Sept 1 Building Blocks and Linear Biopolymers Flashcards
what kind of polymers are DNA RNA and protein?
informational polymers
what is a polymer?
chain of monomers linked by covalent bonds
what constitutes the information in informational polymers?
the order of the different kids of monomers in the polymer chain, the “sequence”
what is the information in the case of DNA, RNA and proteins?
the DNA/RNA/protein sequence
What is the common generic structure of an informational biopolymer?
- a common element, all monomers of that class of informational biopolymer have the same
- a “characteristic” element that makes each monomer specific and different
what are the names of the different structure and what they do?
common elements: “backbone”, bind by covalent bonds with other monomers
characteristic elements: “side chains” that protrude from the backbone
how many joining sites does the common element need to have to make a linear polymer?
TWO joining sites (monomers can join on both sites)
how many joining sites on the common element to make branched polymers?
THREE joining sites (can make branching)
are informational biopolymers linear or branched? and why?
what happens in some cases?
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)
what type of monomers are informational biopolymers made of?
asymmetric monomers
what does asymmetric monomers mean?
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
what does this create in the polymer?
it creates an asymmetric polymer
there is an A end and there is a B end and they are chemically distinct
in what direction does the polymer chain growth go?
the growth only occurs at one end, it is unidirectional
what is the convention when depicting biopolymers on paper?
the growing side is on the right
monomers are added on the right end
what are the two major types of informational biopolymer units?
nucleotides (DNA and RNA) and amino acids (proteins)
for nucleic acids, what is the monomer and the typical chain length?
DNA:
nucleotides
10^3 to 10^8
RNA:
nucleotides
20 to 10^4
for proteins, what is the monomer and the typical chain length?
amino acids
100 to 1000
what is the common element that forms the backbone of nucleotides?
pentose sugar phosphate (heterocyclic base)
5C sugar and a PO4 (phosphate) attached to the 5th carbon
what are the joining sites on the common element?
the 5’ phosphate:
the acid
negative charge
the 3’ hydroxyl (OH)
to which end are monomers added in the growth of a nucleic acid?
the 3’ hydroxyl (OH) end
what is the difference in the nucleotides between RNA and DNA?
RNA has ribose sugar, OH found on 2’ carbon
DNA has 2-deoxyribose sugar, missing OH on the 2’ carbon (only an H there)
how does the absence of a hydroxyl group on the 2’ of DNA sugar affect it?
DNA is much more resistant to chain cleavage by hydrolysis therefore it has greater stability
what is the bond between the pentose sugar and the base?
N-glycosidic bond
(nitrogen bonded to a sugar)
What are purines?
adenine and guanine
what are pyrimidines?
uracil thymine and cytosine
be able to draw the structure of the common element of nucleic acids (ribose AND deoxyribose)
check slides for reference
what is the bond between the different nucleotides?
phosphodiester bond
what is it called a phosphoDIester bond?
ester bond to the 5’ OH of the downstream nucleotide and an ester bond to the 3’ OH of the upstream nucleotide
what is the characteristic element of the amino acid?
the side chain (R)
draw and describe the general structure of an amino acid
central carbon linked to a carboxyl group (acidic), an amino group (basic) (and then the R chain)
which stereoisomers of amino acids are used in protein synthesis?
the L (not the D)
what are the two joining sites on the common element of the amino acid?
the amino (NH2) group and the carboxyl (COOH) group
where is the monomer polarity reflected in nucleotides?
reflected in the polymer, so we speak of the 5’ and 3’ end
where is the monomer polarity reflected in amino acids?
reflected in the polymer, so we speak of amino terminus (N terminus) and carboxyl terminus (C terminus) of a protein
to which end of the protein polymer are monomers added?
added to the carboxyl (COOH) end
how many different types of side chains are there and therefore the three classes of amino acid?
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)
what is the link between amino acids called?
peptide bond
(bond between the carboxyl group of one amino acid to the amino group of another amino acid)
what do monomers need to be in order to be incorporated into the growing polymer chain?
need to be “energised”
two phosphates are added (phosphorolated, less stable more prone to react etc)
what is the high energy form of nucleotide monomers?
nucleoside tri-phosphates (NTPs)
what are the different NTPs for the ribose sugar? (RNA)
ATP
CTP
GTP
UTP
what are the different NTPs for the deoxyribose sugar? (DNA)
dATP
dCTP
dGTP
dTTP
what happens when the NTP is incorporated into a growing chain?
the outer two phosphates are kicked out
one phosphate is left
what is the high energy form of the amino acid monomers?
amino acyl-tRNA esters
a tRNA is added to the carboxyl end and a high energy ester bond is created
what happens after the amino acid is incorporated at the end of a growing protein chain?
the tRNA molecule is “kicked out”
what enzymes catalyse the adding of monomers to the chain? (for DNA, RNA and protein)
DNA polymerase (DNA)
RNA polymerase (RNA)
ribosome (protein)
what are the templates that these enzymes are associated with? (for DNA, RNA and protein)
DNA: DNA
RNA: DNA
protein: mRNA
what are the two DNA strands held together by?
and what is the relationship between them?
hydrogen bonds between the complimentary base pairs (watson crick)
the two strands are antiparallel
how are the different elements of DNA organised in the double helix?
the sugar phosphate backbones are on the outside
the base pairs are stacked on the inside
how can the base pairs in the inside of the DNA structure be read?
by DNA binding proteins
they bind to grooves (major or minor)
can identify specific sequences without having to separate the strands
how are DNA strands separated and re-associated?
can be separated by breaking the hydrogen bonds with heat –> denaturation
can be re-associated by reforming the hydrogen bonds –> renaturation
why is DNA denaturation and renaturation important?
important in biological processes such as DNA replication and transcription
exploited in many experimental techniques in molecular biology and genomics
what is the Tm, what does it depend on and how does having a higher proportion of G-C base pairs affect it?
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
how many hydrogen bonds between G and C?
3
how many hydrogen bonds between A and T?
2
why is Tm higher when there are more G-C base pairs?
triple bonds are harder to break
more energy needed –> higher temperature
what is another property of DNA and what it is important for?
DNA can bend about its long axis
important in DNA protein interactions and in the folding of DNA into compact condensed structure
on which carbon does the base bind in a nucleic acid?
on the 1’ carbon
what is the difference between uracil and thymine? and what does that change
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
**
what is the structure of a nucleotide without the phosphate called?
nucleoside
what is the substrate for the enzymes called?
nucleoside triphosphate
(and then 2PO4s are kicked out)
to which end of the tRNA are amino acids bonded?
the 3’ end
what allows the DNA to bend?
internal structure and other elements
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
