Chpt 4 Nucleic Acids Flashcards
what are the 2 types of nucleic acids?
DNA and RNA
what are the 3 chemical components of all nucleic acids?
- (pentose) sugar
- organic (nitrogenous) base
- phosphate group
why are they called ‘nucleic’ acids?
the guy who discovered them found them in cell nuclei
what’s the main difference between DNA and RNA?
the nature of the sugar component is different
in a nucleic acid, which of the sugar’s carbons is the BASE usually connected to?
prime C1
in a nucleic acid, which of the sugar’s carbons is the PHOSPHATE usually connected to?
prime C5
In DNA and RNA, how are chains of nucleic acids connected to one another?
the phosphate group from one nucleic acid (attached at C5) connects with the other nucleic acid at C3
what are the 2 bases that a nucleic acid can have
purine or pyrimidine
why are the carbons in a nucleic acid’s sugar called ‘prime’ carbons?
to keep them from getting mixed up with the carbons from the base and phosphate
what are the two types of purine bases that a nucleic acid can have?
adenine and guanine
what are the 3 types of pyrimidine bases that a nucleic acid can have?
cytosine, uracil and thymine
uracil is only in RNA
what base can RNA have that DNA can NOT have?
RNA has uracil instead of thymine
what is a (nitrogenous) base, as found in nucleic acids?
an organic molecule that contains the element nitrogen and acts as a base in chemical reactions.
how many classes of (nitrogenous) bases are there?
2 (purine and pyrimidine)
Are (nitrogenous) bases in nucleic acids polar or non-polar?
non-polar
are (nitrogenous) bases planar or 3D?
planar
how many different (nitrogenous) bases are there?
A lot, but we only need to know the 5 that are in DNA and RNA for our class
are (nitrogenous) bases aromatic?
yes
why does Shimko call the (nitrogenous) bases heterogenous?
because they are rings that include atoms other than just carbons and hydrogens.
They have nitrogen
what role does the sugar/pentose play in the structure of a nucleic acid?
it serves as the backbone of the structure
what is ribose?
a cyclic sugar whose :
- ring(?) has 5 carbons, and oxygen, and an aldehyde group
- structure has has 3 OH groups on it
is ribose found in DNA or RNA?
RNA
in order to draw a ‘stereochemically correct’ nucleic acid, where should the (nitrogenous) base be located relative to the 5C carbon?
the base and the 5C carbon must be drawn on the same side of the ring
(on a flat representation, they must both be pointed up or both be pointing down)
what is the difference between a DEOxyribose and a ribose?
ribose has OH groups on its C2 and C3 carbons. Deoxyribose has H on its C2 carbon instead.
Which part of the nucleotide is used to give the molecule its name?
its base
what is a nucleoSIDE?
essentially it’s what you call the part of the nucleotide comprised by the sugar and the base
(if you’re referring to the sugar, the base, and the phosphate group, you call it a regular old nucleoTIDE)
why do we care about nucleosides when they’re just part of the nucleotide?
the nucleoside is the part of the nucleotide that gives rise to distinctions between DNA molecules and RNA molecules
what are nucleoSIDES derived from?
ribose
WHY are nitrogenous bases non-polar?
Because they have delocalization in their aromatic rings
what’s the difference between a uracil molecule (from RNA) and a thymine molecule (from DNA)?
the thymine has a methyl group that the uracil doesn’t have
which is more stable: RNA or DNA
DNA
what was RNA good at before it was replaced by DNA and protein?
- storing and carrying genetic information
2. catalyzing chemical reactions
what are ribosomes?
structures within the cells of living things that make/synthesize protein.
They are made of RNA and protein
why/how was RNA originally able to carry genetic information (before it was replaced by DNA)?
It’s varied structure allowed it to carry genetic info (much in the way its varied structure allows to to fulfill its current role in signaling templates for mRNA translation)
what is translation?
the process by which a protein is synthesized from the information contained in a molecule of messenger RNA (mRNA)
why/how was RNA originally able to serve as a catalyst (before it was replaced by DNA)?
it’s ability to fold into specific shapes
must’ve been able to bind to reaction ingredients and then bring them together
are RNA molecules still catalytically active (even though they’ve been replaced in this role by proteins)?
yes. RNA molecules that can do this are called RNAses or RNA enzymes)
what has replaced RNA in its original genetic information storage role?
DNA
what has replaced RNA in its original catalytic role?
proteins (read enzymes, which do what RNA used to do)
how/where does a pentose bind to a base to create a nucleoSIDE?
The base replaces the OH group on the sugar’s prime 1 carbon
how/where does a base bind to a pentose to create a nucleoSIDE?
the base’s bottom H is removed (via condensation) so the remaining chunk can replace the OH on the sugar’s prime carbon
what reaction enables a sugar and base to bind to create a nucleoside?
condensation
what would you call a nucleoside that had adenine as the base and ribose as the sugar?
adenosine
what would you call a nucleoside that had adenine as the base and deoxyribose as the sugar?
deoxyadenosine
when you draw a nucleotide, do you draw the 5 prime carbon on the right or left?
left
when you draw a nucleotide, do you draw the 1 prime carbon on the right or left?
right
when you draw a nucleotide, do you draw your base and phosphate above the sugar ring or below the sugar ring?
above
what would you call a nucleoside that had guanine as the base and ribose as the sugar?
guanosine
what would you call a nucleoside that had cytosine as the base and ribose as the sugar?
cytidine
what would you call a nucleoside that had uracil as the base and ribose as the sugar?
uridine
what would you call a nucleoside that had thymine as the base and ribose as the sugar?
thymidine
what’s the difference in how you name nucleoSIDES and nucleoTIDES?
the name of the nucleoTIDE has to include the number of phosphates you have
exp. a nucleoTIDE with adenine as the base and a single phosphate group would be ADENOSINE MONOPHOSPHATE (AMP)
what would you call a nucleoTIDE that had: thymine as the base, DEOXYribose as the sugar, and three phosphates?
deoxythymidine triphosphate
what is a phosphodiester bond?
the bond between two nucleotides
what do you call the bond between two nucleotides?
phosphodiester bond
Is a phosphodiester bond considered to have high energy or low energy?
high
what does adenine do hydrogen bonds with during base pairing in DNA?
