Session 4.3b - Lecture 1 - Protein Structure Flashcards
Slides 12-23
Which amino acids have positively charged side chains?
Lysine
Arginine
Histidine (usually - although this is a little bit weird)
Which amino acids have negatively charged side chains?
Glutamate
Aspartate
What is different about histidine compared to the rest of its group? Name the other members of its group.
Histidine is an amino acid with a positively charged side chain, so is basic. However, it is weakly basic compared to lysine and arginine.
Glutamate and aspartate are part of which group?
Negatively charged side chains
Why are some amino acids positively or negatively charged?
This depends on the nature of the group - comes down to the pKa
What is the pKa?
The negative log (-log or p) of the acid dissociation constant (Ka)
What is Ka?
The acid dissociation constant
What is the acid dissociation constant?
Ka
What is the negative log of the acid dissociation constant named, and what does this determine?
pKa
(negative log [p] of acid dissociation constant [Ka])
Whether an amino acid is positively or negatively charged
What is pKR?
It is the pK specifically related to the pK value of the side chain of an amino acid, not thinking about the rest of the amino acid residue.
What do we denote the pK specific to an amino acid side chain?
pKR
What is the pKR value of lysine?
10.5
What are the pK values of Lysine, Arginine and Histidine?
Higher
Lysine 10.5
Arginine 12.5
Histidine 6.0
What does the pK value mean?
The pK value is the pH at which there’s no overall net charge on an acid or a base
OR
The point where there’s equal amounts of protonated and deprotonated forms (1:1 relationship)
The pH at which there’s no overall net charge on an acid or a base is called what?
pK
The point where there’s equal amounts of protonated and deprotonated forms (1:1 relationship) can be represented by what?
The pK value
Lysine has a pK value of 10.5. At what pH will lysine have no net charge?
10.5
Lysine has a pK value of 10.5. At what pH will there be equal protonated and deprotonated forms of lysine?
10.5
In what form does lysine appear at physiological pH?
Physiological pH is ~7.4.
Lysine has a pKa of 10.5.
This means it is always protonated at physiological pH (accepted a proton) and in positive charge form.
How do glutamate and aspartate appear at physiological pH?
These appear as anions, ionised forms of glutamic acid and aspartic acid
This means they have donated their protons and have become negatively charged.
What does it mean for their pK value if glutamate and aspartate are negatively charged at physiological pH?
They have low pK values.
What are the pK values of Glutamate and Aspartate?
Glutamate 4.3
Aspartate 2.8
(Lower)
Positively charged R groups have a _____ pKR value?
higher
Negatively charged R groups have a _____ pKR value?
lower
If the pH of the solution < the pK value then the group will be __________
protonated
general rule - note pK is lazy, should write pKa
If the pH of the solution > the pK value then the group will be __________
deprotonated
general rule - note pK is lazy, should write pKa
If the pH of the solution ____ the pK value then the group will be protonated
Fill in the blank, choose ONE:
Less than <
Equal =
More than >
Less than
<
(general rule - note pK is lazy, should write pKa)
If the pH of the solution ____ the pK value then the group will be deprotonated
Fill in the blank, choose ONE:
Less than <
Equal =
More than >
More than
>
(general rule - note pK is lazy, should write pKa)
Why do lysine and arginine appear protonated at physiological pH?
Physiological pH ~7
Their pK values are higher than pH so they are protonated
Why do glutamate and aspartate appear deprotonated at physiological pH?
Physiological pH ~7
Their pK values are lower than pH so they are deprotonated
What charge do lysine and arginine have a physiological pH?
+ve because their pK values are higher than the pH, thus are protonated
What charge do glutamate and aspartate have a physiological pH?
-ve because their pK values are lower than the pH, thus are deprotonated
Protonated and deprotonated does not necessarily mean what?
That things have a positive or negative charge.
What is physiological pH?
7.4
~7
What is the predominant form of each of the following amino acids shown below?
Lysine pK = 10.5
CH2CH2CH2CH2NH2 + H+ CH2CH2CH2CH2NH3+
CH2CH2CH2CH2NH3+
If the pH of the solution < the pK value then the group will be protonated
(positively charged)
What is the predominant form of each of the following amino acids shown below?
