Exam 1: Molecules and Cells/Water, pH, and Buffers/Nucleic Acids/Nucleic Acid Structure

Question 1

hold atoms together to form molecules.

Answer 1

Covalent bonds

Question 2

maintain biological structure and determine molecular interactions.

Answer 2

Noncovalent bonds (or weak chemical forces)

Question 3

Types of noncovalent bonds:

Answer 3

1. Van der Waals Interactions: result of electron cloud fluctuations that allow attractions to occur between positively charged nuclei and electrons of nearby atoms
2. Hydrogen Bonds: form between a hydrogen atom, covalently bonded to an oxygen or nitrogen, and a second oxygen or nitrogen
3. Ionic Interactions: result of attractive forces between oppositely charged groups, such as negative carboxyl groups and positive amino groups
4. Hydrophobic Interactions: due to the strong tendency of water to exclude nonpolar groups or molecules, because water molecules prefer the stronger interactions between water molecules

Question 4

Compared to similar liquids, water has a higher:

1.

2.

3.

4.

Answer 4

1. Boiling point
2. Melting point
3. Heat of vaporization
4. Surface tension

Question 5

The unusual properties of water are due to its molecular structure:

a) Water is a polar molecule: The electronegative O atom and the two H atoms form a dipole that makes the molecule polar.
b) Hydrogen bonds are formed by interactions between the polar water molecules: H2O molecules in liquid water interact with an average of 4.4 other molecules to form a random, H-bonded network. These intermolecular attractions are responsible for the high boiling point, etc. of water.

Answer 5

Question 6

The H bonds in ice form a rigid structure which holds the water molecules apart.

Because of its structure, it is sometimes called ice, or structure

Answer 6

hexagonal, open lattice

Question 7

The average lifetime of an H-bond between two H2O molecules is picoseconds (1 psec = 10-12 sec).

Answer 7

9.5 picoseconds

Question 8

Because water is a polar molecule, it is an excellent for many substances including

Answer 8

solvent,

ionic substances such as salts.

Question 9

H2O molecules form around ions.

Answer 9

hydration shells

Negative partial charges on oxygen will be attracted to the positive charge of Na+, while the partial positive charges on the hydrogens will be attracted to the negative charge of Cl-.

Question 10

Water Has a High Dielectric Constant

Answer 10

The ability of water to surround ions in dipole interactions and diminish their attraction for one another is a measure of its dielectric constant, D

Question 11

water molecules form around hydrophobic solutes.

Answer 11

clathrate structures

Question 12

Water Forms , which accounts for its excellent solvent properties.

Answer 12

H Bonds with Polar Solutes

Question 13

Water molecules produce with molecules. Examples are fatty acids with a polar group (carboxyl group) at the end of a long nonpolar chain.

Answer 13

micelles

amphiphilic: means that there a two chemical natures within one molecule

Question 14

two nonpolar tails instead of one results in a very different structure than amphiphilic molecules containing just one nonpolar tail – a instead of a micelle.

Answer 14

bilayer

Question 15

the lipid bilayer helps to maintain the different concentrations of ions on the inside and outside of the membrane.

Answer 15

Question 16

What are colligative properties?

Give examples for water

Answer 16

Properties that only depend on the number of solute particles per unit volume of solvent and not on the chemical nature of the solute.

EX:

• freezing point depression
• boiling point elevation
• vapor pressure lowering

osmotic pressure effects

They only depend on the amount of molecules mixed into the water.

Mixing certain starches or proteins with water can lower the freezing point of water than 32 degrees, for example. All these molecules are doing is interfering with the ability of the water molecules to form a crystal hexagonal structure, so you have to slow down the water molecules even more to get them to freeze.

Question 17

Ions in solution, such as the Na+ and Cl- ions of NaCl, interact with H2O molecules to form:

a) clathrate structures
b) hexagonal ice
c) micelles
d) osmotic pressure
e) hydration shells

Answer 17

e) hydration shells

Question 18

The structure of water in the form of normal ice can be described as “hexagonal ice”. This is because:

a) ice crystals always have six sides
b) hydration shells consist of six H2O molecules
c) the minimum number of water molecules around any closed path of H-bonded molecules is six
d) clathrate structures of water molecules are composed of six H2O molecules e) ice floats on liquid water

Answer 18

c) the minimum number of water molecules around any closed path of H-bonded molecules is six

