2.4 Proteins

Essential idea: Proteins have a very wide range of functions in living organisms

Syllabus Reference

https://quizlet.com/_8tread?x=1jqt&i=28b19k

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2.4 Proteins

Vocabulary

Understandings

2.4 Proteins

Understandings

Syllabus Reference

Watch this!

2.4 Proteins

Watch this

Helpful Video

2.4 Proteins

What is anabolism?

2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.

Anabolism: the synthesis of complex molecules in living organisms from simpler ones

Catabolism: is the set of metabolic pathways that breaks down molecules into smaller units

2.4 Proteins

General Amino Acid Structure

2.4.U1 Amino acids are linked together by condensation to form polypeptides.

• Who?
• What?
• Where?
• How?

2.4 Proteins

Where do proteins come from?

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

Proteins

Proteins do the nitty-gritty jobs of every living cell.

Proteins are made of long strings of individual building blocks known as amino acids.

2.4 Proteins

Where do proteins come from?

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

Ribosomes are the molecules within cells that facilitate the formation of peptide bonds and hence where polypeptides are synthesized

2.4 Proteins

Where do proteins come from?

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

2.4 Proteins

The central dogma of genetics

• Genes are simply codes for making polypeptides
• DNA is stored in the nucleus, yet polypeptides are produced in the cytoplasm
• mRNA is a message from the nucleus to the ribosome
• The genetic code is the sequence of bases on mRNA – tells the ribosomes which amino acids to use

3 base pairs = 1 amino acid = 1 codon

peptide bond

2.4 Proteins

Where do proteins come from?

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

3 base pairs = 1 amino acid

2.4 Proteins

Where do proteins come from?

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

There are 22 amino acids, but only 20 amino acids are encoded by the universal genetic code and 2 rare amino acids

2.4 Proteins

Where do proteins come from?

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

You do NOT need to know their names!

2.4 Proteins

There are 20 amino acids naturally incorporated into proteins

2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

If a polypeptide contains just 7 amino acids there can be 20⁷ = 1,280,000,000 possible polypeptides generated.

Given that polypeptides can contain up to 30,000 amino acids (e.g. Titin) the different possible combinations of polypeptides are effectively infinite.

2.4 Proteins

Why are there infinite possibilities of polypeptides?

2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

1. Could be any length
2. 20 possible amino acids
3. Any order or combination

2.4 Proteins

2.4.U4 The amino acid sequence of polypeptides is coded for by genes.

Ribosomes are the site of polypeptide synthesis, but ribosomes need a template – the messenger RNA, which, in turn, is translated by transfer RNA molecules which, in turn, carry specific amino acids.

Challenge: Where does the messenger RNA come from?

2 = di

3 or more = poly

1. What are the elements in amino acids?
2. What chemical groups are involved in proteins?
3. What bonds are used in proteins?
4. How many amino acids are needed in the body?

2.4 Proteins

How do amino acids bond together?

Challenge: what happens to the long chains of proteins?

2.4 Proteins

How do amino acids bond together?

Starter

Challenge: what happens to the long chains of proteins?

1. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)……

(2 specific amino acids (L-Cysteine and L-Methionine) contains a Sulphur atom in its R group. So N, H, C, O & S.

2. Proteins consist of an alpha (central) carbon atom linked to an amino group, a carboxyl group, a hydrogen atom, and a variable component called a side chain (R)

3. Peptide bonds….. Hydrogen, Ionic and Disulfide Bonds (Some hydrophilic and hydrophobic bonds)

4. 20 Amino Acids (2 rare amino acids)

2. Amino acids contain an amino group, a carboxyl group, a carbon and a unique variable R group

2.4 Proteins

What is the structure of an amino acid?

Task 1

amino group

carboxyl group

R group

(basic)

(acidic)

2.4 Proteins

What is the general amino acids structure?

1. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)……

(Cysteine and Methionine) contains a Sulphur

2.4 Proteins

2.4 Proteins

What is the backbone structure of an amino acid?

2.4 U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Amino acids contain an amino group, a carboxyl group, a carbon and a unique variable R group

2.4 Proteins

What is the backbone structure of an amino acid?

