Amino acids and protein folding

Summary

This video explains the critical role of proteins in cellular functions, detailing how amino acids link to form complex protein structures. It describes the 20 amino acids humans use, highlighting those we can synthesize and those we must obtain from our diet. The video also explores how amino acids' side chains affect protein folding and function. Finally, it outlines protein structures—primary, secondary, tertiary, and quaternary—and explains how they contribute to the protein's stability and role in biological processes.

Takeaways

• 🧬 Proteins are long chains of amino acids, connected by peptide bonds and folded into complex shapes.
• 🧪 Humans use 20 amino acids, some of which we can synthesize, while others must be obtained through diet (essential amino acids).
• 💪 Five amino acids are dispensable as the body can produce them anytime, while six are conditionally essential (made under specific conditions).
• 🍽 Nine amino acids are essential and must be obtained from food sources like meat, eggs, and dairy.
• ⚛️ Amino acids have both an amine group (NH2) and a carboxylic acid group (COOH), and can form zwitterions at physiological pH due to their dual charges.
• 🌊 Amino acids are classified as hydrophobic (water-hating) or hydrophilic (water-loving) based on their side chains, affecting protein folding.
• 🔄 Amino acids link through condensation reactions to form peptide bonds, releasing water molecules during the process.
• 🌀 Proteins have multiple levels of structure: primary (amino acid sequence), secondary (alpha helices, beta sheets), tertiary (3D folding), and quaternary (multiple polypeptide chains).
• 🔗 Peptide bonds are strengthened by resonance, making the structure more stable and resistant to breaking.
• 🧩 Protein folding is influenced by hydrogen bonds, disulfide bridges, and hydrophobic interactions, helping them maintain their structure and function.

Q & A

What is the basic structure of a protein?

A protein is made up of long chains of amino acids that are linked by peptide bonds. These chains fold into a specific shape, which determines the protein's function.

How many amino acids do humans use in protein synthesis, and what are they called?

Humans use 20 amino acids for protein synthesis. Some examples include alanine, arginine, cysteine, glycine, lysine, methionine, phenylalanine, and tryptophan.

What are the different categories of amino acids based on their production in the body?

Amino acids are categorized into three groups: dispensable (which the body can make), conditionally essential (which the body can make but not always), and essential (which the body cannot make and must be obtained through diet).

What determines the charge of an amino acid at a specific pH?

The charge of an amino acid depends on the pH and its side chain. At physiological pH (7.4), the amine group is positively charged and the carboxyl group is negatively charged, making it a zwitterion.

How do peptide bonds form between amino acids?

Peptide bonds form through a condensation reaction, where the carboxyl group of one amino acid binds with the amine group of another, releasing a water molecule.

What is chirality in the context of amino acids, and why is it important?

Chirality refers to the existence of two mirror-image forms (enantiomers) of amino acids. Proteins in living organisms are only made from the 'left' or 'L' form of amino acids, which is crucial for their proper function.

What are the four levels of protein structure, and what do they represent?

The four levels are: primary (sequence of amino acids), secondary (alpha helices or beta sheets), tertiary (overall 3D shape of the protein), and quaternary (arrangement of multiple polypeptide chains in a larger protein complex).

What is the role of hydrogen bonding in the secondary structure of proteins?

Hydrogen bonds stabilize both alpha helices and beta sheets, which are types of secondary structures. These bonds form between the CO and NH groups of amino acids, providing stability to the protein.

How do hydrophobic amino acids influence protein folding?

Hydrophobic amino acids tend to orient themselves toward the inside of the protein, avoiding contact with water. This helps shape the protein's structure and contributes to the formation of the tertiary structure.

What is an example of a protein with quaternary structure, and how does it form?

Hemoglobin is an example of a protein with quaternary structure. It is made up of four polypeptide subunits that come together in a specific arrangement to form a functional protein complex.

Outlines

00:00

🔬 Understanding Proteins and Amino Acids

Proteins are essential for cellular functions and are composed of long chains of amino acids linked by peptide bonds. These chains fold into specific shapes to form functional proteins. The human body uses 20 amino acids, categorized into dispensable, conditionally essential, and essential. Dispensable amino acids can be produced by the body, conditionally essential ones are produced most of the time, and essential ones must be obtained from the diet. Amino acids contain an amine group (NH2) and a carboxylic acid group (COOH), making them zwitterions at physiological pH. The side chains of these amino acids determine their properties, such as being hydrophilic or hydrophobic, which influences protein structure. The behavior of these amino acids, like their charge, varies with pH levels.

