Session 4.1a - Pre-Reading [Book] Flashcards
Lippincott's Illustrated Reviews Biochemistry Chapter 1 pp1-12 https://meded.lwwhealthlibrary.com/content.aspx?sectionid=49716372&bookid=774 http://www.uobabylon.edu.iq/eprints/paper_11_9137_715.pdf
What are the most abundant and functionally diverse molecules in living systems?
Proteins
What does virtually every life process depend on?
The class of macromolecules known as proteins.
Give an example of a function of enzymes and polypeptide hormones?
They direct and regulate metabolism in the body.
What can direct and regulate metabolism in the body?
Enzymes and polypeptide hormones.
What do contractile proteins in muscles do?
Permit movement
What proteins permit movement in muscle?
Contractile proteins
What type of molecule is collagen?
A protein
What is the function of collagen in bone?
It forms a framework for the deposition of calcium phosphate crystals, acting like the steel cables in reinforced concrete.
What proteins can you find in the bloodstream?
- Haemoglobin
- Plasma albumin
Where can you find haemoglobin and plasma albumin and what do they do (broadly)?
In the bloodstream, shuttle molecules essential to life
What is the function of immunoglobulins?
To fight infectious bacteria and viruses
What proteins fight infectious bacteria and viruses?
Immunoglobulins
What is the role of a protein?
They display an incredible diversity of functions!
What is common to all proteins?
Their structure; they are linear polymers of amino acids
What are linear polymers of amino acids called?
Proteins
What are proteins made up of?
Amino acids
How are proteins formed?
Simple building blocks (amino acids) join to form proteins that have unique 3D structures, making them capable of performing specific biological functions.
How many amino acids are found in nature?
More than 300 different amino acids have been described in nature
How many amino acids code for mammalian proteins?
Only 20 are commonly found as constituents of mammalian proteins
How are amino acids coded for in humans?
There are only 20 amino acids that are coded for by DNA in mammalian proteins
What is the genetic material in the cell?
DNA
What does DNA code for in humans?
20 amino acids which join to form proteins
What does each amino acid have?
- A carboxyl group,
- A primary amino group, and
- A distinctive side chain (“R-group”)
bonded to the - a-carbon atom
(Figure 1.1A).
Which is the only amino acid that doesn’t have a carboxyl group?
Proline, which has a secondary amino group
What is the side chain of an amino acid often known as?
The “R-group”
What is the “R-group”?
The amino acid side chain
What are the carboxyl, amino group and side chain bonded to in amino acids?
The a-carbon atom
What is physiological pH?
Approximately pH 7.4
What is the significance of pH 7.4?
It is (approximately) physiological pH
What are the electrochemical properties of amino acids at physiological pH?
(~ pH 7.4)
- carboxyl group is dissociated
- amino group is protonated
What happens to the carboxyl group of amino acids at physiological pH?
It is dissociated, forming the negatively charged carboxylate ion (COO-)
What is dissociated in amino acids at physiological pH?
The carboxyl group
Is the carboxyl group negatively or positively charged at physiological pH?
Negatively charged
What is the carboxylate ion?
COO-
What is COO- known as?
The carboxylate ion
What happens to the amino group of amino acids at physiological pH?
It is protonated (NH3+)
What is protonated in amino acids at physiological pH?
The amino group
Is the amino group negatively or positively charged at physiological pH?
Positively charged
Describe the chemical formula of the amino group in an amino acid at physiological pH.
NH3+
How are the carboxyl and amino groups combined in proteins?
Almost all of these are combined through peptide linkage
Where does peptide linkage occur in amino acids?
Between the carboxyl and amino groups
Carboxyl and amino groups of _____ _____ combine to form ________
amino acids, proteins
Although at physiological pH, the carboxyl group of amino acids is negatively charged and the amino group positively charged. Why (in general) do these not react?
They are combined with each other through peptide linkage and are therefore not available for chemical reaction. (Fig. 1.1B)
In general, carboxyl and amino groups of proteins are not available for chemical reaction because they are bonded together by peptide linkage. What bonding is the exception to this?
Hydrogen bond formation (Fig. 1.1B)
Which part of the amino acid dictates the role an amino acid plays in a protein?
