Proteins Structure 4a'

Summary

This lecture explores the intricate relationship between genes and proteins, focusing on the translation process and the genetic code. It delves into the composition of RNA, the structure of proteins, and the significance of amino acids. The lecture also discusses the concept of colinearity between genes and proteins, demonstrating how the sequence of a gene directly corresponds to the sequence of a protein. Additionally, it covers the historical experiments that led to the understanding of the genetic code as a triplet code, highlighting the pivotal role of in vitro translation and RNA synthesis in decoding how specific nucleotide sequences dictate amino acid formation.

Takeaways

• 🧬 The lecture introduces the concept of translation in genetics, focusing on the synthesis of proteins from mRNA by ribosomes and other cellular components.
• 📚 mRNA and tRNA constitute over 95% of RNA in a cell, with mRNA making up only 1-2%, indicating their stability and importance in cellular transcription.
• 🔑 The genetic code is the link between the nucleotide sequence of a gene and the amino acid sequence of the protein it encodes.
• 🌟 Proteins are crucial for an organism's phenotype, acting as enzymes to catalyze chemical reactions and forming structural components of cells.
• 🔍 Understanding protein structure is essential for comprehending genes, as proteins are encoded by genes and reflect the information they contain.
• 📝 Amino acids, the monomer subunits of proteins, are polymerized into polypeptides through peptide bonds, forming the primary structure of proteins.
• 🌀 The secondary structure of proteins, such as alpha-helices and beta-sheets, arises from hydrogen bonding between amino acids, contributing to the protein's overall shape.
• 🧬 Tertiary structure refers to the three-dimensional conformation of a single polypeptide chain, influenced by its secondary structures and amino acid interactions.
• 🤝 Quinary structure describes the arrangement of multiple polypeptide chains in a protein complex, held together by various weak bonds.
• 🔄 The concept of colinearity between genes and proteins was demonstrated by Charles Yanofsky, showing that the sequence of a gene directly corresponds to the sequence of its protein product.
• 🧬 The genetic code is a triplet code, with three nucleotides specifying a single amino acid, and is non-overlapping, meaning each codon is read individually.

Q & A

What are the main components involved in protein synthesis?

Protein synthesis involves messenger RNA (mRNA), transfer RNA (tRNA), and ribosomes. mRNA is read by ribosomes, and tRNA brings the appropriate amino acids to the ribosome to generate proteins.

What percentage of RNA in a cell is made up of rRNA and tRNA?

rRNA and tRNA make up over 95% of RNA in a cell.

How does the stability of rRNA and tRNA compare to mRNA?

rRNA and tRNA are more stable than mRNA and do not get degraded and turned over as fast.

What is the relationship between the nucleotide sequence of a gene and the amino acid sequence of a protein?

The genetic code describes the relationship, where the nucleotide sequence of the gene specifies the amino acid sequence of the protein.

What are the 20 different subunits that make up proteins called?

The 20 different subunits that make up proteins are called amino acids.

What is a polypeptide and how is it formed?

A polypeptide is a polymer composed of amino acids, also known as peptides. It is formed by peptide bonds created through condensation reactions between the amino group of one amino acid and the carboxy group of another.

What are the four levels of protein structure?

The four levels of protein structure are primary (linear sequence of amino acids), secondary (regular repeated structures like alpha helix and beta pleated sheets), tertiary (three-dimensional structure of a single polypeptide chain), and quinary (structure of multiple subunit proteins).

What is the significance of the directionality of polypeptides and mRNA?

The amino terminus of a polypeptide is lined up with the five prime end of the mRNA, and the carboxy terminus with the three prime end, indicating the direction of translation from the mRNA to the protein.

How was the colinearity of genes and proteins first demonstrated?

Colinearity was first demonstrated by Charles Yanofsky in 1963 through his work with the trpA gene in E. coli. He induced mutations and showed that each mutation created an amino acid substitution in the same order as the mutations in the gene.

What does the genetic code being non-overlapping mean?

The genetic code being non-overlapping means that each triplet of bases (codon) is read individually without overlapping into the next triplet, ensuring a specific and consistent translation of the mRNA sequence into amino acids.

How did experiments with T4 phage contribute to understanding the genetic code?

Experiments with T4 phage showed that mutations causing an addition or deletion of one or two bases resulted in nonfunctional proteins, while three base additions or deletions close together resulted in functional proteins with only small changes, indicating that the genetic code is read in triplets.

