Proteins Part 2

Summary

This presentation covers the second part of protein structure, focusing on amino acid sequencing and peptide bonds. The speaker explains how amino acids form proteins, discussing the specific sequences in insulin and how peptide bonds link them. The difference between simple and conjugated proteins is highlighted, with an emphasis on the role of prosthetic groups like lipids and carbohydrates in conjugated proteins. The session also explains naming conventions for peptides and the significance of N-terminal and C-terminal ends in amino acid sequences.

Takeaways

• 🧬 The presentation discusses the structure and sequence of proteins, focusing on insulin as the first sequenced protein.
• 🔗 Insulin has two chains, and its amino acids are linked by peptide bonds in a specific order that should not be altered.
• 🧪 Each amino acid in a protein is referred to as an 'amino acid residue' when it's part of the protein structure.
• 🔍 Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of another, resulting in a peptide bond.
• 📏 Proteins are read from the N-terminal (left side) to the C-terminal (right side) based on the presence of free amino and carboxyl groups.
• 📚 Amino acid sequences can be represented by their three-letter abbreviations or single-letter abbreviations for larger proteins.
• 🧩 A tripeptide consists of three amino acid residues connected by two peptide bonds.
• 🧪 The nomenclature of peptides involves using the '-yl' suffix for amino acids at the N-terminal except for the last one, which retains its full name.
• 🏗️ Proteins are classified as either simple or conjugated based on their composition: simple proteins contain only amino acids, while conjugated proteins have additional non-amino acid components called prosthetic groups.
• 💡 Examples of conjugated proteins include lipoproteins (lipid prosthetic group), glycoproteins (carbohydrate prosthetic group), and metalloproteins (metal prosthetic group).

Q & A

What is the primary structure of insulin?

The primary structure of insulin consists of two chains of amino acids. Each chain has a specific sequence, such as glycine, isoleucine, valine, glutamic acid, and asparagine on one chain, while the other chain includes phenylalanine, valine, and alanine. This sequence is crucial and should not be altered.

What is a peptide bond, and how is it formed?

A peptide bond is a type of covalent bond that links amino acids together in a protein. It is formed when the carboxyl group of one amino acid reacts with the amino group of another, releasing water and creating the bond between the nitrogen and carbon atoms.

What is the difference between an amino acid and an amino acid residue?

An amino acid refers to the molecule in its free form, while an amino acid residue refers to an amino acid that is part of a protein chain.

How is a protein sequence read and organized?

Protein sequences are read from left to right, starting with the N-terminal (free amino group) on the left and ending with the C-terminal (free carboxyl group) on the right.

What is the difference between a peptide, oligopeptide, and polypeptide?

A peptide consists of a few amino acids linked together. An oligopeptide refers to a short chain of amino acids, and a polypeptide refers to a larger chain. A protein typically consists of one or more long polypeptides.

What is a tripeptide, and how many peptide bonds does it contain?

A tripeptide is a molecule composed of three amino acid residues. It contains two peptide bonds linking the three residues together.

What are the naming conventions for peptides?

Peptides are named starting from the N-terminal. The suffix '-yl' is added to the name of the amino acid, except for the amino acid at the C-terminal, which keeps its full name. For example, a tripeptide of alanine, leucine, and glycine is named alanil-leucil-glycine.

What is the difference between simple proteins and conjugated proteins?

Simple proteins consist only of amino acid residues and no other components. Conjugated proteins contain one or more non-amino acid entities, called prosthetic groups, which can be organic or inorganic molecules, such as lipids, carbohydrates, or metals.

What are prosthetic groups in proteins?

Prosthetic groups are non-amino acid entities found in conjugated proteins. They can include lipids, carbohydrates, or metals and are essential for the protein's function.

Why is the amino acid sequence crucial in proteins like insulin?

The sequence of amino acids in a protein like insulin determines its structure and function. If the sequence is altered, it could disrupt the protein's ability to function correctly.