2.4 U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

How do amino acids join together?

2.4 U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

Methionine and Cysteine

2.4 Proteins

Why is this amino acid special?

Guiding Questions

What are the different groups of amino acids?

Do you remember A, T, C and G?

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2.4 Proteins

What are the different groups of amino acids?

Challenge: How many amino acids can be made from 24 base pairs?

1 amino acid = 1 codon = 3 base pairs

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Some amino acids have evenly distributed electrons = non-polar

2.4 Proteins

How do amino acids contribute to protein structure and function?

Syllabus Reference

2.4 Proteins

How does amino acids structure differ?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

• Some amino acids have unevenly distributed electrons = polar

2.4 Proteins

How does amino acids structure differ?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Some amino acids are ionic (electrically charged - either positively or negatively)

2.4 Proteins

How does amino acids structure differ?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Challenge: I am confused, why does that matter?

• there is an uneven distribution of electron density.

2.4 Proteins

What is polarity?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Hydrophilic

Hydrophobic

2.4 Proteins

What is ionic?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Amino Acids

Amino Acids

Hydrophilic

2.4 Proteins

Summary

Checkpoint

Proteins are made from amino acids

Amino acids contain a amine and carboxyl group

Amino acids join together through a condensation reaction

Amino acids join together by peptide bonds

Amino acids are made from C, H, O, N, S and Se

There are 20 amino acids essential to the body

Polar and ionic amino acids are hydrophilic

Non-polar amino acids are hydrophobic

2.4 Proteins

Walk around, touch the ground and think of sleeping on a cloud

Brain Break

• Download Avogadro here

• Draw glycine, the simplest amino acid
• Use the optimise tool to render the molecule in 3D
• Use the hand tool to move it around
• Take a screenshot to upload to ManageBac

2.4 Proteins

Molecular Visualisation Software

Plenary

2.4 Proteins

Interactive Molecular Drawing Program

Checkpoint

2.4 Proteins

Proteins have four levels of organization

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Primary structure is the �amino acid sequence. This relates to the order of amino acids

2.4 Proteins

What is primary structure?

Task 1

2.4 Proteins

What is primary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

The amino acid sequence is coded for by DNA and is unique for each kind of protein

2.4 Proteins

What is primary structure?

Task 1

2.4 Proteins

What is primary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

The amino acid sequence determines how the polypeptide will fold into its 3D shape

2.4 Proteins

What is primary structure?

Task 1

2.4 Proteins

What is primary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Even a slight change in the amino acid sequence can cause the protein to malfunction

For example,

mis-formed haemoglobin causes sickle cell disease

2.4 Proteins

What is primary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

What is primary structure?

Task 1

2.4 Proteins

Stop, Pair and Share

Checkpoint

2.4 Proteins

Proteins have four levels of organization

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Secondary structure results from hydrogen bonding between the oxygen of one amino acid and the hydrogen of another

2.4 Proteins

What is secondary structure?

Task 1

2.4 Proteins

What is secondary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

What is a beta pleated sheet?

Task 1

2.4 Proteins

What is secondary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

The alpha helix is a coiled secondary structure due to a hydrogen bond every fourth amino acid

2.4 Proteins

What is an alpha helix?

Task 1

2.4 Proteins

What is secondary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

You can see several places in this haemoglobin molecule where an alpha helix has formed

2.4 Proteins

What is secondary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

The beta pleated sheet is formed by hydrogen bonds between parallel parts of the protein

2.4 Proteins

What is beta pleated sheet?

Task 1

2.4 Proteins

What is secondary structure?

Task 3

2.4 Proteins

What is beta pleated sheet?

Task 1

2.4 Proteins

What is secondary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

A single polypeptide may have portions with both types of secondary structure

2.4 Proteins

What is secondary structure?