Aspartate pK = 2.8
CH2COOH CH2COO- + H+
CH2COO-
If the pH of the solution > the pK value then the group will be deprotonated
(negatively charged)
Is lysine postively or negatively charged at physiological pH?
Physiological pH = 7.4
pH < pK so group is protonated
= positively charged
Is aspartate postively or negatively charged at physiological pH?
Physiological pH = 7.4
pH > pK so group is deprotonated
= negatively charged
What are the chemical structures for aspartate and aspartic acid?
Aspartate = CH2COO-
Aspartic acid = CH2COOH
Will you find lysine in its deprotonated form at physiological pH?
YES, just because the PREDOMINANT form of it will be protonated at physiological pH, doesn’t mean there aren’t any other molecules of the deprotonated form, just that the protonated form is much more likely.
(Remember it is an equilibrium equation, and Henderson-Hasselbach can be used to work out the ratio of protonated:deprotonated)
Will you find aspartate in its protonated form at physiological pH?
YES, just because the PREDOMINANT form of it will be deprotonated at physiological pH, doesn’t mean there aren’t any other molecules of the protonated form, just that the deprotonated form is much more likely.
(Remember it is an equilibrium equation, and Henderson-Hasselbach can be used to work out the ratio of protonated:deprotonated)
Will you find lysine in its protonated form at physiological pH?
Yes, predominantly
Will you find arginine in its deprotonated form at physiological pH?
Yes, predominantly
How can we work out the proportions of a protonated:deprotonated amino acid in solution, such as lysine?
Via the Henderson-Hasselbalch equation
What can you use the Henderson-Hasselbalch equation for?
Working out the proportions of protonated:deprotonated amino acids in solution.
What do we get when put amino acids together?
A protein
When amino acids form a protein, what structural levels do we get?
4 different levels of protein structure (primary, secondary, tertiary and quaternary structure)
The ‘beads on a string model’ refers to which level of protein structure?
Primary structure.
What is the primary structure?
The linear amino acid sequence of the polypeptide chain
What does the primary structure tell us?
Only tells us which different amino acids come on one after another.
How do we notate the amino acid structure in a protein?
We write them down from N terminus to C terminus left to right, by convention.
- If not specified we assume it is this way around by convention (similar to 5’ and 3’ DNA).
What is the secondary structure?
Local spatial arrangement of polypeptide backbone - the conformations like helices etc.
(small sequence of our protein folding into standard conformation)
Which structure of the protein is responsible for a small sequence of the protein folding into standard conformation?
The secondary structure
What is the tertiary structure?
The overall 3- dimensional configuration of the protein
What gives us the overall 3D structure of the protein?
Localised regions can further fold up to give the overall 3D structure
Localised regions of the protein can further fold up to give us what?
The overall 3D structure/tertiary structure
In textbooks, which structure is typically depicted for proteins?
The tertiary structure
What is the quaternary structure?
Association between different polypeptides to form a multi-subunit protein
Which structure of proteins is not seen in all proteins?
The quaternary structure is not seen in all proteins but in probably quite a lot of them.
Which structures involves interaction between >1 polypeptide?
The quaternary structure
In the quaternary structure, where is one linear amino acid chain?
One linear amino acid chain = one polypeptide sequence
So in the quaternary structure this is one subunit
> 1 subunit gives a quaternary structure, involving proteins fitting together
Fig. 14
Label the image
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Draw the four structures of a protein.
See slide 14
Primary - Lys-Lys-Gly-Gly-Leu-Val-Ala-His
Secondary - alpha-helix
Tertiary - 3D configuration
Quaternary - >1 subunit
Why do proteins fold up/how can they fold up?
This comes down to do with the chemical nature of proteins themselves - the basis for all the folding is to do with the peptide bond which joins the 2 amino acids together.
What is peptide bond formation?
The linking of two amino acids is accompanied by the abstraction of a molecule of water
What is the basis for all the folding in a protein?
The peptide bond
What type of reaction is a peptide bond?