Outlines

00:00

🔬 Introduction to Protein Structures

The speaker introduces the second part of the lecture on proteins, focusing on their structures. It begins with a review of amino acids and highlights the primary structure of insulin, which was the first protein sequenced. The speaker explains that amino acids in insulin are arranged in a specific sequence, emphasizing the importance of this order for proper function. The peptide bond, which links amino acids, is introduced, and the convention of reading amino acid sequences from left to right (N-terminus to C-terminus) is explained.

05:01

🧬 Peptide Bonds and Amino Acid Residues

The speaker delves into peptide bonds and the distinction between amino acids and amino acid residues. A residue refers to an amino acid that is part of a protein. The formation of peptide bonds is demonstrated, with the example of a tripeptide made of alanine, phenylalanine, and serine. The speaker explains how peptides, oligopeptides, and polypeptides are classified based on the number of amino acids linked together, with tripeptides having two peptide bonds.

10:02

🔗 Formation of Peptide Bonds

The speaker details the formation of peptide bonds between amino acids. A peptide bond is formed when the carboxyl group of one amino acid reacts with the amino group of another. This bond links the amino acids together, and the sequence is always read from the N-terminal (left) to the C-terminal (right). The N-terminal is named after its free amino group, while the C-terminal is named after its free carboxyl group.

15:03

🧩 Naming Peptides Based on Structure

This section explains the rules for naming peptides based on their sequence and structure. The speaker introduces the use of suffixes to name peptides, where 'yl' replaces 'ine' or 'e' for each amino acid except the C-terminal amino acid, which retains its full name. An example of a tripeptide, alanil-leucil-glycine, is provided to demonstrate the naming convention. The importance of starting from the N-terminal when naming peptides is emphasized.

20:03

🧪 Classification of Proteins

Proteins are classified based on their chemical composition. The first type, simple proteins, consists only of amino acid residues without any additional components. These proteins may have one or more subunits. The second type, conjugated proteins, contains non-amino acid components known as prosthetic groups. These groups can be organic or inorganic, as seen in lipoproteins (lipid prosthetic group), glycoproteins (carbohydrate prosthetic group), and metalloproteins (metal prosthetic group).

Keywords

💡Amino Acid

Amino acids are the building blocks of proteins. In the video, they are discussed as individual units that, when connected, form proteins. For example, insulin is made up of chains of amino acids. Each amino acid in a sequence is referred to as a 'residue' once it becomes part of a protein.

💡Peptide Bond

A peptide bond is a chemical bond that connects amino acids together in a protein. The video explains how peptide bonds form between the carboxyl group of one amino acid and the amino group of another, creating long chains called polypeptides or proteins. This bond is essential for the protein's structure.

💡Primary Structure

The primary structure of a protein refers to the specific sequence of amino acids in a polypeptide chain. The video highlights insulin's primary structure, showing how amino acids like glycine, valine, and asparagine are arranged in a specific order, which is crucial for the protein's function.

💡Insulin

Insulin is a protein hormone discussed as the first to be sequenced, meaning its amino acid order was identified. The video uses insulin's structure to explain protein sequencing and how each amino acid in insulin is connected via peptide bonds in two chains (A and B chains).

💡N-terminal and C-terminal

These terms describe the two ends of a protein. The N-terminal is the start of a protein, where the amino group is free, while the C-terminal is the end, where the carboxyl group is free. In the video, the sequence of amino acids is read from the N-terminal to the C-terminal, which is a key convention in protein chemistry.

💡Tripeptide

A tripeptide is a chain consisting of three amino acid residues linked by peptide bonds. The video gives an example of a tripeptide formed from alanine, phenylalanine, and serine. It explains how these three amino acids are connected and named based on their positions in the sequence.

💡Polypeptide

A polypeptide is a long chain of amino acids linked by peptide bonds, forming part of a protein. The video contrasts shorter peptides (like tripeptides) with larger polypeptides, such as hemoglobin, to explain the different sizes and structures proteins can take based on the number of amino acids.

💡Residue

An amino acid residue is what remains of an amino acid after it is incorporated into a protein. The term is used to emphasize that the amino acid is now part of a larger structure. The video explains this when discussing the difference between individual amino acids and those linked together in proteins.