05:01

🧩 Formation and Structure of Peptide Bonds

Amino acids form peptide bonds through a condensation reaction where the carboxyl group of one amino acid binds with the amine group of another, releasing water. This bond is strong due to the resonance property of molecules, which stabilizes the peptide chain. Amino acids exhibit chirality, existing as left (L) or right (D) oriented forms, but proteins are only made from L-amino acids. Protein synthesis occurs in ribosomes using mRNA as a blueprint for the amino acid sequence. The growing chain may be processed in the endoplasmic reticulum or directly in the cytosol. Proteins have multiple structural levels: primary (sequence of amino acids), secondary (alpha helices and beta sheets), tertiary (overall 3D shape), and quaternary (multiple polypeptides forming a complex structure). Each level contributes to the protein's stability and function.

10:02

🌀 Protein Folding and Structure

Protein folding involves amino acids orienting themselves to minimize unfavorable interactions. Hydrophobic amino acids tend to hide inside the protein, avoiding water, while hydrophilic ones face outward. Tertiary structure forms as the polypeptide twists and turns, similar to tangled headphones, stabilizing through interactions like disulfide bridges and hydrophobic effects. Quaternary structure involves multiple polypeptide chains forming a larger, functional protein, such as hemoglobin, which has four subunits arranged tetrahedrally. The summary reviews the classifications of amino acids and the hierarchical organization of protein structure, emphasizing how each level contributes to the final protein's function and stability.

Keywords

💡Protein

Proteins are essential macromolecules that perform a variety of functions within cells. In the video, proteins are described as long chains of amino acids that are folded into specific shapes to carry out their functions. They are fundamental to cellular processes and structure.

💡Amino Acids

Amino acids are the building blocks of proteins, linked by peptide bonds. The video explains that humans use 20 different amino acids to form proteins, with each amino acid having a specific side chain that influences the protein's structure and function.

💡Peptide Bonds

Peptide bonds are the chemical connections between amino acids in a protein. The video highlights that peptide bonds are created through a condensation reaction, resulting in the formation of a stable chain of amino acids, which is essential for building the primary structure of proteins.

💡Essential Amino Acids

These are amino acids that humans cannot synthesize and must obtain from their diet. The video lists nine essential amino acids, including lysine, methionine, and tryptophan, which are crucial for protein synthesis and overall health.

💡Hydrophobic and Hydrophilic

Hydrophobic refers to molecules or amino acid side chains that repel water, while hydrophilic refers to those that attract water. The video discusses how hydrophobic amino acids avoid water by orienting themselves inside a protein, whereas hydrophilic ones tend to be exposed on the surface, contributing to the protein's structure.

💡Primary Structure

The primary structure of a protein is the linear sequence of amino acids connected by peptide bonds. The video uses this as the foundation upon which more complex structures of proteins are built, forming the basis for the protein's overall function.

💡Secondary Structure

Secondary structure refers to the folding of amino acid chains into alpha helices or beta pleated sheets. These structures are stabilized by hydrogen bonds and are crucial for a protein's stability and function, as highlighted in the video.

💡Tertiary Structure

The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, formed through interactions like disulfide bridges and hydrophobic interactions. The video explains how this structure is critical for determining the protein's function in the body.

💡Quaternary Structure

The quaternary structure involves multiple polypeptide chains coming together to form a functional protein. The video uses hemoglobin as an example, where four subunits combine to form a larger, functional protein structure.

💡Zwitter Ion

A zwitter ion is a molecule that has both positive and negative charges but is electrically neutral overall. The video explains that amino acids are zwitter ions at physiological pH, with their amine group carrying a positive charge and their carboxyl group carrying a negative charge.

Highlights

Proteins are vital for the normal function of a cell, consisting of long chains of amino acids bound by peptide bonds.

Humans use 20 amino acids in protein synthesis, including essential and non-essential types.

Amino acids are categorized into dispensable, conditionally essential, and essential based on whether the body can produce them.

Essential amino acids, such as lysine, tryptophan, and valine, cannot be synthesized by the body and must be obtained through diet.

At physiological pH, amino acids exist as zwitterions, carrying both positive and negative charges.

The side chains of amino acids determine their properties, such as hydrophilic (water-loving) or hydrophobic (water-hating) behavior.