Outlines

00:00

🧬 Introduction to Translation and Genetic Code

This lecture introduces the topic of translation, which is the process of converting the genetic code into proteins. It emphasizes the importance of mRNA and tRNA, which together make up over 95% of cellular RNA and are more stable than mRNA. The genetic code is described as the relationship between the nucleotide sequence of a gene and the amino acid sequence of the protein it encodes. Proteins, which are crucial for an organism's phenotype, are composed of amino acids and are encoded by genes. The lecture promises to delve into the structure of proteins, the genetic code, and the molecular details of translation.

05:00

🌀 Protein Structure and Amino Acids

The paragraph discusses the structure of proteins, which are polymers made up of amino acids. There are 20 different amino acids that form the building blocks of proteins. Each amino acid has an amino group, a carboxy group, and a unique side chain (R group) that gives it distinct properties. The amino acids are linked together by peptide bonds, which are formed through a condensation reaction. The paragraph also explains the directionality of polypeptides and mRNA, noting that the amino terminus of a protein aligns with the 5' end of mRNA, and the carboxy terminus aligns with the 3' end.

10:00

🔍 Levels of Protein Structure

This section explains the four levels of protein structure: primary, secondary, tertiary, and quinary. The primary structure refers to the sequence of amino acids. Secondary structures, such as alpha-helices and beta-sheets, are formed through hydrogen bonding. Tertiary structure is the three-dimensional shape of a single polypeptide chain, influenced by secondary structures and R group interactions. Quinary structure pertains to multi-subunit proteins, where multiple polypeptides come together to form a complex. The paragraph also touches on the general shapes of proteins, such as globular and fibrous, and the concept of domains within proteins that have specific functions.

15:02

🧵 Colinearity of Genes and Proteins

The concept of colinearity between genes and proteins is introduced, which means that the linear sequence of bases in a gene corresponds to the linear sequence of amino acids in the protein. This was first demonstrated by Charles Yanofsky in 1963 through his work with the trpA gene in E. coli. He induced mutations and showed that each mutation corresponded to an amino acid substitution in the same order along the protein. The paragraph also discusses the non-overlapping nature of the genetic code, where each set of three nucleotides (codon) codes for a single amino acid.

20:04

🧪 Decoding the Genetic Code

The paragraph describes how the genetic code was deciphered in the 1960s. Scientists used cell-free translation systems to isolate cellular components capable of protein synthesis. They could control the mRNA sequence to observe which proteins were produced. Additionally, in vitro synthesis of RNA allowed scientists to create specific mRNA sequences to test. Through experiments with base additions and deletions, they discovered that one or two base changes could disrupt protein function, while three closely placed base changes could result in a functional protein with minor amino acid sequence alterations. This led to the understanding that the genetic code is read in non-overlapping triplets, each coding for a specific amino acid.

Keywords

💡mRNA

mRNA, or messenger RNA, is a type of RNA that plays a crucial role in protein synthesis. In the script, it's mentioned that mRNA is read by ribosomes during translation to generate proteins. The mRNA sequence is transcribed from DNA and carries the genetic information to be translated into a sequence of amino acids, which will form a protein. The script emphasizes that mRNA, along with rRNA and tRNA, makes up over 95% of RNA in a cell, highlighting its importance in cellular processes.

💡tRNA

tRNA, or transfer RNA, is another type of RNA that is essential for protein synthesis. It acts as an adapter molecule that reads the mRNA sequence and brings the appropriate amino acid to the growing polypeptide chain. The script mentions that tRNA, along with rRNA, constitutes over 95% of RNA in a cell, indicating its abundance and significance in the translation process.

💡Ribosomes

Ribosomes are cellular structures that facilitate the synthesis of proteins by translating mRNA into a sequence of amino acids. They are composed of ribosomal RNA (rRNA) and proteins. In the script, ribosomes are described as the site where mRNA is read during translation, emphasizing their central role in protein synthesis.

💡Genetic Code

The genetic code refers to the set of rules by which information encoded in genetic material (DNA or mRNA) is translated into proteins. The script explains that the genetic code describes the relationship between the nucleotide sequence of a gene and the amino acid sequence of the protein it specifies. It is a triplet code, with each set of three nucleotides, or codon, corresponding to a specific amino acid.

