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Nucleic Acids - RNA and DNA Structure - Biochemistry

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This content provides a foundational overview of nucleic acids, specifically DNA and RNA, detailing their structural differences, components, and the nomenclature of their building blocks (nucleotides and nucleosides).

one of the topics that are commonly

taught in a biochemistry course

are nucleic acids

now you might be wondering what exactly

are nucleic acids

and there are two

forms of nucleic acids i'm sure you

heard of them dna and rna

dna stands for

deoxyribonucleic acid

rna is simply

ribonucleic acid but both of these are

different types of nucleic acids

as you can see dna is

a double-stranded nucleic acid it forms

an alpha helix

whereas rna is

a single stranded

nucleic acid so that's one difference

between the two there are other differences

differences

now dna

is mostly located in the nucleus

particularly in eukaryotes

whereas rna you could find it outside of

the nucleus

and dna basically its function is to

store the genetic information

it serves as the library of the cell

whereas rna it can be used to transfer

genetic information

from one part of the cell to another and

it can also be used to synthesize protein

protein

there's different types of rna you have

ribosomal rna

transfer rna and messenger rna

so if you see

trna that's

transfer rna if you see mrna that's

messenger rna and then rrna is ribosomal rna

rna

dna and rna are both polymers

now you might be wondering what exactly

is a polymer

a polymer is basically a long molecule

made up of tiny units called monomers

and the monomers that make up dna

and rna

are known as nucleotides

now there's different types of nucleotides

nucleotides

but they all have

three basic parts to it

so each nucleotide has a pentose sugar

and

a phosphate group

so p stands for phosphate s is for sugar

b is for base

now in dna the type of sugar that we have

have

is a five carbon sugar known as deoxyribose

now i'm going to compare it to rna so

you can see the difference

rna has a ribose sugar instead of a

deoxyribose sugar it still has a

nitrogenous base and

and

it has a phosphate group

but the difference

is an extra hydroxyl group now let's go

ahead and number the carbons on the

ribose sugar

this is carbon 1 that's where the

nitrogenous base is attached to

carbon 2 3

3 4

and carbon 5 is outside

of the pentose ring

and that's where the phosphate group is

attached to

so in dna

notice that we don't have

a hydroxyl group on carbon 2

and so that is why it's called deoxyribose

deoxyribose

it's a deoxyribose sugar because

it's lacking in oxygen

whereas in rna

you have a ribose sugar that's why rnase

is called ribonucleic acid but dna is called

called

deoxyribonucleic acid

but besides that

they both have a phosphate group

now let's focus on the nitrogenous bases

found in dna and in rna

so dna contains the bases adenine guanine

guanine cytosine

cytosine

and thymine

in rna

the bases are adenine guanine

guanine

cytosine but instead of thymine it's

uracil and so that's another difference

between rna and dna it's a typical test

question so make sure you're aware of

that difference

so uracil is found in rna

now the nitrogenous bases that we've

been talking about can be divided

into these two categories purines

purines

and pyrimidines

now the purines

contain two rings

one of the ring is basically a six

membered ring and the other one is

a five-membered ring

pyrimidines on the other hand contain

only one ring and it's a six membered ring

now the purines they need to be aware of

are adenine

and guanine

the pyrimidines include cytosine

thymine and uracil

now let's talk about drawing these

structures and also how to number them

for some of you you may need to

be able to draw these structures on your

tests and for those of you who don't

need to memorize it

you can fast forward this section

or you can

sit back relax grab a bag of popcorn and

so let's start with

on the left side i'm going to draw adenine

adenine

and on the right side

i'm going to draw guanine

now in the first ring

they both contain

two nitrogen atoms

in the second ring

they also contain two

two

so both adenine and guanine has that uh

that same structure

so if you start with the base structure

it can help you to remember

now both adenine and guanine they have a

double bond in the middle

and they have another double bond in

this position

now let's talk about

where they're different

by the way there's a hydrogen here