💡Conjugated Protein

Conjugated proteins are proteins that contain non-amino acid components, known as prosthetic groups, in addition to amino acids. The video provides examples like glycoproteins (which have carbohydrate groups) and lipoproteins (which have lipid groups), explaining how these extra components affect protein function.

💡Simple Protein

A simple protein is composed only of amino acids, without any prosthetic groups or other non-amino acid entities. The video contrasts simple proteins with conjugated proteins, explaining that some simple proteins can have multiple subunits but still consist solely of amino acids.

Highlights

Introduction to protein structure, with a focus on peptide bonds and amino acid residues.

Explanation of the primary structure of insulin and its sequence of amino acids.

Insulin's two chains are made up of specific amino acids arranged in a fixed sequence.

The importance of peptide bonds in linking amino acids to form proteins.

Reading amino acid sequences from the N-terminal to the C-terminal.

Definition and description of peptide, oligopeptide, and polypeptide based on amino acid chain length.

Use of abbreviations (three-letter and single-letter) to simplify large protein sequences.

Formation of peptide bonds: the bonding of the amino group of one amino acid with the carboxyl group of another.

Explanation of N-terminal and C-terminal in protein sequences.

Naming conventions for peptides based on their amino acid sequence.

Classification of proteins into simple proteins (composed only of amino acids) and conjugated proteins (containing non-amino acid components).

The prosthetic group in conjugated proteins can be organic (like lipids or carbohydrates) or inorganic (like metals).

Example of conjugated proteins: glycoproteins, where the prosthetic group is a carbohydrate.

Explanation of tripeptides, including naming conventions and peptide bond formation.

Introduction to prosthetic groups in conjugated proteins, highlighting their functional importance.