Question 19

If the initial pH of a solution is pH 8.0 and acid is added to increase the hydrogen ion concentration 100-fold, the final pH of the solution will be:

a) pH 8.0
b) pH 6.0
c) pH 7.0
d) pH 1.0
e) none of the above

Answer 19

b) pH 6.0

Question 20

In the phosphate buffer system, which buffers the intracellular fluid of cells, excess acidity [H+] is neutralized to form H2PO4- by reaction with:

a) OH-
b) NaH2PO4
c) H2O
d) HPO42-
e) H2CO3

Answer 20

d) HPO42-

Question 21

Which of the following nucleic acid bases are pyrimidines only?

a) guanine, adenine
b) cytosine, uracil, thymine
c) guanine, cytosine, adenine, thymine
d) guanine, adenine, thymine
e) guanine, cytosine, adenine, uracil

Answer 21

b) cytosine, uracil, thymine

Question 22

Which bases are the pyrimidines commonly found in RNA?

a) guanine, cytosine
b) guanine, adenine
c) cytosine, uracil
d) adenine, uracil
e) adenine, thymine

Answer 22

c) cytosine, uracil

Question 23

Which of the following is a nucleoside?

a) adenine
b) adenosine
c) adenosine 5’-monophosphate
d) adenylic acid
e) 3’, 5’-cyclic AMP

Answer 23

b) adenosine

Question 24

All of the following nucleotides are substrates for the synthesis of RNA or DNA in cells except:

a) thymidine 5’-triphosphate
b) uridine 5’-triphosphate
c) deoxycytidine 5’-triphosphate
d) deoxyadenosine 5’-triphosphate
e) guanosine 5’-triphosphate

Answer 24

a) thymidine 5’-triphosphate

- I think this should be deoxythymidine. Thymine is only found in DNA; therefore it would have to be deoxy?

Question 25

Small nuclear RNAs (snRNAs) have all of the following characteristics except: a) involved in the processing of hnRNA into mature transcripts b) form complexes called small nuclear ribonucleoprotein paticles (snRNPs) with specific proteins c) have sedimentation coefficients of 16 S, 23 S, and 5 S d) found mainly in the nucleus of eukaryotes e) consist of 100 to 200 nucleotides

Answer 25

c) have sedimentation coefficients of 16 S, 23 S, and 5 S

Question 26

Restriction endonucleases are used to isolate and clone DNA fragments such as genes that encode important proteins. Assuming that the four nucleotides in DNA are randomly distributed and present in equal proportions, what would be the average size in base pairs of the DNA fragments produced by a “six-cutter” restriction enzyme (one that cuts DNA molecules at a specific sequence 6 nucleotides in length)? a) 256 b) 1024 c) 4096 d) 16384 e) 65536

Answer 26

c) 4096

Question 27

The chain termination method of DNA sequencing is the most widely used procedure to determine the sequential order of nucleotides in DNA molecules including entire genomes. Along with the substrates for DNA polymerase (dATP, dGTP, dCTP, and dTTP), which other nucleotide must be added to the sequencing reaction mixture? a) 3’, 5’-cyclic AMP (cAMP) b) deoxycytidine 5’-diphosphate (dCDP) c) 3’, 5’-cyclic GMP (cGMP) d) 2’, 3’-dideoxynucleoside 5’-triphosphate e) uridine 3’-monophosphate (3’-UMP)

Answer 27

d) 2’, 3’-dideoxynucleoside 5’-triphosphate

Question 28

Which is the type of DNA that exists as a left-handed double helix and can be produced by synthetic oligonucleotides consisting of alternating pyrimidine-purine nucleotides? a) B-DNA b) double-helical DNA:RNA hybrids c) A-DNA d) Z-DNA e) double-helical regions of RNA chains

Answer 28

d) Z-DNA

Question 29

a) M. phlei b) S. marcescens c) E. coli d) Pneumococcus e) Yeast

Answer 29

e) Yeast A=T is only a double bond, while GC forms triples bonds. This means that compounds with more A=T bonds will be easier to break, and therefore have a lower melting point.