It is the nature of the side chains
What is the role of the side chain in amino acids?
It is their nature that dictates the role an amino acid plays in a protein.
Why is the side chain that dictates the role of an amino acid plays in a protein?
- The carboxyl group and amino groups are constant in amino acids so they do not dictate the unique role of amino acids.
- Furthermore, they are bounded by peptide linkage so they do not have electrochemical properties that can react.
- The side chains are unique and convey different properties to the amino acid
- These are not electrochemically locked so they can react with other amino acids, and it is these individual reactions with unique amino acid sequences to perform unique conformations and therefore proteins
How are amino acids classified?
According to the properties of their side chains
Give an example of how amino acids can be classified.
Into nonpolar or polar
What is nonpolar?
An even distribution of electrons
What is polar?
An uneven distribution of electrons
How do you describe compounds with an even distribution of electrons?
Nonpolar
How do you describe compounds with an uneven distribution of electrons?
Polar
Give an example of polar molecules.
Acids and bases (Fig. 1.2 and 1.3)
Which molecules can react: polar or nonpolar?
Polar molecules (because they have an uneven distribution of electrons, so they have free electrochemical properties)
Draw the structural features of amino acids in their fully protonated form
+H3N, COOH, H, R, Ca
See Fig. 1.1
Fig. 1.1a
Label and caption this image
+H3N
Draw amino acids combined through peptide linkages (in their fully protonated form)
-NH-C(-R)H-CO-NH-C(-R)H-CO-
See Fig. 1.1B
Fig. 1.1B
Label and caption the image
R
Where are the dissociable hydrogen ions found in amino acids?
On the carboxyl and amino groups
What is the rough pK value for the carboxylate side chain in nonpolar amino acids?
2.3 (this is the value for glycine)
What is the approximate pK value for the amino group in nonpolar amino acids?
9.6 (this is the pK value for glycine)
What are the nonpolar amino acids?
Glycine Alanine Valine Leucine Isoleucine Phenylalanine Tryptophan Methionine Proline
What is the side chain for glycine?
H
What is the side chain for alanine?
CH3
What is the side chain for valine?
CH-CH3-CH3
What is the side chain for leucine?
CH2-CH-CH3-CH3
What is the side chain for isoleucine?
H-C-CH3-CH2-CH3
What is the side chain for phenylalanine?
CH2-benzene ring
What is the side chain for tryptophan?
CH2-C-CH-NH-benzene ring
What is the side chain for methionine?
CH2-CH2-S-CH3
What is the side chain for proline?
CH2-CH2-CH2-N2
Fig. 1.2
Label and caption the image
Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline
NONPOLAR SIDE CHAINS
Classification of the 20 amino acids commonly found in proteins, according to the charge and polarity of their side chains at acidic pH is shown here and continues in Figure 1.3.
Each amino acid is shown in its fully protonated form, with dissociable hydrogen ions represented in red print. The pK values for the a-carboxyl and a-amino groups of the nonpolar amino acids are similar to those shown for glycine. (Continued in Figure 1.3.)
Which amino acids have uncharged polar side chains?
Serine Threonine Tyrosine Asparagine Glutamine Cysteine
What is the side chain for serine?
H-C(H)-OH
What is the side chain for threonine?
H-C(-CH3)-OH
What is the side chain for tyrosine?
CH2-benzene ring-OH
What is the side chain for asparagine?
CH2-C(-NH2)=O
What is the side chain for glutamine?
CH2-CH2-C(-NH2)=O
What is the side chain for cysteine?
CH2-SH
What are the pK values of tyrosine’s side chains?
COOH
What are the pK values of cysteine’s side chains?
COOH
What are the amino acids with acidic side chains?
Aspartic acid
Glutamic acid
What is the side chain of aspartic acid?
CH2-COOH
What is the side chain for glutamic acid?
CH2-CH2-COOH
What are the pK values for aspartic acid?
COOH
What are the pK values for glutamatic acid?
COOH
What are the amino acids with basic side chains?
Histidine
Lysine
Arginine
What is the side chain of histidine?
CH2-C=CH-NH-CH-NH
What is the side chain of lysine?
CH2-CH2-CH2-CH2-NH3
What is the side chain of arginine?