Transcripts

hello welcome to this uh

presentation on proteins part two

today i'm going to discuss to you the

second part of protein and

in this lecture you will

learn the different structures

of proteins so let's go

okay so in the previous lecture

i uh i showed to you the structure of

different amino acids

and as you can as you can see in this uh

in this slide um i have here the

structure of structure of

or primary structure of insulin insulin

is the

very first protein that has been

sequenced

when i say sequence

the amino acid the amino acid content

has been or have been identified

the amino acids in order so as you can

see in this uh

in the picture of um

insulin there are two chains and then

from your left from the from your left

side

to the right side what appears are the

following

glycine isolation valine

glutamic acid glutamine and so on

okay the right most

amino acid is asparagine and on the

chain b you have phenylalanine valine

and on the last the last amino acid in

the chain

in the chain b is alanine now

as you can see here there is a sequence

okay my insulin and your insulin

must have the same order

of amino acid okay this should not be

the order

must not be altered

okay as you can see here there are how

many amino acids in the chain

1 2 3 4 5 6

7 8 9 10 11 12

13 14 15 16 17 18 19

20 21 this is the 21st

amino acid but if i'm not mistaken uh

um counting

okay now um this amino acids

are linked together they are not

separated

although in this uh in the picture

you don't see a bond but basically each

of the 21 amino acids are connected

by each of the 21 amino acids are

connected by the bond by a bond

similar to the amino acids here in the

chain

b okay so you call the band

peptide band or in uh

this is also known as amide amide bond

okay so at this point we will see

how peptide bond is form

okay by uh by convention in practice

normally the amino acid sequence

in protein is red from left to right

okay so from your left you have glycine

and then on your right you have um

asparagine

okay so we read the amino acid sequence

from n to c

terminal okay from your left side

to the right side okay and at this point

we will see how peptide bond

or peptide bonds are formed or in other

words how

um amino acids are linked together

in a protein so i have here

the this is how peptide bonds

this is how peptide bonds uh look like

okay

this is the peptide bond okay and this

is another

peptide band so in this uh

in this structure this short

this short peptides okay have

three amino acid residues okay

when i say amino acid residues

okay these are the amino acids that are

part of the protein so here in the chain

a

in the in the chain a of insulin

there are 21 amino acid residues

okay take note that i added the word

residue because uh i'm referring to the

amino acid that is

part of the protein

all right now um

if the amino acid is separated

or i'm if i'm referring to individual

amino acid

i would just say amino acid but if the

if i'm referring to amino acid that is

part of the protein i would refer to it

as amino acid

residue okay so in this

short peptide okay in the short peptide

there are three amino acid residues

by the way if it is uh

if there are only three or if there are

only two or more uh

there are two or more amino acids okay

in the chain we just call it peptide

in our case in this uh in this

in this picture there are

three amino acids uh residue

so we just call it tripeptide

okay tripeptide because there are three

amino acid residues

the word protein or polypeptide

is used when we are referring to a large

molecule or large

if there are many rather if there are

main amino acid residues

okay connected so

if there are only a few amino acid

residues connected

we refer to this as a peptide

oligopeptide short short pep

you know short protein

okay so here there are

three amino acids amino acid residues in

the

in the peptide or in the tripeptide so

that's

alanine phenylalanine and serine okay

the three amino acids are uh

the three amino acid residues are

connected by peptide bond so this is

one peptide and another peptide

so as i said this is a tri

okay this is tripeptide

okay tripeptide because there are three

okay three amino acid residues and the

tripeptide

is connected by how many peptide bonds

there are two peptide bonds

okay um

the sequence is named using the three

letter abbreviation

alanine for or allah for alanine

fe for phenyl alanine and sir for

serene okay however we can

also use um the one letter or single

letter abbreviation for each

say for example for allah you have a

and then phenylalanine is f

and serene is s usually

we use the single letter abbreviation if

the protein

is very large okay something like

something like uh

hemoglobin okay and if we are referring

to

a very long okay polypeptide

because if we use the the the name word

complete name

the sequence would be very very large

okay

even if we are using the three-letter

abbreviation the

sequence would be very very long okay

and we don't want

we don't want large space that's why uh

biochemists or scientists have have

simply use or adapt the

single letter abbreviation

okay previously i showed to you the

structure of tripeptide

i have shown you the the form

in which the three amino acid residues

are

are connected now the question is how do

we form

peptide bond okay in this uh

in this structure or in this picture i'm

going to show you how

the peptide bond or peptide bonds are

formed

okay so let's refer to this as um amino

acid one

okay and this is the amino acid two

okay so remember that uh

on the left side you have the n

okay you have the amino group on the

right side you have the carboxyl group

and likewise in the amino acid two this

is how we

this is how we draw okay

uh our r stands for

the side chain of the amino acid

okay and uh the good thing about this is

it's color-coded

okay what we will do is

we're just gonna remove this

oh here from the carboxyl group

and we remove the hydrogen from

the amino group okay

and remember that an amino

an amino group the nitrogen here has

lone pair of electron okay

has lone pair of electron and the lone

pair of electron in the nitrogen

will be used to form a bond

okay between the nitrogen and

the carbon so when this nitrogen bonds

to the

when this nitrogen bonds to the carbon

and this is actually the peptide

bond okay the carbonyl group

remains okay the nitrogen here is

attached to the carbon the height one

hydrogen here

remains okay and if you remember

if you recall my uh my presentation in

organic chemistry i

told you that an an amide

okay has a general formula of

r or any alkyl group or any uh

group of carbon atoms okay

it has carbonyl okay the whole thing

this is carbonyl group remember

and it's connected to

[Music]

amino amino group

okay does not matter if you put the

right the hydrogen

above so this is the this is the peptide

band

okay now as you notice that

in the amino acid 2 this is the amino

acid residue number two

the the carboxyl group

okay the carboxyl group is

unaffected okay the carboxyl group is

in top okay

and on the on the amino acid

one okay the amino group

is inta okay

it's not part it's not part of the

[Music]