Condensation reaction (removal of water)
Which groups react to form a peptide bond?
The carboxyl group and amino group
What atoms are bonded in a peptide bond?
Carbon - nitrogen
What are the functional groups involved in a peptide bond?
Carboxyl group (COO-) to form a carbonyl oxygen (C=O)
Amino group (NH3+) to form an amide group (N-H)
Fig. 15
Label the equation.
Amino acid 1 + amino acid 2
–removal of water–>
peptide with amino terminus, peptide bond and carboxyl terminus.
Draw the formation of a peptide bond.
[AA]R1 + [AA]R2 --H2O--> NH3+ amino terminus -H-C-R1- O=C-N-H peptide bond -H-C-R2- COO- carboxyl terminus
Why is the peptide bond important?
Peptide bonds are:
- planar
- rigid
- exhibit a trans conformation
- bonds on either side of it are free to rotate
Fig. 16
What does this image show?
Several amino acids joined together, with alpha carbons from constituent amino acids together.
Peptide bond (C-N) visible from the carbonyl-oxygen (C=O) and amide-hydrogen (N-H)
What is the peptide unit?
One central carbon to the next
Fig. 16
If we took a peptide unit and turned it around to face you, what would you see?
It is all in one plane; they’re flat (planar).
What part of a protein is planar?
Peptide bonds
Which atoms all line in one plane?
Ca, C, O, N, H and Ca all aline in the same plane
Fig, 16
Label the image
Amino terminus
Draw a peptide containing 4 amino acids in planar structure, and label.
See Fig. 16
Is there movement in amino acids?
Peptide bonds are planar/flat in structure, but there is movement around some of the other things.
What configuration do peptide bonds lie in?
PLANAR
Can peptide bonds move?
No, they are RIGID
Can C-N bonds rotate?
Normally, they can yes, but they are rigid in peptide bond.
Why are peptide bonds unable to rotate?
Although C-N bonds can rotate in other molecules, peptide bonds undergo DELOCALISATION, creating resonance forms.
Delocalisation does what to a peptide bond?
Makes it rigid and unable to rotate
What are resonance structures in proteins?
Delocalisation of electrons in a peptide bond, causing rigidity of the C-N bond.
Why do we get delocalisation in peptide bonds?
These electrons that are important to making up this carbonyl bond in the protein delocalise across the C-N bond.
What does delocalisation/resonance forms mean for the peptide bond in proteins?
The electrons from the C=O bond can delocalise over the C-N bond, giving the C-N bond partial double bond characteristics (e.g. rigidity, planar, shorter)
What are double bond characteristics, and how can they apply to peptide bonds?
The electrons from the C=O bond can delocalise over the C-N bond, giving the C-N bond partial double bond characteristics.
Double bonds in things like alkanes are inflexible, whereas things can rotate around a single bond, hence giving rigidity in the single C-N bond.
Fig. 17
Label the image
Peptide-bond resonance structures
What does delocalisation mean for bond length in the peptide bond?
Delocalisation of the C=O means C-N bond has double bond characteristics.
This means the C-N bond is a little bit shorter than you’d expect it to be (reminiscent more of a double bond than a single bond).
What does a shorter bond length mean?
A shorter bond length means a bond is a little stronger.
Draw the peptide-bond resonance structures
C-C=O-N-H-C
C-C-O-=N+-H-C
Why are peptide bonds rigid?
Due to the delocalisation of electrons from the C=O to the C-N, giving it double bond characteristics.
What does the delocalisation of a peptide bond mean for the partial charges?
The O=C-N becomes an O–C=N+
What does the delocalisation of electrons from the C=O affect the properties of the peptide (C-N) bond?
The peptide bond C-N has partial double bond characteristics.
Unable to rotate - contributes to planarity
Peptide bonds can feature in different conformations. What are they?
- Trans
- Cis
What is the trans conformation of a peptide bond?
Carbonyl-oxygen (C=O) on one side of the bond and amide-hydrogen (N-H) on another.
What is the conformation when the C=O and N-H bonds are on opposite sides?
Trans
What is the cis conformation of a peptide bond?
