building blocks and linear biopolymers

Question 1

What is a polymer?

Answer 1

A polymer is a covalent bond-linked chain of
monomers.

Question 2

What is an informational polymer?

Answer 2

An informational polymer has more than one kind of
monomer, and the order of the different kinds of
monomer in the polymer chain is the information.

Question 3

What is the information in DNA, RNA, and protein?

Answer 3

The information in DNA, RNA, and protein is the
DNA sequence, the RNA sequence, and the protein
sequence, respectively.

Question 4

What is the generic structure of informational
biopolymer monomers?

Answer 4

The generic structure of informational biopolymer
monomers includes a common element shared by
all the different monomers for that class of
informational biopolymer and a characteristic
element that makes each monomer different from
the others.

Question 5

What is the function of the common element in
informational biopolymer monomers?

Answer 5

The common element forms the polymer
“backbone” by covalent bonding between
monomers.

Question 6

What is the function of the characteristic elements
in informational biopolymer monomers?

Answer 6

The characteristic elements form “side-chains” that
protrude from the polymer backbone.

Question 7

What is the information in an informational
biopolymer?

Answer 7

the order of the monomer units, which is the
sequence.

Question 8

What is the maximum number of monomer units
that can be joined together if the monomer has only
one joining site in the common element?

Answer 8

at most two monomer units can
be joined together. (no polymer)

Question 9

What is the difference between a monomer with no
joining sites exposed at ends and a monomer with
two joining sites exposed at ends?

Answer 9

A monomer with no joining sites exposed at ends
cannot have further chain growth, while a monomer
with two joining sites exposed at ends can have
further chain growth.

Question 10

What type of polymers can be made if the monomer
has three joining sites in the common element?

Answer 10

branched polymers

Question 11

Are informational biopolymers branched or linear?

Answer 11

Informational biopolymers are linear and not
branched.

Question 12

What is the difference between linear and branched
informational biopolymers?

Answer 12

Linear informational biopolymers have two ends,
while branched informational biopolymers have
more than two ends.

Question 13

What is an example of a circular (but unbranched)
molecule in bacteria and some viruses?

Answer 13

An example of a circular (but unbranched) molecule
in bacteria and some viruses is the genomic DNA
molecule.

Question 14

What is the difference between the two joining sites
in informational biopolymer monomers?

Answer 14

The two sites are different.

Question 15

What is the consequence of the asymmetry of
monomers in informational biopolymers?

Answer 15

The asymmetry of the monomers directly drives an
asymmetry of the polymer.

Question 16

What is the convention when showing biopolymer
representations on a sheet of paper?

Answer 16

The convention is to depict the orientation in which
unidirectional polymer chain growth occurs in the
rightward direction.

Question 17

What are the two major types of informational
biopolymer monomer units?

Answer 17

nucleotides and
amino acids.

Question 18

What is the typical chain length of DNA?

Answer 18

~10^3 to ~10^8.

Question 19

What is the typical chain length of RNA?

Answer 19

~20 to ~10^4

Question 20

What is the typical chain length of protein?

Answer 20

~100 to ~10^3

Question 21

What is the characteristic element of nucleotides?

Answer 21

A heterocyclic base.

Question 22

What are the two joining sites on the common
element of nucleotides?

Answer 22

The 5’ phosphate and the 3’ OH (hydroxyl)

Question 23

How is nucleic acid polymer growth achieved?

Answer 23

ALWAYS by addition of monomers to the 3’ end.

Question 24

What is the difference between the pentose sugar in
DNA and RNA?

Answer 24

Deoxyribose is missing the 2’ hydroxyl of ribose.

Question 25

What makes DNA much more resistant to chain cleavage by hydrolysis?

Answer 25

The absence of 2’-OH.

Question 26

What is the bond that connects the nitrogen atoms from the amino group in the nucleotides and the anomeric carbon (C1) of the ribose sugar structure ?

Answer 26

N-glycosidic bond.

Question 27

What are the heterocyclic bases of nucleotides? (2groups with each a few bases)

Answer 27

The heterocyclic base are Pyrimidines and Purines. Purine is present in Adenine(A) and guanine (G). Pyrimidine is present in cytosine (C), thymine (T) and Uracil(U).

Question 28

What is the significance of the presence of T instead of U in DNA?

Answer 28

The presence of T instead of U in DNA makes some chemical damage easier to repair. (thanks to the methyl group)

Question 29

What is the polarity of a DNA molecule?

Answer 29

A DNA molecule has a 5' end and a 3' end.

Question 30

What is the link between adjacent nucleotides in a DNA molecule?

Answer 30

The link between adjacent nucleotides in a DNA molecule is a phosphodiester bond.

Question 31

What is the common element that forms the polymer backbone in amino acids?

