Chem 474: Biochem I

Front 1

What functional group separates DNA and RNA?

Back 1

RNA contains an OH functional group on the 2nd Carbon. DNA contains a Hydrogen.

Front 2

RIbose is the 5-carbon sugar used in DNA and RNA however the 5-carbon sugar could take many conformations. Explain why DNA and RNA does not utilize the use of any other 5-carbon sugar conformation.

Back 2

Ribose is the most stable conformation of the 5-carbon sugar because it has the lowest steric hinderence.

Front 3

Which of conformation (Syn or Anti) is the most stable for the ribose of DNA and RNA?

Back 3

Anti conformation is most stable because there is no steric hinderance.

Front 4

What is the difference between Nucleotides and nucleosides?

Back 4

Nucleosides is just the ribose while nucleotide contains the ribose and the phosphate.

Front 5

T/F: Nucleic acids are bidirectional

Back 5

False. Nucleic Acids are unidirectional

Front 6

DNA Base Pairs are held together by what type of bond?

Back 6

H-Bonds

Front 7

Name all of the different forces acting upon a DNA Double Helical structure and what specific components of the DNA double helical structure these forces are affecting

Back 7

1. Hydrogen Bonds bond base pairs together. Normally, Hydrogen bonds are present on single stranded DNA but when two strands are placed in close proximity a new Hydrogen bond is formed.

2. Hydrophobic interactions drive the formation of double stranded DNA. Nucleotides contain hydrophobic bases and hydrophilic backbones. When the strands come together, the hydrophobic bases bond together using H-bonds. H-bonds are also stronger in hydrophobic environments.

3. Van der Waals interactions are formed due to the stacking of the base pairs on top of each other.

4. Electrostatic interactions. Phosphates are (-) and so the formation of double stranded DNA is highly unfavorable energetically. However, due to the electrostatic interaction between the phosphates and the ions (Na+ and Mg2+) as well as the water, this neutralizes the negative charge of the phosphate which helps to allow the formation of the double strands.

Front 8

What is the ratio of G to C in a DNA double helix?

A. 2:1

B. 4:1

C. 1:1

D. 3:1

E. Is variable

Back 8

C. 1:1

Because in a DNA double helix you will always have a G paired with C. This is explained by Chargaffs Rule

Front 9

What is the ratio of G to C in an mRNA?

A. 2:1

B. 4:1

C. 1:1

D. 3:1

E. Is variable

Back 9

E. Is Variable

Because mRNA exists as either single stranded or double stranded depending on the organism. So it can either be 1:1 or 1:0

Front 10

T/F: Two DNA chains with complementary sequences will form a double helix

Back 10

True

Front 11

approximately what degree is each base off center?

Back 11

36 degrees.

Front 12

T/F: The sugar phosphate backbone are on the outside and bases are stacked on the inside

Back 12

True

Front 13

Which form of DNA is the most common?

Back 13

B-DNA

Front 14

Why are major and minor grooves specific to A-T and G-C?

Back 14

It helps to make certain sequences recognizable (i.e. TATA Box)

Front 15

Which grooves (major or minor) accommodates proteins better?

Back 15

Major

Front 16

During what situations would you form A-DNA?

Back 16

1. Dehydrated DNA

2. Double stranded RNA

Front 17

Which of the following is false in regards to A-DNA?

A. It is formed in dehydrated DNA

B. It is shorter and thicker

C. It is a left-handed helix

D. Bases are not parallel to the axis

E. It is formed in double stranded RNA

Back 17

C. It is left-handed helix

Front 18

T/F: The sugar of the A-DNA is C-2' endo while the sugar of B-DNA is C-3' endo

Back 18

False. The sugar of the A-DNA is C-3' endo and the sugar of the B-DNA is C-2' endo.

Front 19

T/F: Z-DNA is sequence specific to alternating AT

Back 19

False. Z-DNA is sequence specific to alternating GC

Front 20

Z-DNA is believed to be involved in what process?