Thymine
what does thymine do hydrogen bonds with during base pairing in DNA?
adenine
How many hydrogen bonds form between each adenine and thymine in DNA base pairing?
2
what does cytosine do hydrogen bonds with during base pairing in DNA?
guanine
what does guanine do hydrogen bonds with during base pairing in DNA?
cytosine
How many hydrogen bonds form between each cytosine and guanine in DNA base pairing?
3
Why is the distance between base pairs’ prime 1 carbons important?
The distance between the prime 1 carbons in a base pair is supposed to be exactly 1.08nm. Anything more or less indicates that the wrong nucleotides were paired and that the organism’s correction mechanisms need to fix it
what does it mean to say that 2 DNA strands are ‘antiparallel’ to one another?
It means one strand is traveling in the 5 prime to 3 prime direction and the other is traveling 3 prime to 5 prime direction
what 4 phenomena drive the double helix shape of DNA strands?
- the shape protects the hydrophobic bases (in the center of the structure) from being exposed to the polar water (surrounding the structure)
- the shape reduces charge repulsion between the negatively charged phosphate groups in the structure’s backbone
- the shape exposes polar regions of the ‘major and minor groves’ to the surrounding polar water (for favorable interactions)
- the shape exposes polar sugars on the structure’s backbone to the surrounding polar water (for favorable interactions)
All of these phenomena are thermodynamically favorable
what 2 characteristics of DNA strands can help protect them from denaturing in high heat?
- the number of base pairs.More base pairs, more heat resistance (A strand with 100 base pairs will be harder to denature with heat than a strand with 10 base pairs)
- The number of guanine to cytosine pairs (because each guanine to cytosine pair has 3 hydrogen bonds where adenine to thymine pairs only have 2)
what does ‘melting temperature’ represent in the context of using heat to denature DNA?
its the temperature range over which half of the DNA in a given sample can be completely denatured with heat
can you re-nature (aka re-anneal) a DNA strand that has been denatured with heat?
Yes
If you cool the DNA (slowly, and gently), it will go back to it’s functional shape
what happens if you try to re-nature a heated DNA strand too fast?
The bases won’t all have time to find their pairs again, so only some of them will bind to their correct partners and the rest will not
You end up with an insoluble structure that needs to be heated and cooled again in order to try and fix it
why does Shimko make such a big deal about proteins?
They make up the enzymes that catalyze living things’ chemical reactions
what are genes?
sequences of DNA
what is (DNA) replication?
copying of DNA
What is (DNA) transcription?
converting DNA into RNA
What is reverse transcription?
conversion of RNA back into DNA
What is (DNA) translation?
making proteins from an RNA template
what is the 3 step sequence for making protein from DNA?
- replication (of DNA)
- Transcription (of DNA to RNA)
- Translation (of RNA to protein)
what are the 3 types of RNA involved in protein making?
mRNA
tRNA
rRNA
What does the polymerase chain reaction (PCR) method accomplish?
it copies DNA exponentially, cheaply
In PCR, what is a primer/what does it do?
Primer is a short nucleic acid sequence (within a larger DNA strand???) that tells the polymerase where to start and stop copying
In PCR, what is a (RNA) polymerase/what does it do?
(RNA) polymerase is an enzyme that moves along the DNA strand, reads its code, and writes the (mRNA) copy
what are the 3 dNTPs (free nucleotides) in PCR
dATP (deoxyadenosine triphosphate)
dCTP(deoxycytidine triphosphate)
dGTP(deoxyguanosine triphosphate)
dTTP(deoxythymidine triphosphate)
Along with temperature control, what 4 components do you need (in your sample) to complete a PCR cycle?
- DNA sample (template)
- Primers
- dNTP (free nucleotides)
- Heat tolerant Polymerases
Where do we get the heat tolerant polymerases for PCR cycles?
from thermophilic (heat loving) archaeal species like vent worms
What are two common polymerases used for PCR cycles?
Taq and PFU
What does it mean to ‘sequence’ a DNA sample?
It means you’re trying to identify the sample by comparing it’s sequence to sequences in known DNA samples
Along with temperature control, what FIVE components do you need (in your sample) to complete a Sanger sequencing cycle?
- DNA sample (template)
- Primers
- dNTP (free nucleotides)
- Heat tolerant Polymerases
- ddNTP
What does ddNTP do in a Sanger sequence?
It stops the extension process so that no more copies of a given DNA strand can be made
What is dsDNA?
your original DNA sample
it stands for double stranded DNA
What is ssDNA
your denatured/split open DNA
it stands for single strand DNA
What is ddNTP (in a Sanger sequence technique)?
Dideoxynucleotide
Why is ddNTP (in a Sanger sequence technique) so called?
Because the sugar has H on both the prime C2 and prime C3 carbons, which prevent it from extending a denatured DNA chain
What are restriction enzymes?
enzymes found in nature that snip or chop out segments of a DNA strand
We can use them to cut DNA so we can do cloning or put the pieces back together in different order