Question 30

cDNA molecules are DNA copies of mRNA transcripts, and therefore contain the protein-coding sequence of a gene uninterrupted by introns. In preparing cDNAs from purified eukaryotic mRNAs, which enzyme is used to synthesize the first cDNA strand? a) DNA polymerase b) reverse transcriptase c) T4 DNA ligase d) Taq DNA polymerase e) SP6 RNA polymerase

Answer 30

b) reverse transcriptase

Question 31

Which of the following would be an appropriate source of the DNA polymerase used in the PCR procedure to amplify specific DNA segments? a) yeast b) adenovirus c) human d) Thermus aquaticus e) Escherichia coli

Answer 31

d) Thermus aquaticus

Question 32

In PCR-based mutagenesis, which component of the PCR reaction mixture is altered to introduce a specific change (mutation) in the nucleotide sequence of a gene that is being amplified by PCR? ## Footnote a) primers b) dATP, dTTP, dGTP, dCTP c) DNA template d) heat-stable DNA polymerase e) thermal cycler conditions

Answer 32

a) primers

Question 33

Which is an example of a polar, uncharged amino acid? a) phenylalanine b) glutamic acid c) lysine d) serine e) leucine

Answer 33

d) serine

Question 34

Which amino acid has the single letter abbreviation “E”? a) phenylalanine b) glutamic acid c) glycine d) serine e) leucine

Answer 34

b) glutamic acid

Question 35

Which amino acid contains a sulfur atom? a) methionine b) tyrosine c) proline d) lysine e) aspartic acid

Answer 35

a) methionine

Question 36

Which amino acid contains a carboxyl group in its R side chain? a) methionine b) tyrosine c) proline d) lysine e) aspartic acid

Answer 36

e) aspartic acid

Question 37

Which amino acid has an R side chain covalently linked to the α-amino group? a) methionine b) tyrosine c) proline d) lysine e) aspartic acid

Answer 37

c) proline

Question 38

The amino acid that can form disulfide bridges (—S—S—) between side chains in the same polypeptide or different polypeptides is: a) proline b) hydroxylysine c) methionine d) γ-carboxyglutamic acid e) cysteine

Answer 38

e) cysteine

Question 39

The peptide Asp—Glu—Ala—Lys—Leu would have an overall net charge at pH 7.0 of: a) +2 b) +1 c) 0 d) -1 e) -2

Answer 39

d) -1

Question 40

What is the number of different amino acid sequences that are possible for a protein that is 100 amino acid residues in length (assuming that only the 20 common amino acids are incorporated into the protein chain)? a) 100 b) 2000 c) 120,000 d) 20²⁰ e) 20¹⁰⁰

Answer 40

e) 20¹⁰⁰

Question 41

Conjugated proteins are proteins that: a) are composed of several different kinds of polypeptide chains b) have a high degree of sequence homology, such as myoglobin and alpha and beta hemoglobin c) contain aromatic amino acids (phenylalanine, tyrosine, tryptophan) that allow spectroscopic measurements of protein concentration d) are on the same branch of the phylogenetic tree because of their shared evolutionary relationship e) contain various chemical constituents as an integral part of their structure

Answer 41

e) contain various chemical constituents as an integral part of their structure

Question 42

Answer 42

nonpermeant solute can be like starch or protein. Water molecules will want to equalize the h20 molecule concentration on each side of the membrane, so it will diffuse through the semipermeable membrane. WATER FLOWS INTO THE TUBE IN ORDER TO EQUALIZE THE CONCENTRATION OF WATER MOLECULES ON EITHER SIDE OF THE MEMBRANE

Question 43

pH equation

Answer 43

Question 44

hydroxide ion concentration and hydrogen ion concentration are related by the equation:

Answer 44

* Kw = [H+][OH-] = 10 ^ -14

Question 45

The Phosphate buffer system buffers and consists of....

Answer 45

the intracellular fluid

Question 46

Too high or too low of a pH in DNA can cause:

Answer 46

- high H+ concentrations in DNA, (low pH) **can break down into fragments, destroying the DNA** - high pH, low H+ ion concentration, (BASIC) **the two DNA strands will separate as a minimum**

Question 47

The Carbonate Buffer system is an important buffer system for . It consists of:

Answer 47

blood plasma. bicarbonate ion [HCO₃^-] and carbonic acid [H₂CO₃]

Question 48

Water molecules form hydrogen bonds with polar solutes. These include solutes containing groups.