so that's an h

if you don't see a hydrogen that means that

that

now adenine

has an nh2 group on this position right

here so that's where it's different

guanine has an nh2 group

and at the same time it has a carbonyl

so if you remember that it can help you

to draw these two structures so that's

the difference between adenine and guanine

guanine

now let's talk about numbering the rings

so this nitrogen represents

represents

number one

and then you need to

count it in a counterclockwise direction

so this is two three four

four

five six

then you move on to

the five member ring

this is seven

and we're going to count it in a

clockwise direction

so this is eight and this is nine

now what you need to know

with purines

is that when you attach them to a ribose

they will be connected let me draw a

i'm just going to draw a box to

represent the ribose just to keep it

simple but what i want you to take from this

this

the ribose ring

is attached to the nitrogenous base

at position 9 when dealing with purines

the permanent is different

but for purines

the ribose

is attached to the n9 position

so it's the ninth position

on a nitrogen atom on a purine ring

so you may need to know that for a test

maybe not it depends on if the teacher

is going to quiz you on that fact

i don't know

now let's move on to

the pyrimidines

so there's three structures that we need

so once again

we're gonna have a six membered ring

with two nitrogen atoms

and four carbon atoms

just like we had in the case of the purines

purines

we only have a six membered ring here

but we're not going to have the

five-member ring for the pyrimidines

but the structure of the membered ring

is very similar

so on the left i'm going to draw

let's start with thymine

and then in the middle i'm going to draw uracil

so all three of these nitrogenous bases

they have the same

general structure

the six-membered ring as you can see

now let's talk about the way we're going

to count it

so this is going to be number one

and we're going to count it in

a clockwise direction

so this is two three

three four

four

five and six

now the ribose will be attached

to the nitrogenous base

at the n1 position

so make sure you uh

keep that in mind

you can add it in your notes

so this is going to be a hydrogen in the

case of thymine

and we're going to have a double bond between

between

positions five and six

and the same is true for

now for thymine we have a carbonyl group

at position four

and another carbonyl group at carbon two

and here we have a hydrogen so that's

thymine now uracil

looks very similar to thymine

thymine has a methyl group but your cell

does not

and so that's the difference between

thymine and uracil

your cell has

a hydrogen if you don't see it it's an

now in the case of cytosine

we have a carbonyl group on carbon 2

just like thymine and uracil

so they're similar in that respect however

however

we do have something different in cytosine

cytosine

and that is we have an nh2 group on

carbon four

and so that's how cytosine differs from

thymine and uracil

it has

this nh2 group

in this position

in addition to that it also has a double bond

bond

between positions

three and four

so those are the three pyrimidines that

you may need to know

and just remember uracil is found only

in rna

thymine is found only in dna

and cytosine is found

now here's a question for you

what is the difference between

between

a nucleotide and

and

a nucleoside

what would you say perhaps you heard of

the word nucleoside

what really

is a nucleoside well let's go back to nucleotides

nucleotides

we know that a nucleotide has three parts

parts

as mentioned before it has a ribose or a

deoxyribose sugar

it has

a nitrogenous base

which could be

a pyrimidine with one ring or a purine

with two rings

now in the case of

a nucleoside it doesn't have three parts

a nucleoside has two parts

it has

the five carbon sugar

and it has

the nitrogenous base

it does not have the phosphate group

so this

is a nucleoside

it's the sugar and the nitrogenous base

but once you add the phosphate group to

a nucleoside then it becomes a

nucleotide so make sure you understand

the difference

and also the name in so let's say

this is cytosine which is one of the

three pyrimidines we talked about

now by itself cytosine

cytosine

now let's focus on the nomenclature

when you add

the ribose sugar to it

it becomes the nucleoside

and it's called citidene

citidene

in the case of rna but

but

and it really depends on the presence of

the oh group on carbon 2.