Task 1

2.4 Proteins

What is secondary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

Stop, Pair and Share

Checkpoint

2.4 Proteins

Use these images to help

Checkpoint

Primary: Amino Acid Sequence

Secondary: Alpha Helix (Hydrogen Bonds)

Secondary: Beta Pleated Sheets(Hydrogen Bonds)

2.4 Proteins

Proteins have four levels of organization

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Tertiary structure depends on the interactions among the R group side chains

2.4 Proteins

What is tertiary structure?

Task 1

2.4 Proteins

What is tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

What is tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

These interactions may include:

• hydrogen bonds
• disulphide bridges
• ionic interactions
• polar (non-polar) associations

2.4 Proteins

What is tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

https://www.youtube.com/watch?v=9YwdeEDrfPI

Types of interactions

Hydrogen bonds between polar side chains

2.4 Proteins

What are the types of interactions?

Task 1

2.4 Proteins

What are the types of interactions (bonds) in a tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Types of interactions

Hydrophobic interactions: amino acids with nonpolar side chains cluster in the centre of the protein, out of contact with water

2.4 Proteins

What are the types of interactions?

Task 1

2.4 Proteins

What are the types of interactions (bonds) in a tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Types of interactions

Ionic bonds between positively and negatively charged side chains

2.4 Proteins

What are the types of interactions?

Task 1

2.4 Proteins

What are the types of interactions (bonds) in a tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Disulfide bridge (strong covalent bonds) between sulfur atoms in the amino acid cysteine

2.4 Proteins

What are the types of interactions?

Task 1

2.4 Proteins

What are the types of interactions (bonds) in a tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

What is keratin?

Task 1

2.4 Proteins

What are the types of interactions (bonds) in a tertiary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

Stop, Pair and Share

Checkpoint

Hydrogen bonds between polar side chains

Disulfide bridge (strong covalent bonds) between sulfur atoms in the amino acid cysteine

Ionic bonds between positively and negatively charged side chains

Hydrophobic interactions: amino acids with nonpolar side chains cluster in the centre of the protein, out of contact with water

2.4 Proteins

Stop, Pair and Share

Checkpoint

https://wordwall.net/resource/23585711

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2.4 Proteins

Walk around, touch the ground and think of sleeping on a cloud

Brain Break

2.4 Proteins

Proteins have four levels of organisation

Task 1

2.4 Proteins

Proteins have four levels of organization

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Quaternary structure results from interactions among separate polypeptide chains.

2.4 Proteins

What is quaternary structure?

Task 1

2.4 Proteins

What is quaternary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

For example, Haemoglobin is composed of 4 polypeptide chains

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Collagen is a fibrous protein consisting of 3 polypeptides coiled like a rope

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2.4 Proteins

What is quaternary structure?

Task 1

2.4 Proteins

What is quaternary structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

2.4 Proteins

Stop, Pair and Share

Checkpoint

2.4 Proteins

Proteins have four levels of organization

Task 3

2.4 Proteins

What is protein structure?

2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Play Fold It!

• Register online here:

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• Download the game

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• Learn the game by solving puzzles offline

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2.4 Proteins

Play Foldit

Checkpoint

2.4 Proteins

Play Foldit

Checkpoint

A couple of cool TED Talks

The protein folding problem

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How online gamers solved the structure of proteins

2.4 Proteins

Cool Ted Ed films

Checkpoint

2.4 Proteins

Ted Ed Films

Checkpoint

Denaturation results in disruption of the secondary, tertiary, or quaternary structure of the protein

2.4 Proteins

What is denaturing?

Task 2

2.4 Proteins

What is denaturation?

2.4 A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

Denaturation may be due to changes in pH, temperature or various chemicals

2.4 Proteins

What is denaturing?

Task 2

2.4 Proteins

What is denaturation?

2.4 A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

Protein function is lost during denaturation, which is often irreversible

2.4 Proteins

What is denaturing?

Task 2

2.4 Proteins

What is denaturation?

2.4 A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

2.4 Proteins

What are the functions of proteins?

