Mullis

Front 59

A plasmid is an example of a common ____.

Back 59

vector

Front 60

the enzyme used to create DNA from RNA is

Back 60

reverse transcriptase

Front 61

The enzyme that catalyzes the formation of a phosphodiester linkage at a break in DNA strand

Back 61

DNA ligase

Front 62

cleaves DNA at sites with inverted repeat sequences referred to as palendromic sequences

Back 62

restriction endonucleases

Front 63

Complementary, single-strand overhangs that are produced by some restriction endonucleases are referred to as

Back 63

sticky ends or cohesive ends

Front 64

The Sanger technique for sequencing DNA involves the use of ___ nucleotide analogs that terminate chain elongation.

Back 64

2',3' dideoxy

Front 65

DNA fragments can be visualized in polyacrylamide gel electrophoresis by staining with ____ which binds to double stranded DAN and fluoresces an intense orange when irradiated by UV light.

Back 65

ethidium bromide

Front 66

The viological role of restriction enzymes in bacteria is to

Back 66

cleave foreign DNA

Front 67

Which of the following DNA sequences contains a 48 base palindromic site?

Back 67

GCATATGC

Front 68

Plasmids used in recombinant DNA technology typically

Back 68

posses a gene for antibiotic resistance, replicate independently of the host genome, are circular double stranded molecules

Front 69

A polylinker site contains

Back 69

many closely spaced restriction enzyme sites

Front 70

Reverse transcriptase is normally found in

Back 70

retroviruses

Front 71

Foreign genes can be inserted into eukaryotic cells by

Back 71

viruses, liposomes, chemical treatment, and microinjections

Front 72

Animals that harbor a foreign gene as a result of recombinant gene manipulation are called

Back 72

transgenic

Front 73

techniques for engineering new proteins by site-directed gene mutations include:

Back 73

oligonucleotide directed mutagenesis and cassette mutagenesis

Front 74

The temperature at which half the DNA helical character is lost is referred to as

Back 74

Tm

Front 75

The difference in RNA bases compared to DNA bases is

Back 75

RNA contains U instead of T

Front 76

What are two primary components of a gene?

Back 76

exons and introns

Front 77

Why are deletion and insertion mutations usually lethal?

Back 77

changes the reading frame

Front 78

What is an advantage of codon degeneracy?

Back 78

it lessens the chance of deleterious mutations

Front 79

A plasmid vector that contains the beta-galactosidase gene and is useful for screening cells with recombined DNA

Back 79

pUC18

Front 80

How can DNA fragments of various sizes be separated?

Back 80

gel electrophoresis

Front 81

A labeled complementary single stranded DNA used in things such as southern blotting

Back 81

DNA probe

Front 82

What is the basis of the Sanger method for DNA sequencing?

Back 82

DNA can be sequenced by controlled termination of replication using 2',3'-dideoxy nucleotide analogs

Front 83

Explain the the basis of the polymerase chain reaction

Back 83

To analyze and amplify specific DNA sequences using 3 steps: 1) strand separation 2) hybridization of primers 3) DNA synthesis

Front 84

Briefly outline the steps necessary to create a recombinant DNA molecule

Back 84

1) Cleave with restriction enzymes
2) Anneal DNA fragments and join with DNA ligase

Front 85

How is a single gene of interest identified on a plate containing many different library clones?

Back 85

screening a genomic library for a specific gene

Front 86

How is gene disruption used to determine the function of a gene?

Back 86

uses process of homologous recombination

Front 87

How is a gene gun used?

Back 87

most effective way of transforming plant cells DNA is coated onto tungsten pellets and they are fired at the target cells with very high velocities

Front 88

Briefly outline how a cDNA library is made

Back 88

complementary DNA for all mRNA that a cell contains can be made, inserted into vectors, and then inserted into bacteria