so this is one two

three four five

there's always going to be an o h group

on carbon three but

but

if we don't have an o h group on carbon

two it's called deoxycitadine

if we do have it

now let's think about this

if the nitrogenous base is called cytosine

cytosine

and if the nucleoside is called citadine

what is the name of the nucleotide that

contains the cytosine nitrogenous base

so it's going to sound weird but it's called

called citadelate

citadelate

chances are you probably don't need to

know that for your tests but for those

of you who may need to know it that's

what the nucleotide is called

so when you hear the word cytosine

it's not referring to this entire

nucleotide but rather just the base

that's in the nucleotide

but if you hear acetylate that's the

entire nucleotide

so here is a summary that can help you

with the nomenclature of nucleosides and nucleotides

nucleotides

on the left we have the nitrogenous base adenine

adenine

once we add a ribose sugar to it

it becomes adenosine

and then if we add the phosphate group

it becomes added excuse me wow i said

that wrong adenylate

adenylate

looking at guanine the situation is similar

similar

as a nucleoside it's guanosine and as a

nucleotide with the phosphate group guanolate

now the nitrogenous base thymine once we

add a ribose sugar to it it becomes thymidine

thymidine

or thymidine if that's how you say it but

but

since thymine is found in dna chances

are it's going to be added to a

deoxyribose sugar

and instead of

thymodylate it becomes deoxy feminically

feminically

in dna

my pronunciation of these names may not

be the best so

don't quote me on that you can look it

up yourself but

these are the names that corresponds to

the nitrogenous base the nucleus sides

and the nucleotides

now let's talk about namin nucleosides

how would you name this particular nucleoside

so the first thing we need to do is identify

identify

the type of nitrogenous base that we

have now based on the structures that we

drew earlier what kind of base do we have

have

well first is it a

a purine

purine

or is it

a pyrimidine

now if you recall pyrimidines are

nitrogenous bases that have only one

ring so because this is a two ring

nitrogenous base

we have a purine

now there's two parents you need to be

familiar with

and that's adenine and guanine so which

one is this is this adenine or guanine

so this particular nitrogenous base

is called guanine

guanine

now what does it become once we add a

guanine plus the ribose sugar

becomes the nucleoside guanosine

guanosine

and so that's what we have here

this is position one two three four

five six seven

seven

eight nine

so as we can see

the purine is attached to the ribose

at the knife position on the nitrogen atom

atom

now what happens to the name

if we put

let's say a methyl group on carbon 8

how do we name this particular nucleoside

well this becomes eight

eight methyl

now what if we remove

a hydroxyl group let's say if we

as in the case of dna

what does it become now

so now we have a deoxyribose

and so this is going to become deoxyguanosine

deoxyguanosine

this is carbon 1 on the ribose sugar

this is 2 3

4 and this is carbon 5.

so now the way we're going to name it

i'm running out of space here so let's

see if i can fit in

it's going to be 8-methyl dash

dash 2-deoxy

guanosine because

because

we don't have the oxygen or the hydroxyl

group rather

on carbon 2 of the rival sugar so now

it's deoxy guanosine

and so that's a simple example of how

you can name a nucleoside with a purine ring

ring

let's try another example

so how can we name this particular nucleoside

so first let's start with the

now we have a one ring nitrogenous base

so that means it's a pyrimidine and we

have three options it's either cytosine

now looking at the nh2 at the top

only one of those three

pyrimidines have the nh2 on the top and

if you remember

this is the nitrogenous base cytosine

cytosine

now combined with the ribose sugar

it becomes the nucleoside called

called citadine

citadine

and so that's the name of this

particular nucleoside

now how will the name change

if we add a methyl group to

so we need to number it this is one two three

three four

four five

five six

six

citadine

and so that's how we can name it

and also remember that

the ribose is attached to the pyrimidine

ring at the n1 position

for the purine it was the n9 position

so just keep that in mind

now let's shift our focus to

name in nucleotides

so we're going to have our

our

our nitrogenous base and

and

a phosphate group

so how can we name this particular nucleotide

so the nitrogen is base that we have

this is g

and so that's guanine

when we combine it with the sugar it

becomes a nucleoside called

called guanosine

guanosine

but now how do we name it once we have

so it becomes

guanolate when the phosphate group

another way in which we can name this

particular nucleotide is we can start

with the name of the nucleoside guanosine

guanosine

and then specify the location of the phosphate

phosphate

so we could say guanosine

dash five

dash monophosphate

because we have one phosphate attached

to the ribose sugar

and so that's how we can name this particular

particular nucleotide

so this time

the nitrogenous base that we're going to use

use is

is adenine

and the phosphate group is going to be

placed in a different position

so you can also see phosphate

represented this way

so how can we name this particular nucleotide

so given the base adenine

once we combine it with the sugar it

becomes the nucleoside adenosine

now the phosphate group

is located

on carbon 3 of the ribose ring

so to put it together we're going to

start with the name of the nucleoside adenosine

adenosine

and then specify the location of the

phosphate group so adenosine

dastery dash mono

mono phosphate

phosphate

and so that's how we can name that

so we're going to use the same

but this time

we're going to have

so let's say if we have three of them

so we're going to start by naming the nucleoside

nucleoside

so if we combine

the ribose sugar

and the nitrogenous base

now we have three phosphate groups

and so it's going to be called

triphosphate trifi3 and it's located on

carbon 5.

