Proteins Part 2
Summary
TLDRThis 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
🔬 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.
🧬 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.
🔗 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.
🧩 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.
🧪 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).
Mindmap
Keywords
💡Amino Acid
💡Peptide Bond
💡Primary Structure
💡Insulin
💡N-terminal and C-terminal
💡Tripeptide
💡Polypeptide
💡Residue
💡Conjugated Protein
💡Simple Protein
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
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