Sept 1 Building Blocks and Linear Biopolymers

Question 1

what kind of polymers are DNA RNA and protein?

Answer 1

informational polymers

Question 2

what is a polymer?

Answer 2

chain of monomers linked by covalent bonds

Question 3

what constitutes the information in informational polymers?

Answer 3

the order of the different kids of monomers in the polymer chain, the “sequence”

Question 4

what is the information in the case of DNA, RNA and proteins?

Answer 4

the DNA/RNA/protein sequence

Question 5

What is the common generic structure of an informational biopolymer?

Answer 5

1. a common element, all monomers of that class of informational biopolymer have the same
2. a “characteristic” element that makes each monomer specific and different

Question 6

what are the names of the different structure and what they do?

Answer 6

common elements: “backbone”, bind by covalent bonds with other monomers
characteristic elements: “side chains” that protrude from the backbone

Question 7

how many joining sites does the common element need to have to make a linear polymer?

Answer 7

TWO joining sites (monomers can join on both sites)

Question 8

how many joining sites on the common element to make branched polymers?

Answer 8

THREE joining sites (can make branching)

Question 9

are informational biopolymers linear or branched? and why?
what happens in some cases?

Answer 9

informational biopolymers are linear
packaging and handling of linear molecules may be more efficient than that of branched molecules
sometimes the two ends can join together, making a circular but unbranched molecule (DNA molecule of bacteria and some viruses)

Question 10

what type of monomers are informational biopolymers made of?

Answer 10

asymmetric monomers

Question 11

what does asymmetric monomers mean?

Answer 11

there are two joining sites per monomer but the two sites are different
A and B
A can only join with B
B can only join with A

Question 12

what does this create in the polymer?

Answer 12

it creates an asymmetric polymer
there is an A end and there is a B end and they are chemically distinct

Question 13

in what direction does the polymer chain growth go?

Answer 13

the growth only occurs at one end, it is unidirectional

Question 14

what is the convention when depicting biopolymers on paper?

Answer 14

the growing side is on the right
monomers are added on the right end

Question 15

what are the two major types of informational biopolymer units?

Answer 15

nucleotides (DNA and RNA) and amino acids (proteins)

Question 16

for nucleic acids, what is the monomer and the typical chain length?

Answer 16

DNA:
nucleotides
10^3 to 10^8
RNA:
nucleotides
20 to 10^4

Question 17

for proteins, what is the monomer and the typical chain length?

Answer 17

amino acids
100 to 1000

Question 18

what is the common element that forms the backbone of nucleotides?

Answer 18

pentose sugar phosphate (heterocyclic base)
5C sugar and a PO4 (phosphate) attached to the 5th carbon

Question 19

what are the joining sites on the common element?

Answer 19

the 5’ phosphate:
the acid
negative charge
the 3’ hydroxyl (OH)

Question 20

to which end are monomers added in the growth of a nucleic acid?

Answer 20

the 3’ hydroxyl (OH) end

Question 21

what is the difference in the nucleotides between RNA and DNA?

Answer 21

RNA has ribose sugar, OH found on 2’ carbon
DNA has 2-deoxyribose sugar, missing OH on the 2’ carbon (only an H there)

Question 22

how does the absence of a hydroxyl group on the 2’ of DNA sugar affect it?

Answer 22

DNA is much more resistant to chain cleavage by hydrolysis therefore it has greater stability

Question 23

what is the bond between the pentose sugar and the base?

Answer 23

N-glycosidic bond
(nitrogen bonded to a sugar)

Question 24

What are purines?

Answer 24

adenine and guanine

Question 25

what are pyrimidines?

Answer 25

uracil thymine and cytosine

Question 26

be able to draw the structure of the common element of nucleic acids (ribose AND deoxyribose)

Answer 26

check slides for reference

Question 27

what is the bond between the different nucleotides?

Answer 27

phosphodiester bond

Question 28

what is it called a phosphoDIester bond?

Answer 28

ester bond to the 5' OH of the downstream nucleotide and an ester bond to the 3' OH of the upstream nucleotide

Question 29

what is the characteristic element of the amino acid?

Answer 29

the side chain (R)

Question 30

draw and describe the general structure of an amino acid

Answer 30

central carbon linked to a carboxyl group (acidic), an amino group (basic) (and then the R chain)

Question 31

which stereoisomers of amino acids are used in protein synthesis?

Answer 31

the L (not the D)

Question 32

what are the two joining sites on the common element of the amino acid?

Answer 32

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

Question 33

where is the monomer polarity reflected in nucleotides?

