lecture 2 Flashcards
whats a polymer
covalent bond-linked chain of monomers
what are informational biopolymers? give examples of this
DNA, RNA, and protein
polymers that have more than one kind of monomer. order of different monomers is the information
what are the two elements of the informational biopolymer monomers?
-a common element (shared by all different monomers for that class of informational biopolymer)
-a characteristic element that makes each monomer different from the others
what forms the backbone of the polymer?
covalent bonding between the common elements of monomers
what forms the side chains of the polymer?
the characteristic elements
what happens if there are no joining sites exposed at ends?
no further growth in polymer chain, only 2 can join together
in what case can we get a branched polymer?
if the monomer has three joining its in the common element
true or false, informational biopolymers can be branched
false, always linear
can cells make branched polymer?
yes, but they arent informational
what type of DNA do some viruses and bacteria have?
circular DNA
true or false, linear molecules may be more efficiently handled than branched molecule
true
what type of monomers are informational biopolymers made of
asymmetric monomers
what are asymmetric monomers?
two joining sites per monomer but the two sites are different (B can only join with A, and A can only join with B)
what does the asymmetry of the monomer lead to?
asymmetry of the polymer (A end and B end distinct)
true or false, for all informational biopolymers DNA, RNA, and protein, growth is bidirectional
false, its unidirectional (only at one end). depicted as added to right end
what is the protein monomer?
amino acid
what is the monomer of DNA and RNA?
nucleotides
what is the characteristic element of nucleotides?
heterocyclic base (rings that have more than one atom). (purines/pyrimidines)
whats the common element that forms the polymer backbone for nucleotides?
pentose sugar phosphate
whats a pentose?
5 carbon sugar
what are the joining sites on the common element
the 5’ phosphate and the 3’ OH (hydroxyl)
true or false nucleic acid polymer growth is by addition of monomers to the 3’ end
true
what are the two ends of the nucleic acid polymer chain?
5’ phosphate end and 3’ hydroxyl end
what do DNA and RNA nucleotides differ in?
pentose sugar
what is the difference between deoxyribose and ribose?
deoxyribose is missing the 2’ hydroxyl of ribose
what sugar is found in RNA?
ribose
what sugar is found in DNA?
deoxyribose
what are the two types of heterocyclic bases for nucleotides?
purines and pyrimidines
what are the purines
adenine and guanine
what are the pyrimidines?
uracil, thymine, and cytosine
what are the two heterocyclic bases that are found specifically in RNA and DNA?
RNA: uracil
DNA: thymine
what is the link between adjacent nucleotides called?
phosphodiester bond
what is the characteristic element of the proteins?
amino acid side chain R
what forms the backbone of an amino acid?
carbon (alpha carbon), linked to a COOH (carboxyl group), and a NH2 group
which stereoisomers of amino acids are used in protein synthesis?
L (NOT D)
what are the two joining sites on the common element of the protein?
-NH2 (AMINO)
-carboxyl (COOH)
which characteristic of the R group differentiates amino acids
basic or acidic group in the R group
how many amino acids?
20 different amino acids
what are the three main classes of amino acids?
-hydrophobic
-hydrophilic
-special
what are the two ends of the amino end?
-amino end
-carboxyl end
how are monomers incorporated into the growing polymer chain?
they are energized
how are monomers energized?
breaking of high energy bond favours the forward reaction
what are nucleotide monomers in the form of?
high energy nucleoside triphosphate (NTPs)
what happens to NTPs?
the outer two phosphates are kicked out when the NTP is incorporated into a growing nucleic acid chain
what are amino acid monomers in the form of before they are added to the polymer?
amino acyl-tRNA esters
what happens when we want to incorporate the amino acyl-tRNA ester into a polymer?
tRNA molecule is kicked out when the next amino acid is incorporated at the end of a growing protein chain (high energy bond releases energy)
what are two things that a monomer needs to join a polymer chain?
-energized
-enzyme (linkage reaction is catalyzed by a specific enzyme)
what does the enzyme that helps create the polymer chain associated to?
associated with a template biopolymer that directs the enzyme to incorporate the correct flavour monomer
what are examples of TEMPLATE biopolymers?
DNA, RNA, mRNA
whats the biopolymer, template, and enzyme for DNA replication?
biopolymer: DNA
template: DNA
enzyme: DNA polymerase
whats the biopolymer, template, and enzyme for protein making?
biopolymer: protein
template: mRNA
enzyme: ribosome
whats the biopolymer, template, and enzyme for RNA?
biopolymer: RNA
template: RNA
enzyme: RNA polymerase
true or false, RNA and protein usually exist as single polymer chain?
true
true or false, DNA is usually single stranded
false, its double stranded
whats RNA involved in?
protein synthesis
what are DNA strands held together by?
H-bonds between complementary bases
what are the complementary bases in DNA called?
Watson crick base pairs
whats the relation between the two DNA STRANDS
antiparallel
what type of helix is DNA assembled in?
right-handed helix termed B DNA
whats on the outside of the DNA helix?
sugar-phosphate backbone
whats on the inside of the DNA helix?
base-pairs
where can DNA-binding proteins make contact with base pairs? what does this allow for?
major or minor grooves
this allows them to identify specific sequences without having to separate the strands
true or false, duplex DNA strands can be separated and re-associated
true
what happens if we break H bonds in the DNA helix? can the bonds reform?
strand denaturation
-denaturated DNA strands can accurately re-form base-paired duplex DNA by formation of H-bonds between complementary base-pair sequences (renaturation)
why are DNA denaturation and renaturation important processes?
is used in important biological processes such as DNA replication and transcription
what is the Tm?
temperature at which the DNA is half melted
what does the Tm depend on?
depends on base composition
which base pairs give a higher Tm?
DNA with a higher proportion of GC base pairs
why does it take more energy to separate a G-C pair than an A-T pair?
G-C: 3 H bonds
A-T: 2 H bonds