💡Amino Acids

Amino acids are the building blocks of proteins. There are 20 different amino acids that make up proteins, each with a distinct side chain (R group) that gives it its unique properties. The script discusses how amino acids are linked together by peptide bonds to form polypeptides, which fold into functional proteins. Understanding the properties of individual amino acids is key to understanding protein structure and function.

💡Peptide Bonds

Peptide bonds are the chemical bonds that link amino acids together in a polypeptide chain. They are formed through a condensation reaction between the amino group of one amino acid and the carboxyl group of another, with the release of a water molecule. The script mentions that peptide bonds have partial double-bond character, which restricts the movement around these bonds, influencing the overall structure of the protein.

💡Primary Structure

The primary structure of a protein refers to the linear sequence of amino acids that make up the polypeptide chain. It is the first level of protein structure organization and is crucial for determining the higher-order structures of the protein. The script explains that the primary structure is the specific order of amino acids, which is written from the N-terminus to the C-terminus, following the convention of DNA's 5' to 3' direction.

💡Secondary Structure

Secondary structure in proteins refers to the local folding patterns that arise from hydrogen bonding between amino acids in a polypeptide chain. The most common secondary structures are the alpha-helix and beta-pleated sheets. The script describes how these structures form due to the regular arrangement of amino acids that allows for hydrogen bonding, which in turn contributes to the overall three-dimensional shape of the protein.

💡Tertiary Structure

Tertiary structure is the overall three-dimensional shape of a single polypeptide chain. It is influenced by the secondary structures within the protein and the interactions between the R groups of amino acids. The script mentions that understanding tertiary structure is important for knowing how a protein will function, as it determines the positioning of functional groups and the protein's interactions with other molecules.

💡Quaternary Structure

Quaternary structure refers to the three-dimensional structure formed by the assembly of multiple polypeptide chains (subunits). These subunits can be the same (homo-oligomers) or different (hetero-oligomers). The script explains that quaternary structure is formed by weak bonds such as hydrogen, electrostatic, and van der Waals forces, and it is the final level of protein structure organization that contributes to the protein's function.

Highlights

Introduction to the lecture series on translation, the genetic code, and proteins.

Messenger RNAs (mRNAs) are read during protein synthesis by ribosomes, tRNAs, and other components.

rRNA and tRNA make up over 95% of RNA in a cell, with mRNA constituting 5% or less.

The genetic code describes the relationship between the nucleotide sequence of a gene and the amino acid sequence of the protein it specifies.

Proteins are essential for the phenotype of an organism, acting as enzymes and structural components of the cell.

Proteins are polymers composed of 20 different amino acids, which are the monomer subunits.

Amino acids are distinguished by their unique R groups, which give them their chemical properties.

Peptide bonds, formed by a condensation reaction, link amino acids together in a polypeptide chain.

Polypeptides have directionality, with the N-terminus aligning with the 5' end of mRNA and the C-terminus with the 3' end.

Proteins form complex structures with four levels of organization: primary, secondary, tertiary, and quaternary.

The primary structure of a protein is the specific order of amino acids in the polypeptide chain.

Secondary structures, such as alpha-helices and beta-sheets, arise from hydrogen bonding between amino acids.

Tertiary structure refers to the three-dimensional structure of a single polypeptide chain.

Quaternary structure is the three-dimensional structure formed by multiple polypeptide chains.

Proteins can be globular or fibrous, with globular proteins being compact and fibrous proteins having a linear shape.

Colinearity between genes and proteins was demonstrated by Charles Yanofsky in 1963, showing a direct correspondence between gene sequence and protein sequence.

The genetic code is a triplet code, with three nucleotides coding for a single amino acid.

The genetic code is non-overlapping, meaning each codon is read individually without overlap.

Experiments with T4 phage by Francis Crick and Sydney Brenner helped determine the nature of the genetic code.

In vitro translation and RNA synthesis techniques in the 1960s allowed scientists to determine which codons coded for which amino acids.