CH2-CH2-CH2-NH-C(-NH2)=NH2
What are the pK values of histidine?
COOH
What are the pK values of lysine?
COOH
What are the pK values of arginine?
COOH
Which amino acids have hydrogen in their side chain that will dissociate?
ALL ACIDIC side chains
- Aspartic acid
- Glutamic acid
ALL BASIC side chains
- Histidine
- Lysine
- Arginine
SOME UNCHARGED POLAR side chains
- Tyrosine
- Cysteine
NO NONPOLAR side chains
Fig. 1.3
Label and caption the image
Classification of the 20 amino acids commonly found in proteins, according to the charge and polarity of their side chains at acidic pH (continued from Figure 1.2).
UNCHARGED POLAR SIDE CHAINS
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine
ACIDIC SIDE CHAINS
Aspartic acid, Glutamatic acid
BASIC SIDE CHAINS
Histidine, Lysine, Arginine
What are the properties of amino acids with nonpolar side chains?
Each of these amino acids has a nonpolar side chain that does not gain or lose protons or participate in hydrogen or ionic bonds (Figure 1.2).
What happens to the protons in amino acids with nonpolar side chains?
They are not gain or lost
What is the bonding of amino acids with nonpolar side chains?
They do not participate in hydrogen or ionic bonds (Figure 1.2).
How can the side chains of nonpolar amino acids be thought of as?
“Oily” or lipid-like
What interactions do amino acids with nonpolar side chains make?
Hydrophobic interactions
Describe the interactions of nonpolar amino acids and explain why they occur?
Nonpolar side chains do not:
- Gain or lose protons
- Participate in hydrogen or ionic bonds
They can be thought of as:
- “Oily” or lipid-like
- Promote hydrophobic interactions
(Figure 2.10)
What sort of environment is an aqueous solution?
A polar environment
Give an example of a polar environment
In aqueous solutions
Where are nonpolar amino acids found in aqueous solutions?
Aqueous solutions are polar, so the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein (Figure 1.4).
What is the hydrophobic effect?
Nonpolar amino acids clustering together in the interior of the protein in a polar environment e.g. aqueous solution
Nonpolar amino acids tend to cluster together in the interior of a protein in nonpolar amino acids. What is this effect known as?
The hydrophobic effect
What is the hydrophobic effect the result of?
The hydrophobicity of the nonpolar R-groups
Why does the hydrophobic effect occur in aqueous solution?
The hydrophobicity of the nonpolar R-groups act like droplets of oil that coalesce in an aqueous environment.
Where do nonpolar R-groups lie in proteins found in aqueous solutions?
They fill up the interior of the folded protein, to help give it its three-dimensional shape.
Where are nonpolar amino acids found in hydrophobic environments?
The nonpolar R-groups are found on the outside surface of the protein (Fig. 1.4)
Give an example of a hydrophobic environment.
A membrane
A membrane is an example of what type of environment?
A hydrophobic environment
Why are nonpolar R-groups found on the outside surface of the protein in membranes?
Membranes are hydrophobic environments, so the R-groups interact with the lipid environment (Fig. 1.4).
What are the hydrophobic interactions of nonpolar amino acids important for?
These hydrophobic interactions are important in stabilising tertiary protein structure
What is the location of nonpolar amino acids in proteins?
The NONPOLAR amino acid side chains interact with HYDROPHOBIC environments.
Therefore, in AQUEOUS solutions, a POLAR environment, nonpolar amino acids cluster together on the INSIDE of the protein,
Whereas in MEMBRANES, a HYDROPHOBIC environment, they cluster together on the OUTSIDE of the protein.
Fig. 1.4
Label and caption the image
Soluble protein
- Nonpolar amino acids cluster in the interior of soluble proteins.
- Polar amino acids cluster on the surface of soluble proteins.
Membrane protein
- Nonpolar amino acids cluster on the surface of membrane proteins. (Cell membrane)
Location of nonpolar amino acids in soluble and membrane proteins.
Draw the location of nonpolar and polar amino acids in a soluble protein (aqueous solution) and a membrane protein.