A. Transcription

B. Translation

C. Replication

D. All of the above

E. None of the above

Back 20

A. Transcription

Front 21

Which of the following contains a left-handed helix?

A. A-DNA

B. B-DNA

C. Z-DNA

D. None of the above

Back 21

C. Z-DNA

Front 22

Which of the following contains a zig-zagging phosphate backbone?

A. A-DNA

B. B-DNA

C. Z-DNA

D. None of the above

Back 22

C. Z-DNA

Front 23

Shape-wise, which of the following is the broadest?

A. A-DNA

B. B-DNA

C. Z-DNA

D. None of the above

Back 23

A. A-DNA

Front 24

Circular DNA is unique to what type(s) of organisms?

Back 24

Archaea and bacteria

Front 25

How does supercoiling affect the overall interaction of the DNA to proteins?

Back 25

Supercoil changes the ability for proteins to interact with the DNA. The more supercoiled a DNA, the less likely that promoter sites will be exposed to allow polymerase to bind and start transcription.

Front 26

T/F: Stem-loops allow for higher order folding

Back 26

True

Front 27

Which of sequences will form a bulge in the following RNA?

5'-AUAAGUGACUACACUUGAA-3'

A. AU and GAA

B. AAGU

C. ACUA

D. CACUUG

E. No bulges will be formed

Back 27

C. ACUA

Front 28

DNA replication is performed _______________ :

A. Conservatively

B. Semiconservatively

C. Completely

D. None of the above

Back 28

B. Semiconservatively.

Front 29

Describe the experiment which determined that DNA replicates semiconservitavely

Back 29

DNA was placed in a solution of nucleotides containing N15 to the point where all new DNA formed contained N15. Then this DNA was placed in a solution of nucleotides containing N14. It was found that during the first replication cycle all daughter DNA showed a signal of intermediates indicating that all daughter cells contained one strand of DNA containing N15 and another containing N14. This indicates that replication occurs semi conservatively. As DNA continues to replicate there displayed a second band now there were signals for the intermediate as well as a signal for N14 indicating that there were two populations of newly replicated DNA. One population contained the one N14 and one N15 DNA, and the other population contained both N14.

Front 30

The more the double strands, the __________ the absorbance of UV on a hipochromism.

A. Higher

B. Lower

C. None of the above

Back 30

B. Lower

Front 31

The more the single strands, the ________ the absorbance of UV on a hipochromism.

A. Higher

B. Lower

C. None of the above

Back 31

A. Higher

Front 32

This type of base pairing results in a decrease of of melting temperature

Back 32

A-T

Front 33

This type of base pairing results in an increase of the melting temperature

Back 33

C-G

Front 34

Under physiological conditions, which of these DNA samples would you expect to absorb more UV light. Assume equimolar amounts

A. 5'-CCCGGG-3'

B. 5'-CGCGCG-3'

C. 5'-GGCGCC-3'

D. 5'-CGGCCG-3'

E. 5'-GCGGCG-3'

Back 34

E. 5'-GCGGCG-3'

Because all the other strands, will likely spontaneously form double bonds with other single strands because they are complementary to each other. The formation of double bonds would decrease UV light absorption

Front 35

What enzyme is directly responsible for DNA replication?

Back 35

DNA polymerase

Front 36

Which of the following is not required for DNA replication?

A. Mg2+

B. Complementary dNTP

C. RNA Polymerase

D. All of the above

E. None of the above

Back 36

C. RNA Polymerase

Front 37

T/F: In order for DNA Polymerase to recognize the DNA for replication it must contain a primer bound to the template and a free 3' OH.

Back 37

True

Front 38

For DNA Replication, elongation proceeds in what direction?

Back 38

5'-3'

Front 39

Which of the following is false?