Transcripts

all right welcome back this is a new

lecture set where we will talk about

translation and the genetic code and a

little bit about proteins right at the

beginning here so this is the first um

recorded lecture for this lecture

set okay so as an introduction messenger

mrnas okay or messenger rnas or mrnas as

we just talked about are read during

protein synthesis the translation by

ribosomes TRNA is and other components

to generate proteins okay R RNA and TRNA

make up over 95% of RNA in a Cell

remember I said in the last lecture said

that rrna makes up 50% rrna plus TRNA

make up 95% of all the RNA in a Cell

they are more stable than mRNA so they

don't get degraded and turned over as

fast and their genes represent over 50%

of the transcription that takes place in

a Cell mRNA makes up 5% or less all the

RNA in a Cell often times only making up

between 1 and 2% of the RNA in a Cell

the genetic code describes the

relationship between the nucleotide

sequence of the Gene and the amino acid

sequence of the protein it specifies so

in this lecture set we'll start by

talking about proteins a little bit then

we'll get into um the genetic code and

we'll get into the molecular details of

translation all right Pro proteins are

the structures that determine much of

the phenotype of an organism they are

responsible as enzymes to catalyze

chemical reactions and also form

structural components of the cell genes

encode proteins so understanding

proteins helps in the understanding of

genes so in case you're asking the

question why are we talking about

proteins um because they're sort of

linked to the information contained

within the genes so before talking about

how proteins are made we'll briefly talk

about protein structure a protein is a

polymer composed of monomer subunits the

protein subunits are called amino acids

and there are 20 different amino acids

that make up proteins amino acids were

once called peptides and so polymer of

amino acids or peptides is called a

polypeptide it makes more sense to call

it a poly amino acid but it's always

called the poly peptid you can think of

a peptide as pretty much equivalent to

an amino acid each amino acid has an

amino group a carboxy group and a side R

Group which is different for each amino

acid and gives each amino acid their

distinctive

properties so here's amino acid

structure you have a central Alpha

carbon you have a carboxy group um

normally there' be an H here but under

physiological conditions in our cells um

it gives up that H have the negative

charge that H ends up on the amino group

so instead of being nh2 it's NH3 and it

has a positive charge here it's aoxy

group amino group Alpha carbon there's

always a hydrogen here and then every

one of those 20 different amino acids

has a different R Group and again the

different R groups then give different

characteristics chemical characteristics

to these different amino acids and so

different books um classify them

differently but a lot of times see the

non-polar ones so in Orange here are the

r groups and you can see that they're

nonpolar there's no charges there's no

unequal distribution of charge you see a

lot of hydrocarbons there um aromatic

amino acids okay so you have the groups

here polar um but neutral okay so they

don't have charges but they have

polarity to them hydroxy group here

hydroxy group there amino group there

carox carox amine there polar AIC amino

acids all right so they have a negative

charge they've given up a hydrogen or

proton a polar Amino or basic amino

acids so they're going to have a

positive charge on these and then

non-standard so non-standard sort of

different um

cysteine here pyly here um you get some

different types of amino acids um they

are non-standard ones so just one way to

look at it we're not going to get into

um in of course such as biochemistry or

something that would be really important

when you're talking about protein

biochemistry to sort of know the

chemistry of all these we're not going

to get into that a lot just be aware of

the different amino acids and they have

to come together then to um form a

polypeptide so amino acids then are

joined together by something called

peptide bonds these are calent bonds

formed by condensation reaction between

the amino group of one amino acid and

the carboxy group of another amino acid

this is a condensation or dehydration

reaction as a molecule of water is

removed every polypeptide has a free

amino group at the N Terminus and a free

carboxy group at the C Terminus so just

like how a polymer of nucleotides DNA

RNA has a five Prime n with a free five

Prime phosphate or a three prime n with

a free thre Prime hydroxy proteins have

a free ENT Terminus or have a free amino

group creating the ENT Terminus on one

end and a free carboxy group but the

other end um which is then the C

Terminus so here's this dehydration

reaction so here's one amino acid there

second amino acid so here's carboxy

group amino group they join together and

this Bond here then is a peptide bond so

it's a dehydration reaction because it

gives up a molecule of water then when

forming this peptide

bond so here's another figure showing

this so this is already a polypeptide

and the next one coming in there's a

carox group there's amino group come

together a molecule water and that

peptide bond forms there and then

directionality of polypeptide and mRNA

we'll talk a little bit more about this

in a bit there's the amino Terminus it's

actually lined up with the five Prim

five Prime end of the MRNA carboxy

Terminus lines up with three prime end