Soluble protein (i.e. aqueous solution - polar environment) - Nonpolar inside; polar outside
Membrane protein (hydrophobic environment) - Nonpolar inside the cell membrane
[Clinical]
What is sickle cel anaemia?
A sickling disease of red blood cells
A sickling disease of red blood cells is known as?
Sickle cell anaemia
[Clinical]
What is the pathophysiology of sickle cell anaemia?
The substitution of polar glutamate by nonpolar valine at the sixth position in the beta subunit of haemoglobin
[Clinical]
What amino acid is substituted in sickle cell anaemia?
Glutamate for valine
What is the significance of the glutamate to valine substitution in sickle cell anaemia?
Glutamate - polar
Valine - nonpolar
At which structural position is valine substituted for glutamate in sickle cell anaemia (a haemoglobinopathy)?
The sixth position in the b subunit of haemoglobin
How does proline differ from other amino acids?
Proline’s side chain and a-amino N form a rigid, five-membered ring structure (Figure 1.5).
Which amino acid has a rigid, fibre-membered ring structure?
Proline (via its side chain and a-amino N)
Describe proline’s amino group.
Proline has a secondary (rather than a primary) amino group (due to its five-membered ring structure).
(The N is bound to two R groups - the central carbon atom and a methane group to form a ring)
What is the classification of amino groups?
Primary, secondary, tertiary
The number relates to the amount of R groups bound to the N
Primary = R1-NH2 Secondary = R1-R2-NH Tertiary = R1-R2-R3-N
What is proline an example of?
An imino acid
Which of the 20 amino acids made from DNA is frequently referred to as an imino acid?
Proline
What is an imino acid?
A molecule that contains both imino (>C=NH) and carboxyl (COOH) functional groups.
What is the difference between an amino and imino acid?
Amino acids have amines: a functional group that contain a basic nitrogen atom with a lone pair
Imino acids have imines: a functional group containing a carbon-nitrogen double bond
What is the biological relevance of the unique geometry of amino acid proline?
- Contributes to the formation of the fibrous structure of collagen
- Interrupts the a-helices found in globular proteins
What amino acid contributes to the formation of the fibrous structure of collagen?
Proline
What amino acid often interrupts the a-helices found in globular proteins?
Proline
Fig. 1.5
Label the secondary and primary amino group. Name the amino acids and caption it.
Comparison of the secondary amino group found in proline with the primary amino group found in other amino acids, such as alanine.
Secondary amino group - Proline
Primary amino group - Alanine
Draw the structure of an amino acid with a secondary amino group and the structure of an amino acid with a primary amino group.
Secondary - proline R2-NH2
Primary - alanine R1-NH3
Describe the properties of amino acids with uncharged polar side chains.
These amino acids have zero net charge at neutral pH
Which uncharged polar amino acids can lose a proton from their side chains?
Cysteine and tyrosine (at alkaline pH)
At what pH can cysteine and tyrosine can lose a proton at what pH?
Alkaline (see Figure 1.3).
What do serine, threonine and tyrosine have in common?
They are amino acids with uncharged polar side chains, which each contain a polar hydroxyl group
Which amino acids contain a polar hydroxyl group?
Serine, threonine and tyrosine
What are the reactive properties of serine, threonine and tyrosine?
They have a polar hydroxyl group, so they can participate in hydrogen bond formation (Figure 1.6)
What do the side chains of asparagine and glutamine contain?
A carbonyl (C=O) and an amide (-NH2) group
Which amino acids contain a carbonyl and an amide group?
Asparagine and glutamine
What are the electrochemical properties of asparagine and lgutamine?
They both contain a carbonyl group and an amide group - both of which can also participate in hydrogen bonds.
What are the electrochemical properties of nonpolar uncharged amino acids?
These can either lose a proton (at alkaline pH) or participate in hydrogen bonds.
Fig. 1.6
Label and caption the diagram.
Hydrogen bond between the phenolic hydroxyl group of tyrosine and another molecule containing a carbonyl group.
Tyrosine
Hydrogen bond
Carbonyl group
Draw a hydrogen bond between the side chain of tyrosine and another molecule containing a carbonyl group.
Tyrosine (H3N-C(-COOH)-H)
-CH2-benzene ring-OH
H hydrogen bonded to O=C (carbonyl group)
See Figure 1.6
What is special about the amino acid cysteine?