Peptide bonds form between the carboxyl group of one amino acid and the amine group of another, releasing a water molecule in the process.

Resonance in peptide bonds strengthens them by allowing electrons to be shared across the molecule.

Amino acids exhibit chirality, meaning they exist in left-handed (L) and right-handed (D) forms, but proteins only use the L-form.

Protein production occurs in ribosomes, which follow the instructions from messenger RNA (mRNA) to assemble amino acids in the correct order.

Proteins have four levels of structure: primary, secondary, tertiary, and quaternary, each adding complexity to the overall protein shape.

Secondary protein structures include alpha helices and beta-pleated sheets, stabilized by hydrogen bonds.

Tertiary structure results from interactions like disulfide bridges and hydrophobic interactions that fold the protein into its final shape.

Quaternary structure forms when multiple polypeptide chains combine, as seen in hemoglobin's tetrahedral arrangement.

Protein structure is essential for function, and its formation relies on various bonds and interactions, each contributing to the final 3D shape.

Transcripts

proteins are vital for the normal

function of a cell essentially a protein

is at its simplest a very long chain of

individual units called amino acids

bound to each other by peptide bonds to

form an amino acid

chain they sort of resemble a string of

beads and they get twisted and folded

into a final protein shape to make a

protein we need to get to know two

things the ingredients which are the

amino acids and the recipe or how the

finished amino acid chain folds into the

protein humans use 20 amino acids in our

day-to-day protein making so we have

alanine Arginine asparagine aspartic

acid cysteine glutamic acid glutamine

glycine histadine isol leucine Lucine

lysine methionine phenol alanine Proline

cine thionine

tryptophan tyrosine and veine pH that's

20 one way to divide these is into the

ones that we make ourselves and the ones

that we cannot make

ourselves there are five amino acids

that are dispensable alanine asparagine

aspartic acid glutamic acid and Cene

because we can make them denovo

ourselves at any time and in good

quantity then there's six of them that

we call conditionally essential because

we can make them most of the time but

not always and these are Arginine

cysteine glutamine glycine Proline and

tyrosine finally there are nine of them

that we cannot make ourselves htin

isoline

Lucine lysine methionine phenol alanine

threonine tryptophan and veine and as a

result we have to obtain them from our

diet we call these the essential amino

acids all right so the amino acid just

from the name you can tell they've got

an amine group or nh2 and also an acid

in this case a carboxilic acid group or

Co the amine and carboxilic acid groups

are both bound to the same carbon called

the alpha carbon now at a physiologic pH

of 7.4 the amine group has a positive

electrical charge and the carboxy group

has a negative

charge having both a positive and a

negative charge makes amino acids a type

of zwitter ion which is German for

hybrid or double

ion now the alpha carbon also has a side

chain sometimes marked as r and this

side chain gives the amino acids certain

properties which can play an important

role in the overall protein

structure first the side chain can be

hydrophilic or hydrophobic so water

loving or water

hating hydrophobic amino acids have

non-polar side chains this might be in

the form of an alkal side group which is

a saturated hydrocarbon seen in veine

glycine alanine Lucine isol leucine

methionine and Proline

alternatively it can be in the form of

an aromatic side group which involves a

six carbon ring like in phenol alanine

tyrosine and

tryptophan now hydrophilic amino acids

have polar side chains these polar side

chains might be acidic like when their

side chains contain additional carboxy

groups like aspartic acid and glutamic

acid other hydrophilic amino acids have

polar side chains that are basic like

lysine histadine and

Arginine at physiological pH the acidic

groups lose a hydrogen and the basic

groups gain a

hydrogen finally some polar side chains

are neutral for example they can contain

hydroxy groups like Cene theanine or

tyrosine or suf hydral groups like

cysteine or carboxamide groups like

asparagine or

glutamine now keep in mind that the

charge and amino acid really depends on

its side chain as well as the

pH for example at a very low PH the

amine group is positive while the

carboxy group is neutral and at a very

high pH the amine group is neutral and

the caroal group has a negative charge

and at a pH that's somewhere in between

both groups are electrically charged and

they cancel each other out resulting in

no net charge for the amino

acid the just right pH also known as the

pi or isoelectric point is different for

every amino acid and it depends on the

specific side

chains for amino acids to link up in a

chain the carboxy group of one amino

acid has to bind to the amine group on

another amino acid creating a single

peptide bond this is a condensation

reaction meaning that two amino acids

are basically smooshed together and the

O from the carboxy group along with one

of the hydrogens from the amine group

get released as a water molecule in the