of an mRNA and we'll talk briefly about

this in a little

bit here then again showing um peptide

bond um joining together the point of

this slide here is um these peptide

bonds actually have a partial double

bond character so all that means is um

at the peptide bond they're not allowed

to rotate freely they can't just circle

around um they're restricted in their

movement it's it's more like um if you

think of a chain the different lengths

of a chain together rather than um sort

of beads um on a string you know beads

on a string you can take that string and

you can twirl it around tie it up do all

of things it's sort of free rotation do

whatever you want but with a chain you

can twist a chain around but there's

kinks in the chain and so sort of like a

partial double bond between every link

of a chain and that's sort of how these

peptide bonds um act or behave um yeah

another side forgot about this one so

again amino acid amino acid coming

together forming peptide bond

dehydration uh reaction all right so

most polypeptides in our cells are

polypeptides average about 200 to 300

amino acids all right so 200 to 300

amino acids linked together is the

average size of most polypeptides and by

convention um I showed you that how the

N Terminus and C Terminus match the five

Prime and three prime NS of DNA and

since DNA is written five Prime to three

prime by convention um proteins if you

were to write out the number of amino

acids in a protein it would be written

from the N Terminus to the C Terminus

from left to right um so proteins form

complex structures um and can classify

those structures into four levels of

organization so uh the first level is

called the primary structure and primary

structure is the specific order of amino

of amino acids or the linear sequence um

it's usually written out in a

three-letter code or a one letter code

again those letter codes are something

you might memorize or look at if you

take a course such as biochemistry so

here's primary structure and again

primary structure they draw it out here

but it's really all it is is the order

of the amino acids and again by

convention you start at the amino end

when listing those amino acids

um here again order of amino acids on

the left that's just the primary

structure uh secondary structure is a

regular repeated structure or pattern in

a polypeptide chain um only parts of the

entire polypeptide form this so um

sometimes it's easier to talk about

tertiary structure first

so tertiary structure okay is the

three-dimensional structure of a

complete polypeptide chain it's also

referred to as its confirmation so this

complete three-dimensional shape of a

polypeptide chain of a single

polypeptide chain secondary structure

then is part of the overall tertiary

structure so there are multiple

secondary

structures within the full tertiary

structure the full of the secondary

structure and the rest of the

polypeptide chain creates the

three-dimensional tertiary structure um

what plays a role in the shape this

tertiary structure takes is of course

the secondary structure within it and

the interaction between the r groups so

we'll get back to secondary structure in

a second so tertiary structure is just

here so it's a

complete threedimensional

structure there's another image here so

it's a full polypeptide chain and it's

three-dimensional structure that it

takes on

all right so getting back to secondary

structure then again a regular repeated

structure regularly repeated not

confirmation regularly repeated

structure in a polypeptide chain only

parts of the polypeptide form this um

the shape of the secondary structure

arises primarily from the hydrogen

bonding between amino acids okay the

most common the most common examples of

secondary structure are the alpha Helix

and the beta pleed sheet all right so

let's take a look here so here's primary

structure secondary structure then is an

alpha Helix okay it's a right-handed

Helix and again the hydrogen bonding is

what determines the structure so you can

see hydrogen bonding here the dotted

lines here dotted lines here dotted

lines here so in general if the r groups

line up just right you'll get hydrogen

bonding between these different amino

acids and it'll take a regular repeated

pattern um which then make up part of

the entire tertiary structure so here's

the whole tertiary structure you can see

here it has one prominent Alpha Helix

and that's it so it's a part of the full

tertiary structure the other secondary

structure common one is a beta pleted

sheet so instead of weaving around each

other it sort of goes back and forth it

turns somewhere and then another run of

amino acids interact with the amino

acids next to it so again these dotted

lines hydrogen bonding is what is

holding it together so again going to

this tertiary structure here so there's

two turquoise ones and there's two um

beta pleated sheets behind it um making

up part of the whole and this next image

here same thing you see the red one two

three Alpha helices start of alpha Helix

there 1 2 3 four five six beta pleted

sheets okay with these two likely

interacting strongly and these two

interacting strongly and but then a lot

of

non identifiable green here so it bends

and it turns and it twist T but it's not

an identifiable secondary structure um

but it still is responsible for making

up the large um or the overall

three-dimensional

shape all right so the last type of

structure is quinary structure so

quinary structure is the confirmation of

a multiple subunit protein okay so it

has to have more than one polypeptide