Answer 48

hydroxyl (-OH)

Question 49

Pyrimidines consist of:

Answer 49

cytosine, thymine, and uracil

Question 50

Purines consist of:

Answer 50

adenine and guanine

Question 51

Sugars include:

Answer 51

ribose and deoxyribose

Question 52

Nucleosides consist of

Answer 52

a base bonded to a sugar

Question 53

Ribonucleosides include:

Answer 53

adenosine, uridine, cytidine, guanosine

Question 54

Deoxyribonucleosides include:

Answer 54

deoxyadenosine, deoxythymidine, deoxycytidine, deoxyguanosine

Question 55

Nucleotides consist of:

Answer 55

1-3 phosphate groups bonded to nucleosides

Question 56

Ribonucleotides (monophosphates) include:

Answer 56

adenosine 5'-monophosphate (AMP), uridine 5'-monophosphate (UMP), guanosine 5'-monophosphate (GMP), cytidine 5'-monophosphate (CMP)

Question 57

Deoxyribonucleotides (monophosphates):

Answer 57

dAMP, dTMP, dGMP, dCMP

Question 58

Diphosphates

Answer 58

ADP, UDP, GDP, CDP; dADP, dTDP, dGDP, dCDP

Question 59

Triphosphates

Answer 59

ATP, UTP, GTP, CTP ; dATP, dTTP, dGTP, dCTP

Question 60

Nucleic acids are linear polymers of nucleotides (polynucleotides) linked 3' to 5' by bridges.

Answer 60

phosphodiester

Question 61

By convention, the sequence of bases in a polynucleotide chain is read from

Answer 61

the free 5' end to the free 3' end.

Question 62

Two fundamental differences between DNA and RNA:

Answer 62

1. DNA contains deoxyribose instead of ribose. 2. DNA contains thymine instead of uracil.

Question 63

Messenger RNA (mRNA):

Answer 63

carries the "message" encoded in genes to the ribosomes, where this information is translated into polypeptide chains

Question 64

Ribosomal RNA (rRNA):

Answer 64

major component (65%) of ribosomes, the sites of protein synthesis

Question 65

Transfer RNA (tRNA):

Answer 65

carries amino acids to the ribosomes, where they are assembled into a polypeptide chain

Question 66

Small Nuclear RNAs (snRNAs):

Answer 66

involved in processing of eukaryotic gene transcripts into mature messenger RNA

Question 67

What is the primary structure of nucleic acids?

Answer 67

Linear sequence of bases along a DNA or RNA strand example: 5'-ATGAAACAAATGTTT-3'

Question 68

What is the secondary structure of nucleic acids?

Answer 68

Formation of double helix by specific base pairing A:T (or A:U) and G:C

Question 69

**Tertiary Structure** _For eukaryotic cells:_ _For prokaryotic cells:_

Answer 69

_For eukaryotic cells:_ organization of DNA into chromosomes by interactions with histone proteins and nonhistone proteins _For prokaryotic cells:_ supercoiling of circular chromosomal DNA molecules such as: * \*E. coli chromosome * \*plasmid DNA molecules * \*mini-chromosomes of organelles including mitochondria

Question 70

Tertiary Structure of DNA: Supercoils

Answer 70

Circular DNA or linear DNA with fixed ends can form supercoils if the two strands of the double helix are underwound (negative supercoils) or overwound (positive supercoils).

Question 71

Tertiary Structure of DNA: Linking Number

Answer 71

The linking number is a parameter that characterizes supercoiled DNA: L = T + W where T = twist, the number of helical turns and W = writhe, the number of times that the double helix crosses over itself

Question 72

Nucleotides, the building blocks of DNA and RNA, are composed of _1 , 2 , and 3 ._

Answer 72

bases, sugars, and phosphate groups.

Question 73

Nucleosides lack

Answer 73

phosphate groups.

Question 74

DNA nucleotides consist of a base (A, T, C, or G), , and 1-3 phosphate groups. RNA nucleotides consist of a base (A, U, C, or G), , and 1-3 phosphate groups.

Answer 74

1. deoxyribose 2. ribose

Question 75

The phosphodiester linkages in DNA and RNA connect the _1_ carbon of one nucleotide with the _2_ carbon of another.

Answer 75

1. 3’ 2. 5’

Question 76

A-T base pairs have _1_ H-bonds, while G-C base pairs have _2_ .

Answer 76

1. two 2. three

Question 77

RNA molecules, particularly _and_ , can have short double helical segments held together by A-U and G-C base pairs.

Answer 77

tRNA and rRNA

Question 78

The percentage of total cell RNA of mRNA is , while tRNA is and rRNA is not including the small RNAs.

Answer 78

1. ~2% 2. 16% 3. 82%,

Question 79

Transcription is the process of . It involves the enzyme .