A. Genes in cellular organisms use DNA

B. Some viruses use RNA as genetic Material

C. In RNA viruses, the genome is replicated by RNA-Dependent RNA polymerase

D. In retroviruses, the genome information flows from RNA to DNA using RNA Dependent DNA Polymerase

E. None of the above.

Back 39

E. None of the above

Front 40

What are the different classes of RNA?

Back 40

1. mRNA

2. tRNA

3. rRNA

4. snRNA

5. Signal Recognition Particle

6. miRNA

7. siRNA

8. Telomerase

Front 41

What is mRNA (messenger RNA) responsible for?

Back 41

1. Acts as a template for protein synthesis during translation.

2. One mRNA produced for one prokaryote gene or groups of gene.

3. Regulate eukaryote mRNA functions structurally

Front 42

What is tRNA (transfer RNA) responsible for?

Back 42

1. Carries activated amino acids to the ribosome for peptide bond formation using mRNA as template.

2. At least one tRNA is designed for each amino acid

Front 43

What is rRNA (Ribsomal RNA) responsible for

Back 43

1. Major component of Ribosome

2. Catalyzes peptide synthesis

Front 44

What is snRNA (Small nuclear RNA) responsible for

Back 44

1 Splicing of mRNA exons

Front 45

What is Signal Recognition Particles responsible for?

Back 45

1. Protein/RNA Complex that targets proteins to specific cell locations

Front 46

What is miRNA (Micro RNA) responsible for?

Back 46

1. Noncoding, ~21 nuicleotide that bind to complementary mRNA and inhibits translation. Acts as a post transcript silencer.

Front 47

What is siRNA (small interfering RNA) responsible for?

Back 47

1. Binds to mRNA and facilitates its degradation

Front 48

What is Telomerase responsible for?

Back 48

1. Protein/RNA enzymes that maintain chromosome ends during DNA Replication

2. It is believed that Telomerase is why you get old.

Front 49

All cellular RNA are synthesized by ______ polymerase

Back 49

RNA Polymerase

Front 50

The process of synthesizing RNA from DNA is called

Back 50

Transcription

Front 51

The process of synthesizing protein from RNA is called

Back 51

Translation

Front 52

T/F: RNA synthesis does not require a primer

Back 52

True

Front 53

Which of the following is False:

A. RNA synthesis requires DNA template, NTP, and either Mg2+ or Mn2+

B. RNA elongation occurs in a 3'->5' direction

C. RNA synthesis does not require a primer

D. No proofreading occurs during RNA synthesis.

Back 53

B. RNA elongation occurs in a 3'->5' direction

Front 54

Synthesized mRNA is complementary to:

Back 54

DNA template strand

Front 55

Hybridization shows that RNA sequences are the same (with exception to uracil) to the

Back 55

DNA coding strand

Front 56

For transcription, DNA must be read in what direction on the template strand

Back 56

3'->5'

Front 57

How many nucleotides encode an amino acid

Back 57

3

Front 58

Which of the following is false?

A. Genetic code is non-overlapping

B. The genetic code has no punctuation

C. The genetic code is degenerate

D. All of the above

E. None of the above

Back 58

E. None of the above

Front 59

Describe the "wobble effect"

Back 59

The wobble effect describes how the third nucleotide in a codon is conservative and provides leeway for the coding for a specific Amino Acid. If for example, the last nucleotide should be a T to code for a Glutamic acid, and the T is instead a C, the wobble affect likely allows for the coding of Glutamic Acid anyway. This helps to reduce the chances of mutations.

Front 60

T/F: Mutations are the same in all species

Back 60

True

Front 61

T/F: mRNA from one species can be translated by another species with exception to mitochondria

Back 61

True

Front 62

Since there are only 20 amino acids, why not use 20 codons and keep the other 44 as stop codons? In other words, why is the genetic code degenerate?

A. Allows for the production of larger quantities of proteins.

B. Allows for an increase in protein diversity

C. Minimizes harmful mutations

D. Saves energy

E. All of the above.

Back 62

C. Minimizes harmufl mutations

Front 63

What four amino acid peptide is most likely encoded in the following mRNA?