that interacts and then it's that

three-dimensional shape of multiple

polypeptides coming together it's

composed of two or more folded

polypeptides or subunits joined together

by weak bonds joined together by

hydrogen electrostatic so polar calent

bonds Vander wals forces different

things that are holding it together if

two different polypeptides come together

they form a hetero dimer heterol for

different dimer for two die for two if

two of the same polypeptides come

together they form a homo dier and so

we've looked at this figure before so

here's one subunit here's another

subunit looks like they just STI this

one turn it upside down and put it

together so that's a homo dier it looks

like two identical subunits there this

is not this is a different

example um myoglobin well here's an

example so the green the red and the

other color green um three different

proteins um coming together interacting

so that would then be an example of

quinary structure all right proteins are

also sometimes identified by their

General overall shape um they can be

called globular proteins or fibrous

proteins so proteins that have compact

shapes so proteins like enzymes or

antibodies are called globular proteins

these proteins can form Pockets when

folded especially enzymes or protruding

parts that interact with other proteins

or other molecules uh parts or sequences

of a protein that have a particular

function are called domains okay so you

can have an entire protein and you can

have a certain part of the protein that

does a certain job and that is called a

domain for example um A protein that

interacts with DNA can have a DNA

binding domain so you can have part of

the protein that binds the DNA and it

still has a whole other part of it that

does some other job um so globular

proteins

example an example here of an enzyme so

it sort of rolls up on itself Compact

and since it's enzyme has an active

sight or a little CFT or an opening

where things take place um examples here

myoglobin is a globular protein it's

compact where collagen is a fibrous

protein okay proteins that are fibrous

can take on a linear shape um they're

longer they're not Co globbed up if you

will and so they're called fibrous

protein so collagen is one keratin that

makes up hair it's fibrous um collagen

is found mainly in the extracellular

Matrix outside of our

cells is is where you find things like

that all right now we're going to talk

about colinearity of a gene and protein

so what is the relationship between

genes and proteins I sort of already

given this away right talking about the

five Prime end of the MRNA corresponds

to the amino Terminus and the three

Prime with the carboxy Terminus well how

do we know this so colinearity of genes

and proteins is the idea that the linear

sequence of the gene corresponds with

the linear sequence of the poly peptide

in other words one end of the gene

corresponds to one end of the protein

that genes and proteins are colinear was

first demonstrated by Charles yanowski

in

1963 he was looking at a

polypeptide um was called trip a that

was part of tryptophan synthesis enzyme

and

ecoli he induced 16 different mutations

in this trip a gene all of which produce

an inactive enzyme he mapped these sites

by recombination analysis

we'll talk later in the course about uh

recombination and it what it is and how

it's a tool to figure out where things

are to put it shortly it was a lot of

work uh he then analyzed the trpe mutant

proteins and discovered that each

mutation created an amino acid

substitution each of these amino acid

substitution was in the same order as

the mutations in the gene in other words

if an amino acid at the beginning of the

polypeptide was mutated this correspond

responded to a mutation at the beginning

of the Gene and amino acid mutation at

the end of the protein corresponded to a

mutation towards the end of the gene

therefore the Gene and protein are

collinear all right so um this is just

showing collinearity here's the DNA

here's the RNA and start codon here so

at the five Prime end of the MRNA you

have the beginning of the polypeptide

which would be the N Terminus and at the

three prime end of the MRNA you have the

end of the protein which would be the

carboxy end so

here's the different types of mutation

inasi looked at in the in what he saw in

the amino acid so normal amino acid had

this particular sequence he made a bunch

of mutations and then he went and

checked where those mutations were so he

knew a446 was the first one or closest

to the five primen and he knew a169 was

closest to three Prim you do the order

of all of them in between you then could

then um uh figure out the amino acid

sequence of the protein and see where

changes were made and when you saw that

the change made closest to the amino

Terminus was closest to the five Prime

and and so on and so forth so that's how

he determined the colinearity uh between

the Gene and

proteins all right we know that DNA

contains the information to code for

proteins how does the information

molecule how or how does in information

molecule with only four different bases

code for 20 different amino acids IDs

two bases could code for 16 different

amino acids and three bases together

could code for

64 okay so the question is are only some

of the 64 three base triplets or codons

used to code for 20 amino acids or are

some of the 20 amino acids coded for by

multiple Triplets of

nucleotides so the genetic code is a

triple code so three nucleotides in row

will code for a single amino acid so we

can see this here Aug codes for

