KH1 Flashcards
what are DNA, RNA and protein
informational biopolymers
what is a polymer
covalent bond linked chain of monomers
what do informational biopolymers have
more than one kind of monomer
what is the information
the order of the different kinds of monomer in polymer chain
sequence is the info
what is the information for DNA, RNA and protein
DNA sequence
RNA sequence
protein sequence
T OR F: informational biopolymer monomers always have different basic structures
FALSE
informational biopolymers have a common generic structure
describe common generic structure of biopolymer monomers
common element - shared by all the different monomers
so, a common element with characteristic elements on top
what makes each monomer different from the others
a characteristic element
what does the common element form
polymer backbone
covalent bonding between monomers (how they join via polymerization)
what do the characteristic elements form
side chains
protrude from polymer backbone
what is the info in an informational biopolymer
order of monomer units (sequence, think of colour memory game)
where does polymer structure arise from
monomer chemistry
if monomer has one joining site in common element
only 2 monomer units can be joined together
cant form a polymer
why cant monomer with one joining site form a polymer
if join 2 together then there arent any joining sites at exposed ends so the chain cant grow anymore
if monomer has two joining sites in common element
can make linear polymers of infinite length
since there is a joining site at the exposed end the chain can grow bigger
if monomer has three joining sites in common element
can make branched polymers
can informational biopolymers be branched
cells can make branched polymers but informational biopolymers are not branched
they are linear
why is it better that informational biopolymers are linear
packing and handling is more efficient - better to fit into chromosomes
better for science bc easier to determine linear structures than branched
how many ends do linear informational biopolymers have
2 ends (“loose ends”)
sometimes can be joined into circular molecule (ex: genomic DNA of bacteria like E. coli)
what are informational biopolymers made from
asymmetric monomers = 2 different joining sites per monomer
(A & B - cant join with itself but only with the other letter, A&B ends are chemically distinct)
asymmetry of monomers drives…
an asymmetry of the polymer
describe growth of informational biopolymers (and convention)
growth only occurs at one end - polymer growth is unidirectional - no exceptions at all
convention = depict growth in rightward direction, monomers are added at the end right)
name the 2 major types of informational biopolymer monomer units
nucleotides and amino acids
name the polymers/monomers/typical chain lengths
nucleic acids (monomer = nucleotides)
DNA ~10^3 - 10^8
RNA ~20-10^4
protein (monomer = amino acids)
~100-10^3 monomer units
what is the characteristic element of a nucleotide
heterocyclic base (ring with 2 different types of atoms)
what is the common element that forms the polymer backbone of a nucleotide
pentose (5 carbon sugar) sugar phosphate
carbons are numbered 1’ 2’ 3’ 4’ 5’
name the 2 joining sites on the common element for a nucleotide
5’ phosphate (acid in nucleic acid, negative charge)
3’ OH (hydroxyl)
how is monomer polarity reflected
in the polymer - 5’ end and 3’ end of a nucleic acid chain
how do nucleic acid polymers grow
always by adding monomers to 3’ end
NEVER THE 5’ end
what is the difference between DNA and RNA
differ in the pentose sugar
deoxyribose is missing 2’ hydroxyl of ribose - only has an H
what does DNA only having an H on 2’ C mean
DNA is more resistant to chain cleave by hydrolysis
greater stability (want DNA to be as stable as possible)
describe the heterocyclic bases of nucleotides
purines
pyrimidines
these are names for the bases that nucleotides are made from
name purines
adenine
guanine
name pyrimidines
uracil
thymine
cytosine
how does nucleotide attach to ribose
N-glycosidic bond
always on 1’ sugar
describe the bases only found in DNA
thymine is only in DNA
uracil is only in RNA
T instead of U makes chemical damage easier to repair in DNA
what is the link between adjacent nucleotides
phosphodiester bond
why is it called a phosphoDIESTER bond
phosphate is joined (ester linkage) to 5’ OH of nucleotide below and then there’s another link to 3’ OH of above nucleotide
what is the characteristic element of a protein
amino acid side chain (R)
what is the common element that forms the polymer backbone of a protein
carbon (alpha carbon)
linked to a COOH (carboxyl) and a NH2 (amino group)
describe stereoisomers of protein synthesis
designated by L and D
only L stereoisomers of amino acids are used in protein synthesis
name 2 joining sites of protein
amino group
carboxyl group
(monomer polarity so amino terminus and carboxyl terminus)
describe protein polymer growth
always by addition of monomers to carboxyl end
describe side chains of amino acids
20 different amino acid side chains
name and briefly describe 3 main classes of amino acid
hydrophobic (8aa)
hydrophilic (includes acidic and basic side chains (if the side chain is acidic or basic, not talking about the polarity), 9aa)
special (3aa)
what is the link between amino acids
peptide bonds
(alpha carbon is linked to amide of other alpha carbon)
how are monomers incorporated into the growing polymer chain
monomers are energized
nucleotide monomers are in the form of high e every nucleoside triphosphates (NTPs)
outer 2 phosphates are kicked out when NTP is incorporated (so only 1 phosphate between sugars)
when it’s deoxyribo how to write
put d in front
dATP
for ribose it’s just (ATP)
what are amino acid monomers in the form of high energy called
amino acyl-tRNA esters
tRNA is kicked out when next aa is added
energized monomers can’t join a growing chain by themselves
linkage is catalyses by specific enzyme
enzyme is associated with a template biopolymer - directs enzyme to incorporate correct monomer (maintain sequence)
describe biopolymer/template/enzyme
DNA - DNA - DNA polymerase
RNA - DNA (transcription) - RNA polymerase
protein - mRNA - ribosome
what form is RNA and protein
single polymer chains
what form is DNA
double stranded
duplex DNA
sugar phosphate backbone on outside
stacked base pairs on inside
what are DNA strands held together by
H bonds (not covalent) between complementary bases (waston-crick base pairs)
the 2 DNA strands are…
ANTIPARALLEL
why is it called BDNA
DNA is generally a right handed helix
describe grooves of DNA
there is a major groove which is larger and a minor groove which is smaller
how many H bonds for A-T
2 H bonds
how many H bonds for C-G
3 H bonds
what does major/minor groove allow for
base pairs to be read by DNA binding proteins binding to grooves (without opening strand)
proteins can bind and have recognition and make contact with base pairs
can duplex DNA strands be separated
YES and they can be reassociated
DNA strands are held together by weak H bonds
breaking H bonds allows strands to separate (by heat)
describe DNA strand separation
melting
denaturation
less than boiling point of water
describe DNA renaturation
denatured DNA can re form base pair duplex DNA by forming H bonds between complementary base pair sequences
why is DNA denaturation and renaturation important
for biological processes like DNA replication and transcription since DNA and RNA polymerases can’t read from outside - must open up DNA
what is the Tm and describe it based on DNA composition
the temp at which the DNA is one half melted
depends on base composition
DNA with higher G-C bonds have a higher Tm since more H bonds (3 instead of 2)
what is Tm a function of
G-C base pair content
takes less energy to separate A-T pair than G-C bc H bonds
can DNA bend
yes it can bend along it’s axis
why is DNA bending important
important in DNA protein interactions and in folding of DNA into compact condensed structures
EX = TATA box binding protein - DNA must fold
is DNA flexible
yaaaa
H bonds are left and right - don’t interfere with flexibility (cooked spaghetti)
sometimes helixes can be more stiff if H bonds align with backbone