so it's adenosine dash

dash 5

that's triphosphate

now this particular nucleotide has a

common name and so sometimes the 5 is

just ignored because it's a very common molecule

molecule

and so it's simply referred to as

adenosine triphosphate

and perhaps you heard of it as

this molecule atp so that's adenosine triphosphate

now there's some other ones

for instance if you hear the word adp it

stands for adenosine diphosphate

so instead of having

just one phosphate group

or three now you have two phosphate groups

groups

so that's adenosine diphosphate

and if you hear

the abbreviation amp

this is

adenosine monophosphate

so there's just one phosphate group

instead of two or three

so what i'm going to do at this point is

draw a

representation of a dna strand

so here we have our sugar

attached to a phosphate group

and then this is going to be attached to

a nitrogenous base

so let's put cytosine in it and

and

over here it's going to be attached to

another phosphate group

and then that's going to be attached

ribose sugar

actually deoxyribose since we're dealing

with dna

and so this

is going to be

adenine this time

and then we're going to have another

another

and let's put thymine in this box

now at this point go ahead and draw the

complementary strand on the right side

using the left side as a starting point

so first let's draw the nitrogenous bases

bases that

that

and then attached to each

nitrogenous base we have the sugar

but notice the direction of the sugar

how it's like pointed up

for the complementary strand it's going

to be pointed down

and then

we're going to have a phosphate group

attached to

it and here we have another phosphate group

group

we're going to talk about the

connectivity of the phosphate group

shortly i just want to complete this first

so what bases

will go in these boxes

now what you need to know is that c

cytosine will always pair up with g

guanine so we need to put g

inside this box

adenine a will always pair up with

thymine and dna

and t will pair up with a

now the next thing you need to put are

the hydrogen bonds

located between these base pairs and so

it's the hydrogen bonds that keep the

two strands in dna attached to each other

other

so there's three hydrogen bonds

connecting c

and g

now between a and t there are two

hydrogen bonds

now if you recall from chemistry

hydrogen bonds exists

whenever hydrogen

is attached to elements such as oxygen

oxygen

nitrogen or fluorine

and an h bond is basically an

intermolecular force that exists between

separate molecules

now for those of you who may want to

review on that

um if you do a youtube search type in

intermolecular forces organic chemistry tutor

tutor

you should see a video that will give you

you

a review on intermolecular forces and

dipole interactions and things like that

now on the left side and

and

also on the right side

this is known as the sugar phosphate backbone

and it makes sense you have your

phosphate groups on the left attached to

now on the sugar this is carbon one two three

three

four and 5.

so notice that the phosphate group

is attached to carbon 3

and carbon 5 of the sugar units

and so this is called

a 3 five

five phosphodiester

phosphodiester linkage

and it's a covalent linkage

a covalent bond is whenever two atoms

are connected to each other by means of

sharing electrons

so whenever two elements or two atoms

come together by sharing electrons they

form a covalent bond

now the next thing i want to mention

is that these two strands these

complementary strands they are

anti-parallel to each other

so the strand on the left

it runs in

the five

now the strand on the right

it goes in the opposite direction so if

we focus on the top sugar unit this is

carbon 1 2

3 4

5. so notice that it's going in

the five to three direction but any

other way

so thus

these two strands

are anti-parallel they run in opposite directions

directions

and so these are some basic things that

you need to know if you have a test

coming up you never know which one of

these facts you might be tested on so

just make sure you know that stuff

now i have one more question for you

write the sequence

for the complementary strand

feel free to pause the video and try it

complementary to 5 is 3

and you need to know that a

pairs up with t

and c pairs up with g

so here we have a

we're going to pair it up with thymine

and here we have t

and let's pair it up with adenine

adenine

and c we're going to pair it up with guanine

guanine

and a is going to go with t

g we're going to pair it up with c

and so

forth so this

is the complementary strand

that's how you can write the sequence

by knowing this piece of information

well that's basically it for this video

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YouTube Transcript:Nucleic Acids - RNA and DNA Structure - Biochemistry

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YouTube Transcript:
Nucleic Acids - RNA and DNA Structure - Biochemistry