Checkpoint

• Structure – e.g. collagen, spider silk
• Hormones – e.g. insulin, glucagon
• Immunity – e.g. immunoglobulins
• Transport – e.g. haemoglobin
• Sensation – e.g. rhodopsin
• Movement – e.g. actin, myosin
• Enzymes – e.g. Rubisco, catalase

• Rubisco
• Insulin
• Immunoglobulins
• Rhodopsin
• Collagen
• Spider silk
• Haemoglobin

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• Choose a protein from the list
• Produce a 3 minute presentation outlining its function and its importance to humans.

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2.4 Proteins

What are protein functions?

Task 2

2.4 Proteins

What are the functions of proteins?

2.4 A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

• Compare globular and fibrous proteins
• State the structure and function of your chosen protein
• Outline the importance of the protein to humans/animals

Folded proteins are placed into two general categories

2.4 Proteins

What are folded protein?

Task 2

2.4 Proteins

What are folded proteins?

2.4 A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

Fibrous proteins have polypeptide chains organised in long fibers or sheets

• Water insoluble
• Very tough physically, may be stretchy
• Form structural components in the body

2.4 Proteins

What are fibrous proteins?

Task 2

2.4 Proteins

What is fibrous proteins?

2.4 A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

Functions of fibrous proteins

Structural proteins function in support

• Insects and spiders use silk fibers to make cocoons and webs
• Collagen and elastin are used in animal tendons and ligaments
• Keratin is the protein in hairs, horns and feathers

2.4 Proteins

What are the functions of fibrous proteins?

Task 2

2.4 Proteins

What are the functions of fibrous proteins?

2.4 A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

2.4 Proteins

What are the functions of fibrous proteins?

2.4 A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

Contractile proteins function in movement

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• Actin and myosin contract to create the cleavage furrow and to move muscles

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• Contractile proteins move cilia and flagella

2.4 Proteins

What are the functions of fibrous proteins?

Task 2

2.4 Proteins

What are the functions of fibrous proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Globular proteins have their chains folded into compact, rounded shapes and are easily water soluble

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Functions of globular proteins

Storage proteins function in the storage of amino acids

• Ovalbumin is the protein in egg whites

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• Casein is the protein in milk, source of amino acids for baby mammals

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Functions of globular proteins

Transport proteins function in the movement of other substances

• Hemoglobin, the iron containing protein in blood, transport oxygen from lungs to other parts of the body (C₃₀₃₂H₄₈₁₆O₈₇₂N₇₈₀S₉Fe₄)
• Membrane transport proteins such as channels for potassium and water

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Hormone proteins function as cellular messenger molecules that help maintain homeostasis

• Insulin: sends message “allow sugar into cells” (when blood glucose levels are high, cells will transport glucose into the cells for use or storage)
• Glucagon: sends message “we need more sugar in the blood” (when blood glucose is too low, cells will release glucose)

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Functions of globular proteins

Receptor proteins allow cells to respond to chemical stimuli

• Growth factor receptors initiate the signal transduction pathway when a growth hormone attaches

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Functions of globular proteins

Cholesterol receptors on the cell membrane allow LDL to be endocytosed into the cell

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Functions of globular proteins

Protective proteins function as protection against disease

• Antibodies combat bacteria and viruses

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Functions of globular proteins

Enzymes speed up chemical reactions

• Amylase and other digestive enzymes hydrolyze polymers in food
• Catalase converts hydrogen peroxide H₂O₂ into water and oxygen gas during cellular respiration

2.4 Proteins

What are the functions of globular proteins?

Task 2

2.4 Proteins

What are the functions of globular proteins?

2.4 U7 Living organisms synthesize many different proteins with a wide range of functions.

Proteome

The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism at a certain time. More specifically, it is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions.

NB: The term is a portmanteau of proteins and genome.

2.4 Proteins

What is the proteome?

Task 2

2.4 Proteins

What is the proteome?

2.4.U8 Every individual has a unique proteome.

2.4 Proteins

What is proteonomics?

Task 2

2.4 Proteins

What is the proteome?

2.4.U8 Every individual has a unique proteome.

2.4 Proteins

Investigating the denaturation of proteins

2.4.A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

Available equipment:

• Waterbaths
• Albumen otherwise known as egg white
• Thermometers
• Colorimeters (optional)

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Your task: determine the temperature stability of albumen

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