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Biol200 > building blocks and linear biopolymers > Flashcards

building blocks and linear biopolymers Flashcards

1
Q

What is a polymer?

A

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

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2
Q

What is an informational polymer?

A

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.

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3
Q

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

A

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

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4
Q

What is the generic structure of informational
biopolymer monomers?

A

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.

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5
Q

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

A

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

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6
Q

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

A

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

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7
Q

What is the information in an informational
biopolymer?

A

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

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8
Q

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?

A

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

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9
Q

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

A

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.

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10
Q

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

A

branched polymers

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11
Q

Are informational biopolymers branched or linear?

A

Informational biopolymers are linear and not
branched.

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12
Q

What is the difference between linear and branched
informational biopolymers?

A

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

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13
Q

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

A

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

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14
Q

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

A

The two sites are different.

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15
Q

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

A

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

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16
Q

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

A

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

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17
Q

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

A

nucleotides and
amino acids.

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18
Q

What is the typical chain length of DNA?

A

~10^3 to ~10^8.

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19
Q

What is the typical chain length of RNA?

A

~20 to ~10^4

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20
Q

What is the typical chain length of protein?

A

~100 to ~10^3

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21
Q

What is the characteristic element of nucleotides?

A

A heterocyclic base.

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22
Q

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

A

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

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23
Q

How is nucleic acid polymer growth achieved?

A

ALWAYS by addition of monomers to the 3’ end.

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24
Q

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

A

Deoxyribose is missing the 2’ hydroxyl of ribose.

25
Q

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

A

The absence of 2’-OH.

26
Q

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 ?

A

N-glycosidic bond.

27
Q

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

A

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).

28
Q

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

A

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

29
Q

What is the polarity of a DNA molecule?

A

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

30
Q

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

A

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

31
Q

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

A

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).

32
Q

What is the characteristic element in amino acids?

A

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

33
Q

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

A

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

34
Q

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

A

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

35
Q

What is the polarity reflected in a protein polymer?

A

The amino terminus and the carboxyl terminus.

36
Q

How does protein polymer growth occur?

A

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

37
Q

How many different amino acid side chains are
there?

A

There are 20 different amino acid side chains.

38
Q

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

A
  1. Hydrophobic
  2. Hydrophilic (includes acidic and basic side chains)
  3. Special
39
Q

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

A

The link is a peptide bond.

40
Q

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

A

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

41
Q

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

A

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

42
Q

What are the different types of nucleotide
monomers?

A

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

43
Q

What are nucleoside triphosphates (NTPs)?

A

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

44
Q

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

A

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

45
Q

What is the form of amino acid monomers?

A

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

46
Q

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

A

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

47
Q

Can even energized monomers join a growing
chain by themselves?

A

Even energized monomers cannot join a growing
chain by themselves

48
Q

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

A

The linkage reaction is catalyzed by a specific
enzyme.

49
Q

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

A

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

50
Q

How are the two strands of DNA held together?

A

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

51
Q

What is the general structure of DNA?

A

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.

52
Q

How do DNA-binding proteins identify specific
sequences?

A

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.

53
Q

What is DNA denaturation?

A

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

54
Q

What is DNA renaturation?

A

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

55
Q

Why is DNA denaturation and renaturation
important during biological processes?

A

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

56
Q

What is Tm in DNA denaturation?

A

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

57
Q

What factors affect the Tm of DNA?

A

The Tm of DNA depends on its base composition.

58
Q

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

A

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.

59
Q

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

A

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.

Biol200 (12 decks)

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