Answer 79

1. RNA synthesis from a DNA template 2. RNA polymerase

Question 80

In prokaryotes, a single mRNA molecule can specify several polypeptides. In contrast, eukaryotic mRNAs encode only one polypeptide. But eukaryotic mRNAs are more complex because they consist of .

Answer 80

protein-coding segments (exons) separated by noncoding intervening sequences (introns) that must be removed

Question 81

Translation is the process of . The process involves messenger RNA, ribosomes, transfer RNA, amino acids, and other molecules.

Answer 81

protein synthesis at ribosomes in cells

Question 82

Ribosomes are composed of and .

Answer 82

1. ribosomal RNA 2. ribosomal proteins

Question 83

rRNA has a complex secondary structure due to:

Answer 83

many short segments of A-U and G-C intrastrand hydrogen bonds.

Question 84

tRNA molecules . They also possess short hydrogen-bonded segments.

Answer 84

1. transfer amino acids to the growing polypeptide chains.

Question 85

Primary structure can be determined by the of DNA sequencing, or by newer sequencing technologies.

Answer 85

dideoxy or chain termination method

Question 86

The dideoxy method uses:

Answer 86

2’,3’-dideoxynucleotides to terminate the growth of DNA chains.

Question 87

The major form of the DNA double helix in cells is

Answer 87

B-DNA

Question 88

B-DNA is a right- handed helix with about per turn of the helix. The bases are almost perpendicular to the helix axis and are stacked nm apart. The pitch, or repeat distance, along the helix is nm.

Answer 88

1. 10 base pairs 2. 0.34 3. 3.4

Question 89

A-DNA is formed by . DNA/RNA hybrid double helices and double helical segments of RNA also have structures like A-DNA.

Answer 89

1. dehydrated DNA fibers

Question 90

is a narrow, left-handed helix formed by synthetic oligonucleotides with an alternating pyrimidine- purine sequence (e.g. GCGCGC).

Answer 90

Z-DNA

Question 91

Tertiary structure is long-range, three-dimensional structure that includes of circular DNA molecules in prokaryotes and packaging of DNA into chromosomes in eukaryotes.

Answer 91

1. supercoiling

Question 92

Supercoils are formed in circular DNA, or linear DNA with fixed ends, if the two strands of the double helix are . Circular bacterial chromosomes are converted to interwound supercoiled circles by .

Answer 92

1. underwound or overwound 2. DNA gyrase (topoisomerase II)

Question 93

The higher-order structure of eukaryotic DNA involves the interaction of DNA with **histones** to produce , the coiling of **nucleosomes** into _chromatin fibers_, and the folding of **chromatin fibers** into _DNA loops_. Also, cruciform structures might be formed from palindrome (inverted repeat) sequences.

Answer 93

1. nucleosomes

Question 94

RNA molecules also have tertiary structure. The secondary structures of transfer RNA (tRNA) molecules are folded into tertiary structures. Ribosomal RNA (rRNA) molecules have many short segments of double helix which interact with numerous ribosomal proteins to form the precise 3-D structures of the small and large ribosomal subunits.

Answer 94

1. cloverleaf 2. L-shaped

Question 95

* The L form is never found in DNA or RNA, so you can always just assume it is the D-Dextro form.

Question 96

nucleotides are linked together by

Answer 96

phosphodiester bonds

Question 97

RNA is stranded

Answer 97

single

Question 98

rRNA has sedimentation coefficients of , , and

Answer 98

5s 16s 23s

Question 99

2% of Human DNA is coding, 98% is non coding

Question 100

In prokaryotes, a single mRNA molecule can contain sequences that encode for several polypeptides, while eukaryotic mRNAs can only code for polypeptide.

Answer 100

one polypeptide.

Question 101

prokaryotic mRNAs can be translated into proteins even before transcription is completed. In eukaryotes, however, transcription occurs in the and translation in the .

Answer 101

1. nucleus 2. cytoplasm

Question 102

Secondary Structure of tRNA molecule

Answer 102

- INTRAstrand hydrogen bonding - 3’ end “acceptor stem” is where the new nucleotides will be added - anticodon specifies which amino acid will be added to the acceptor stem

Question 103

The Dideoxy or Chain Termination Method of DNA Sequencing

Answer 103

Question 104

the angle of the causes the major and minor grooves

Answer 104

glycosidic bonds