5'-AUGCAUGGAUAGGUCGUAAAGGA-3'

A. MHGR

B. MRPT

C. MGPT

D. MDRS

E. MARA

Back 63

D. MDRS

AUG-GAU-AGG-UCG

Methionine, Aspartic Acid, Arginine, Serine

Front 64

What mutation results in the formation of sickle cell anemia?

Back 64

a single point mutation converting a thymine to an adenine causes the subsequent Amino Acid Valine to be formed instead of glutamic acid. Valine is a hydrophobic AA which makes a polymerization to form a sickle cell.

Front 65

Why is sickle cell anemia dangerous?

Back 65

The shape of sickle cell causes the cells to aggregate in blood vessels and capillaries. This can cause blood vessels and in particular capillaries to break down.

Front 66

Explain how RNA polymerase can recognize the correct sequence on DNA for a gene in Eukaryotic cells during Transcription

Back 66

Eukaryotes contain TATA boxes which help to guide RNA polymerase to find the promoter sites. Additionally, Eukaryotes have enhancer sequences called CAAT Box which can be found further upstream.

Front 67

Explain how RNA polymerase can recognize correct sequence on DNA for a gene in prokaryote cells during Transcription

Back 67

Prokaryotes ahve Pribnow Box and a -35 region which helps to guide RNA polymerase to promoter sites.

Front 68

In prokaryotes, what serves as a terminator signal?

Back 68

Prokaryotes have hairpin structures which serves as a terminator signal

Front 69

Which protein serves to terminate transcription?

Back 69

Rho

Front 70

In eukaryotes how is mRNA modified following the termination of transcription?

Back 70

A poly A tail is added to the 3' end.

Front 71

Which of the following is false?

A. tRNA contains an amino acid attachment site at the 3'-end

B. Amino acid is carried as an activated amine

C. Anticodon serves as the mRNA template recognition site

D. The attachment of amino acid and t-RNA is catalyzed by aminoacyl-tRNA synthetase

Back 71

B. Amino acid is carried as an activated amine

Front 72

T/F: The attachment of Amino Acids by tRNA to the mRNA is an ATP driven process

Back 72

True

Front 73

What type of bond is used by tRNA?

Back 73

Esther bonds.

Front 74

Where is mRNA translated?

Back 74

Ribosome

Front 75

Protein synthesis in bacteria starts with ______ carried by an initiator tRNA

Back 75

fMet

Front 76

In prokaryotes, the initial AUG is preceded by

Back 76

Shine Delgarno

Front 77

T/F: Shine Delgarno is a pyrimidine-rich sequence

Back 77

False. It is Purine Rich

Front 78

In Eukaryotes, after the initiator AUG located, what is established?

Back 78

Reading Frame

Front 79

What three codons are read as stop sequences?

Back 79

UAA, UAG, UGA

Front 80

T/F: mRNA from one species can be translated by the ribosome of other species

Back 80

True

Front 81

T/F: Eukaryotic genes are discontinuous

Back 81

True

Front 82

T/F: Introns are unimportant segments of DNA which are excised from the coding region prior to the DNA exiting the nucleus

Back 82

False. 80% of the genome has been assigned functions including those outside protein-coding regions (exons)

Front 83

What protein conducts the splicing of mRNA?

Back 83

Splicesome

Front 84

What are Ribozymes

Back 84

Catalytic RNA molecules

Front 85

T/F: RNA can serve as both a genome and a catalyst

Back 85

True

Front 86

What evidence has been seen to support the idea that RNA was the origin of all modern day organisms

Back 86

The idea that RNA is pre-biotic and self replicating meaning that it can act as both a genome and as an enzyme.

Front 87

Describe SELEX

Back 87

SELEX allows for the selection and activation of RNA sequences which allows for new functions that would not otherwise occur in nature