methionine AGC codes for serine okay and

so on and so

forth and so but there's still lots of

questions like how do we figure this out

or how did science figure out well first

the genetic code is non-overlapping in

other words each triplet of bases is

read individually and then the next full

triplet of bases all right so figure

here what that means so one here could

be 1 2 3 and you can imagine then two

could be the second third and fourth

three could be the third fourth and

fifth that would be an overlapping code

it turns out that's not how it works

it's nonoverlapping so one two three

nucleotides code for amino acid then

it's a shift to four oops four five6

code for the second 7 8 n that trip

closer to the third so it's a

nonoverlapping

code all right so how was it

demonstrated that the genetic code was a

tripli code well Francis Crick Sydney

brener and colleagues did experiments

with a T4 virulent bacteria phage trying

to determine the nature of the genetic

code so again now they're working with

bacteria phages or viruses that infect

bacterial cells because you can grow

lots of them up and you can do really

fine tuning of uh the genetics in these

types of experiments so they discovered

while isolating mutants of this phage

and the particular types of mutants they

are looking for were that preferentially

added or deleted a base so while

isolating mutants for this phage they

discovered that mutations which cause an

addition or a deletion of one or two

bases resulted in a nonfunctional

protein while an addition or deltion of

three bases relatively close to one

another resulted in a functional protein

with only small changes in the amino

acid sequence so one or two base

additions deletions completely stop

translation three base additions delions

close to one another did

not um result in the stopping of the

protein they resulted in A protein that

was pretty similar so what does this

look like then so here's wild type

protein mutagenesis by base addition all

right so you're can add one base here

and it will mess up all the rest so

after three in here messes up all the

rest of the amino acids all right same

thing if you added two

but if three were added I think this

next slide shows that so here you DNA

and if you get 1 2 three mutations close

together you'll the MRNA still translat

or transcribes fine and you get

relatively the same amino acid sequence

so this is altered so a couple of amino

acids are different than what would be

in the wild type Gene before it was

mutated um but then Downstream of that

again Downstream of that um you get all

the same amino acids so the protein

slightly altered but still usually in

these cases still works so that's how

they discovered one or two base

additions cause problems three that are

close together then usually return the

protein to

um functionality um they also discovered

revertant right so if they had one base

addition or deletion they could get the

opposite happening and they could revert

back to normal and that's what this

slide also had here so Genesis here

mutation changes everything another

mutation just a little bit down the way

returns you got Arginine Serene Serene

Argin returns or reverts the protein

back to near Wild type function okay so

again apart from those two amino acids

here um all the others are the same so

that's what a revertant is it's a

mutation that has been reverted back to

Wild type function you can tell it's not

exactly the same but the functionality

of the protein um is close enough to

what the wild type

go all right so how was it figured out

which codons which three nucleotides

together coded for which amino acids

there are two techniques in the 1960s

that made this possible one was cell

free or in vitro

translation okay in vitro in a test tube

or without

cells and in in vitro

translation the scientists had the

ability to make cell-free extracts all

right so they are able to extract or

take apart cells and use the components

within within a um test tube and all

those components then when they isolated

them were able to carry out protein

synthesis all right so they're able to

take apart a cell isolate the parts that

could make um a protein or could

translate and then they could control

what mRNA was used to make the protein

so they could put in a very specific

sequence and see what protein got made

in that

process and they able to control what

mRNA was in because the other um

technique they had was invitro synthesis

of RNA they could specifically

synthesize RNA of the nucleotides they

wanted to within limits it started where

it was a probability thing um and then

they got better and better at it so they

could put together exact

um sequences of um mRNA so they would do

things like put together all A's or all

C's or all G's that would be how they

would start and then they would do

things I think slide here shows this

they would do things where they would

put a a two a d nucleotide together a u

and a c and allow the U and C to go

together um randomly so sometimes you'd

get

ucu sometimes you'd get CU c um you get

these two possibilities and then you'd

get a protein that came out of that inal

translation of serene and Lucine so you

knew Serene had to be either ucu or CU

and Lucine had to be the other one so

they did a lot of these um

two nucleotides together and they always

got two different options of codons and

they would always get two different

amino acids that were made then they

went to triplets and then you get lots

of different options here and then they

went to putting together single

nucleotides in different um percentages