peptide formation however the carboxyl

group of amino acid 1

is used in the peptide formation

and then the amino group amino group of

the

amino acid 2 is used in the peptide

formation now by convention as i said

we read or we identified the sequence

beginning from the left

to the right okay from left

to right now the

left most amino acid residue is called

the

n terminal okay

and the amino acid residue at the

right most right most in the sequence

is called it's called

c terminal okay

now let me explain to you why the

leftmost

amino acid is referred to as

n-terminal as you can see in the

in this uh picture okay

in this picture the

the end or the left most the left-most

amino acid

has three

amino group okay so

the leftmost amino acid in the chain

has three amino group meaning

the amino group is not

involved in the peptide formation

okay and the amino acid residue at the

right side

okay extreme right has free

okay it has free carboxyl group

that's why it's called the

amino acid at the c terminal

okay c terminal so

if you have a sequence say

a c v

uh g and then f

okay i have how many amino acid residues

i have

five so you call this penta

okay penta

okay how many amino acid residues there

are five that's why

pentapeptide how many um

how many peptide bonds there are four

so one two

three four peptide bond

what is the amino acid at the

n-terminal that's alanine

okay because the alanine

does have an n

terminal or free

amino group

okay what is the amino acid at the c

terminal it's the

phenyl alanine why because phenylalanine

has free carboxyl group

it's carboxylic acid its carboxyl group

is not uh involved in the peptide

formation

okay unlike uh the amino acids here

their their pep

uh their amino acid or their amino group

and their carboxyl groups are involved

or participated in the peptide formation

okay so it's just very easy the

leftmost amino acid is the n-terminal

and then the right-most amino acid

is the amino acid at the c-terminal

okay and because it has

three amino group the

c terminal is uh due to the presence of

presence of three carboxyl

groups or carboxyl group

okay at this point we will see how

peptides

are named okay for example

it says here the c terminal

amino acid residue keeps its

full name okay remember the c terminal

uh amino acid residue that's the amino

acid at the

right most okay in the chain because

um that amino acid residue has

uh the carboxyl group okay

now the rule the rule is it says

um yl suffix

is added to replace ine

or e acid ending of the

amino acid name okay except

for tryptophan which

uh yl is added to the name

when you have a sequence for example

alanine

okay let us and

glycine okay i'm just using the single

letter abbreviation

alanine or allah

okay the complete is alanine

okay remember it ends with y um i and e

so this i and e will just be replaced by

a suffix

yl so that becomes a

la nil okay and then the

the middle amino acid residue is leosine

okay leosine

okay the ine once again will be replaced

by yl so that becomes

la you seal okay

now it says here that i

would like to say again the c terminal

amino acid residue

keeps its full amino acid name okay

what's the amino acid

at the c terminal that is glycine

okay so to name this uh to name this

stripe peptide

you'll have to say alanil layucial

okay and leosil glycine

um the peptide name has no

um space in between okay

so this is a tri

this is a try peptide

tripeptide because there are three amino

acids three amino acid residues and the

three amino acid residues are linked by

two

peptide bonds what's the name of this

tripeptide

alanil leucil glycine

you always begin the naming from the

n terminal

okay at this point we will now classify

the protein okay

based on chemical composition

now there are many proteins in fact in a

in a cell there are

so many proteins and they vary in a

shape function and they vary in

composition okay the first class is

called

simple protein in which

only amino acid residues are present

no other component except amino

acid okay in a simple protein

there could be more than one subunit

okay when we say subunit they are uh

something like um this could be

polypeptide okay there could be one or

more polypeptides

in uh in a protein say for example this

is uh

this is protein okay and another

polypeptide

this is subunit subunit a and this is

subunit b

okay but the whole thing is one

protein but it contains two subunits

okay it's a simple protein

if there are no other

non amino acid component

so again simple protein is

if there is only or there are only

amino acid present okay

it could be a mono subunit

or mono uh mono subunit yes

okay next is conjugated protein

okay it says here a protein that has

one or more none okay it says here

none amino acid entity

okay in simple protein only

amino acid entities are present okay

now in conjugated protein the non-amino

acid

entities are called prosthetic

groups okay the non-amino acid

entities are prosthetic group

now uh there could be one or more

polypeptide chain or there could be

two or more subunits okay

the prostatic group or the non-amino

acid component may be organic

or in organic example

lipoprotein the prosthetic group is

lipids okay glycoprotein

the prosthetic group is carbohydrates

metal protein

some metals become

part of the prosthetic group