The side chain contains a sulfhydryl group (-SH)
Which amino acid contains a sulfhydryl group (-SH)?
Cysteine
Why is cysteine biological important?
Its side chain contains a sulfhydryl group (-SH), which is an important component of the active site of many enzymes.
Which amino acid is an important component of the active site of many enzymes and why?
Cysteine, because it contains a sulfhydryl group (-SH).
What can occur to two cysteines in proteins?
The -SH groups of two cysteines can become oxidised to form a dimer (cystine).
What happens when two -SH groups from two cysteines become oxidised to form a dimer?
This creates a covalent cross-link called a disulfide bond.
What type of bond is a disulfide bond?
Covalent bond between two sulfurs (-S-S-)
Which amino acid can form disulfide bonds?
Cysteine (because it has an -SH group)
What is the biological significance of disulfide bonds?
Many extracellular proteins are stabilised by disulfide bonds.
Give an example of extracellular protein stabilisation.
Disulfide bonds (from cysteine residues; -S-S-).
What is albumin?
A blood protein that functions as a transporter for a variety of molecules
What blood protein is stabilised by disulfide bonds?
Albumin
Which amino acids can be phosphorylated?
Serine, threonine and rarely, tyrosine.
What is phosphorylation?
Addition of a phosphate group
Why can serine, threonine and (rarely) tyrosine be phosphorylated?
Due to their polar hydroxyl group on their side chain, acting as a site of attachment
Which amino acids can serve as sites of attachment for oligosaccharide chains in glycoproteins?
Asparagine, serine or threonine
How do asparagine, serine or threonine act as a site of attachment for oligosaccharide chains in glycoproteins?
Asparagine - amide group
Serine or threonine - hydroxyl group
Define oligosaccharide chains in glycoproteins.
Oligosaccharide - “few sugars” - a small amount of monosaccharide units forming a carbohydrate
Glycoproteins - proteins with carbohydrate groups attached to the polypeptide chain
Which amino acids are proton donors?
Aspartic and glutamic acid (acidic side chains).
Amino acids with acidic side chains are proton ______
donors
Amino acids that are proton donors have ______ side chains
acidic
How are aspartic and glutamic acid found at physiologic pH?
The side chains are FULLY IONISED, containing a NEGATIVELY charged carboxylate group (-COO-)
How do aspartic and glutamic acid appear in their fully ionised form?
Negatively charged carboxylate group (-COO-)
When are aspartic and glutamic acid found with a negatively charged carboxylate group?
At physiologic pH (side chains fully ionised).
What is the name of aspartic and glutamic acid at physiologic pH?
Aspartate and glutamate, respectively
this emphasises that these amino acids are negatively charged at physiologic pH - see Figure 1.3
Which amino acids accept protons?
Basic amino acids (see Figure 1.3)
Amino acids with basic side chains are proton ______
acceptors
Amino acids that are proton acceptors have ______ side chains
basic
How do lysine and arginine appear at physiologic pH?
Their side chains are fully ionised and positively charged
Which amino acids have fully ionised and positively charged side chains at physiologic pH?
Arginine and Lysine
How does histidine appear at physiologic pH?
It is weakly basic, so the free amino acid is largely uncharged
Which amino acid is weakly basic?
Histidine
What are the properties of a weakly basic amino acid?
E.g. histidine; its free amino acid is largely uncharged
What form does histidine take when incorporated into a protein?
This depends on the ionic environment provided by the polypeptide chains of the protein; so can be positively charged or neutral.
Why can histidine be positively charged or neutral?
Because it is weakly basic, so it depends on the ionic environment surrounding it
What is the biological relevance of histidine?
Histidine is weakly basic so can have a positively charged or neutral status depending on its environment.
This is significant because it contributes to the role it plays in the functioning of proteins such as haemoglobin (see Mechanisms of the Bohr effect).
Why is histidine important in haemoglobin?
Histidine is weakly basic so can have a positively charged or neutral status depending on its environment.
This is significant because it contributes to the role it plays in the functioning of proteins such as haemoglobin (see Mechanisms of the Bohr effect).