Answer 33

reflected in the polymer, so we speak of the 5' and 3' end

Question 34

where is the monomer polarity reflected in amino acids?

Answer 34

reflected in the polymer, so we speak of amino terminus (N terminus) and carboxyl terminus (C terminus) of a protein

Question 35

to which end of the protein polymer are monomers added?

Answer 35

added to the carboxyl (COOH) end

Question 36

how many different types of side chains are there and therefore the three classes of amino acid?

Answer 36

20 different amino acid side chains the chemical properties define the main classes of amino acid 1. hydrophobic (8 amino acids) 2. hydrophilic (9 amino acids) 3. special (3 amino acids)

Question 37

what is the link between amino acids called?

Answer 37

peptide bond (bond between the carboxyl group of one amino acid to the amino group of another amino acid)

Question 38

what do monomers need to be in order to be incorporated into the growing polymer chain?

Answer 38

need to be "energised" two phosphates are added (phosphorolated, less stable more prone to react etc)

Question 39

what is the high energy form of nucleotide monomers?

Answer 39

nucleoside tri-phosphates (NTPs)

Question 40

what are the different NTPs for the ribose sugar? (RNA)

Answer 40

ATP CTP GTP UTP

Question 41

what are the different NTPs for the deoxyribose sugar? (DNA)

Answer 41

dATP dCTP dGTP dTTP

Question 42

what happens when the NTP is incorporated into a growing chain?

Answer 42

the outer two phosphates are kicked out one phosphate is left

Question 43

what is the high energy form of the amino acid monomers?

Answer 43

amino acyl-tRNA esters a tRNA is added to the carboxyl end and a high energy ester bond is created

Question 44

what happens after the amino acid is incorporated at the end of a growing protein chain?

Answer 44

the tRNA molecule is "kicked out"

Question 45

what enzymes catalyse the adding of monomers to the chain? (for DNA, RNA and protein)

Answer 45

DNA polymerase (DNA) RNA polymerase (RNA) ribosome (protein)

Question 46

what are the templates that these enzymes are associated with? (for DNA, RNA and protein)

Answer 46

DNA: DNA RNA: DNA protein: mRNA

Question 47

what are the two DNA strands held together by? and what is the relationship between them?

Answer 47

hydrogen bonds between the complimentary base pairs (watson crick) the two strands are antiparallel

Question 48

how are the different elements of DNA organised in the double helix?

Answer 48

the sugar phosphate backbones are on the outside the base pairs are stacked on the inside

Question 49

how can the base pairs in the inside of the DNA structure be read?

Answer 49

by DNA binding proteins they bind to grooves (major or minor) can identify specific sequences without having to separate the strands

Question 50

how are DNA strands separated and re-associated?

Answer 50

can be separated by breaking the hydrogen bonds with heat --> denaturation can be re-associated by reforming the hydrogen bonds --> renaturation

Question 51

why is DNA denaturation and renaturation important?

Answer 51

important in biological processes such as DNA replication and transcription exploited in many experimental techniques in molecular biology and genomics

Question 52

what is the Tm, what does it depend on and how does having a higher proportion of G-C base pairs affect it?

Answer 52

the Tm is the temperature at which the DNA is 50% melted the Tm of the DNA depends on its base composition more G-C base pairs = higher Tm

Question 53

how many hydrogen bonds between G and C?

Answer 53

3

Question 54

how many hydrogen bonds between A and T?

Answer 54

2

Question 55

why is Tm higher when there are more G-C base pairs?

Answer 55

triple bonds are harder to break more energy needed --> higher temperature

Question 56

what is another property of DNA and what it is important for?

Answer 56

DNA can bend about its long axis important in DNA protein interactions and in the folding of DNA into compact condensed structure

Question 57

on which carbon does the base bind in a nucleic acid?

Answer 57

on the 1' carbon

Question 58

what is the difference between uracil and thymine? and what does that change

Answer 58

there is a methyl group on thymine, and on uracil there is no (only CH) see slide 16 for picture the methyl group makes it easier to repair damage if there is some in the DNA

Question 59

# **** what is the structure of a nucleotide without the phosphate called?

Answer 59

nucleoside

Question 60

what is the substrate for the enzymes called?

Answer 60

nucleoside triphosphate | (and then 2PO4s are kicked out)

Question 61

to which end of the tRNA are amino acids bonded?

Answer 61

the 3' end

Question 62

what allows the DNA to bend? | internal structure and other elements

Answer 62

hydrogen bonds are transverse, no H bonds along the axis of the polymer the backbones do not contact each other --> can bond TATA box-binding proteins that attach to DNA, bend it and prepare it for transcription