formation of an amide Bond well

technically being a single Bond it

actually has the properties of a

structurally stronger double bond thanks

to the property of

resonance now resonance is a property of

a molecule where electrons get shared

across the molecule while keeping the

arrangement of atoms the

same basically the electrons from

neighboring functional groups in the

amino acid are borrowed and that makes

peptide bonds stronger and more

stable so amino acids are essentially a

carboxy group an amine group a side

chain and a hydrogen all bound to an

alpha

carbon now there's an interesting

geometric property here called chirality

which means that each amino acid can

exist in two forms that look like mirror

images of each other these two forms are

called en anomers of each

other we have the left or level oriented

amino acids as well as the right or

dextro oriented amino acids while

similar these are definitely not the

same think of it like a pair of shoes

even though they're made out of the same

materials and generally look alike the

left and the right shoe are not

interchangeable at least not without a

lot of pain

involved as it turns out proteins are

only made out of level oriented amino

acids now protein production itself

happens in cellular structures called

ribosomes which use the messenger RNA

which is essentially a blueprint that

tells the ribosome exactly the order of

amino acids that are

needed at this point the protein is just

a growing string of amino acids as it

grows it's either being injected into

another organel called the endoplasmic

reticulum which will help the protein

take shape or it's being translated

directly into the cytool now the

proteins have multiple levels of

structure to them primary secondary

tertiary and quinary structure creating

a hierarchy as an analogy think about

the alphabet it can be used to create

Words which can make simple sentences

which can further be made into complex

sentences as an example the letters

themselves would be considered the

primary structure then simple words like

exam and ours would represent secondary

structures tertiary structure would be

when the entire chain folds together

maybe making a simple sentence like the

exam is in 2

hours and the quadin structure might

actually be a few peptide chains coming

together to form a more complex protein

making a complex sentence that says the

exam is in 2 hours and I haven't slept

at

all when it comes to proteins the

primary structure is simple enough it's

just a linear sequence of amino acids

connected through peptide bonds like a

String of

Pearls now the peptide bonds between the

amino acids are very rigid but by

comparison the single bonds connecting

the amide functional group of the

peptide bond to the alac carbon are

flexible that allows significant freedom

of rotation and through that rotation

the protein can fold into one of the two

types of secondary structure Alpha helix

or beta pleated

sheets the alpha Helix resembles a

spring the helical structure brings the

co of the first amino acid near the the

NH of the fifth amino acid the second Co

gets near the sixth NH and so on in

other words each of these instances is

separated by four amino

acids having the O and H get close to

one another allows for a strong hydrogen

bond to form and that makes the alpha

helical structure really

stable beta pleated sheets also rely on

hydrogen bonding but slightly

differently imagine a neatly folded

piece of paper in beta completed sheets

hydrogen bonds form between the NH on

one flap of paper and the co on another

flap of paper and these bonds almost

hold or glue the sheets

together that makes beta ple sheets

really stable as

well now tertiary structure is the

overall shape of the polypeptide chain

and it includes the secondary structures

as well as other features for example

two sulfur containing cyes can bind to

form a disulfide

bridge

also hydrophobic amino acids form bonds

with one another and Orient themselves

toward the inside of the protein in that

way they avoid contact with water it's

like the hydrophobic amino acids are

being a bit

shy basically the way a polypeptide

chain twists and turns to form its

tertiary structure is kind of like the

way headphones get tangled up in your

pocket quadrin structure is the final

level and it's the level at which

multiple polypeptide chains come

together to form a larger protein

structure a classic example involves the

four polypeptide subunits that have come

together to form a single hemoglobin

protein which is roughly a tetrahedral

Arrangement all right as a quick recap

there are 20 amino acids five

dispensable six conditionally essential

and nine

essential the primary structure of a

protein is the linear sequence of amino

acids the secondary structure includes

both Al Alpha helix or beta pleed sheets

both of which rely on hydrogen

bonds the tertiary structure binds the

secondary structures through various

other Bond interactions like disulfide

Bridges or hydrophobic

reactions and the quadrin structure

creates the final shape of a protein by

connecting multiple polypeptides in the

form of tertiary

structures helping current and future

clinicians Focus learn retain and Thrive

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