Answer 31

The common element that forms the polymer backbone in proteins is a carbon (the alpha carbon) linked to a COOH (carboxyl) group and a NH (amino group).

Question 32

What is the characteristic element in amino acids?

Answer 32

The characteristic element in amino acids is the amino acid side chain (R).

Question 33

What is the significance of only using L stereoisomers of amino acids in protein synthesis?

Answer 33

Only using L stereoisomers of amino acids in protein synthesis ensures that the protein is folded correctly.

Question 34

What are the two joining sites on the common element in amino acids?

Answer 34

the amino (NH2) group and the carboxyl (COOH) group.

Question 35

What is the polarity reflected in a protein polymer?

Answer 35

The amino terminus and the carboxyl terminus.

Question 36

How does protein polymer growth occur?

Answer 36

It occurs by addition of monomers to the carboxyl (COOH) end.

Question 37

How many different amino acid side chains are there?

Answer 37

There are 20 different amino acid side chains.

Question 38

What are the three main classes of amino acid based on their chemical properties?

Answer 38

1. Hydrophobic 2. Hydrophilic (includes acidic and basic side chains) 3. Special

Question 39

What is the link between adjacent amino acids in a protein chain?

Answer 39

The link is a peptide bond.

Question 40

To which end would the next amino acid be added in a growing protein chain?

Answer 40

The next amino acid would be added to the carboxyl (COOH) end.

Question 41

In what form are nucleotide monomers in order to be incorporated into the growing polymer chain?

Answer 41

Nucleotide monomers are in the form of high-energy nucleoside triphosphates (NTPs).

Question 42

What are the different types of nucleotide monomers?

Answer 42

The different types are ribo-ATP, CTP, GTP, UTP, and deoxyribo-dATP, dCTP, dGTP, and dTTP.

Question 43

What are nucleoside triphosphates (NTPs)?

Answer 43

Nucleoside triphosphates (NTPs) are high-energy molecules that include ATP, CTP, GTP, and UTP, among others.

Question 44

What happens to the outer two phosphates of NTPs when they are incorporated into a growing nucleic acid chain?

Answer 44

The outer two phosphates are "kicked out" when the NTP is incorporated into a growing nucleic acid chain

Question 45

What is the form of amino acid monomers?

Answer 45

Amino acid monomers are in the form of high-energy amino acyl-tRNA esters.

Question 46

What happens to the tRNA molecule when the next amino acid is incorporated at the end of a growing protein chain?

Answer 46

The tRNA molecule is "kicked out" when the next amino acid is incorporated at the end of a growing protein chain.

Question 47

Can even energized monomers join a growing chain by themselves?

Answer 47

Even energized monomers cannot join a growing chain by themselves

Question 48

What catalyzes the linkage reaction between monomers in a growing polymer chain?

Answer 48

The linkage reaction is catalyzed by a specific enzyme.

Question 49

What is the difference between DNA, RNA, in terms of their physical structure?

Answer 49

RNA and protein usually exist as single polymer chains, but DNA is usually double-stranded (duplex DNA).

Question 50

How are the two strands of DNA held together?

Answer 50

The two DNA strands are held together by H-bonds between complementary bases, which are called Watson-Crick base pairs.

Question 51

What is the general structure of DNA?

Answer 51

DNA is generally in a right-handed helix termed “B” DNA with sugar-phosphate backbones on the outside and base-pairs stacked on the inside.

Question 52

How do DNA-binding proteins identify specific sequences?

Answer 52

DNA-binding proteins can make contact with base-pairs at the major or minor grooves and identify specific sequences without having to separate the strands.

Question 53

What is DNA denaturation?

Answer 53

DNA denaturation is the breaking of H-bonds between base pairs, allowing the strands to separate.

Question 54

What is DNA renaturation?

Answer 54

DNA renaturation is the re-association of denatured DNA strands by formation of H-bonds between complementary base-pair sequences.

Question 55

Why is DNA denaturation and renaturation important during biological processes?

Answer 55

DNA denaturation and renaturation are important during biological processes such as DNA replication and transcription, because double stranded DNA can't be read.

Question 56

What is Tm in DNA denaturation?

Answer 56

Tm is the temperature at which the DNA is one-half melted.

Question 57

What factors affect the Tm of DNA?

Answer 57

The Tm of DNA depends on its base composition.

Question 58

What is the relationship between G-C base pairs and Tm? (and why)

Answer 58

DNA with a higher proportion of G-C base pairs has a higher Tm. A G-C base pair has 3 H-bonds. An A-T base pair has 2 H-bonds. It takes more energy to separate a G-C base pair than an A-T base-pair.

Question 59

What is the significance of DNA bending about its long axis?

Answer 59

DNA bending is important in DNA-protein interactions and in the folding of DNA into compact condensed structures. H-bonds don't intervene in the flexibility- like cooked spaghetti.