Carbonyl-oxygen (C=O) on one side of the bond and amide-hydrogen (N-H) on the SAME.
What is the conformation when the C=O and N-H bonds are on the same side?
Cis
As well as the C=O and N-H being on the same side on Cis conformations, what other groups are on the same side?
The R groups
What conformation are proteins ALWAYS in?
Trans
Why do we not find proteins in the Cis conformation?
The R groups are much closer together, thus causing steric hindrance
Why is it important that proteins are in the trans orientation?
This allows the peptide bonds to have flexibility
Which part of the protein is rigid and planar and which part can rotate?
Peptide bonds are rigid and planar but the bonds on either side of them can rotate.
What are the properties of a trans conformation in peptide bonds?
Ca on opposite sides of peptide bond
What are the properties of a cis conformation in peptide bonds?
Ca on same sides of peptide bond
Steric clashes
Fig. 18
Label the image
Trans - Ca on opposite sides of peptide bond
Cis - Ca on same side of peptide bond
Steric clashes
Draw a trans and cis conformation of proteins.
Trans - Ca on opposite sides of peptide bond (1)
Cis - Ca on same side of peptide bond (1) Steric clashes (1)
What is the Cα-N bond called in amino acids?
Phi bond
What is the Phi bond?
Cα-N single bond
What is the Cα-C bond called?
Psi bond
What is the Psi bond?
Cα-C single bond
What does this symbol notate?
ψ
Psi in the Greek alphabet
What does this symbol notate?
φ
Phi in the Greek alphabet?
What is the symbol for Psi in the Greek alphabet?
ψ
What is the symbol for Phi in the Greek alphabet?
φ
What is the significance of the Psi and Phi bonds?
These can rotate, allowing not any conformation but lots of different bond angles, leading to flexibility and therefore development of our 3D structure and proteins.
What part of the protein can rotate to give us flexibility?
The Psi (C-C) and Phi (C-N) bonds
Fig. 19
Label the image
Psi and Phi bond appropriately labelled
Psi - Cα-C
Phi - Cα-N
Draw a short peptide depicted a psi and phi bond.
-N-H-C–H-R-C=O-N-H-phi-C-H–R-psi-C=O-N-H-C-H-R-C=O
What forms a protein?
Amino acids joined by peptide bonds
What does the amino acid sequence of a protein determine?
- The way in which the polypeptide chain folds
- The physical characteristics of the protein
What are the physical characteristics and the way a protein folds determined by?
The amino acid sequence of a protein
What is the importance of amino acids in proteins?
It allows them to come in a huge variety of shapes, forms and have different characteristics.
Fig. 20
Label this image
Amino-terminal end
Carboxyl-terminal end
Red = R groups
Yellow = Peptide bond
Serine, glycine, tyrosine, alanine and leucine
Draw the protein of serine, glycine, tyrosine, alanine and leucine.
NH3+ Amino-terminal end
C-H-
O=C-N-H repeated
Coo- carboxyl-terminal end
Serine = CH2OH Glycine = H Tyrosine = CH2-benzene-OH Alanine = CH3 Leucine = CH2-CH-CH3-CH3
What are the electrical characteristics of a protein defined by?
Its isoelectric point (pI)
What is the isoelectric point (pI) of proteins?
The isoelectric point, pI, of a protein is the pH at which there is no overall net charge.
How is the pI calculated?
Basically, it is the pKa of the entire protein.
Name a protein with a pI of ~1 and a protein with a pI of 11.
Pepsin, pI = <1.0
Lysozyme, pI = 11.0
Name some acidic proteins.
Protein/pI
Pepsin <1.0 Egg albumin 4.6 Serum albumin 4.9 Urease 5.0 β-lactoglobulin 5.2 Haemoglobin 6.8
Name a neutral protein
Protein/pI
Myoglobin 7.0
Name some basic proteins.
Protein/pI
Chymotrypsinogen 9.5
Cytochrome c 10.7
Lysozyme 11.0
Name the functions of the following proteins.
Pepsin Egg albumin Serum albumin Urease β-Lactoglobulin
Pepsin - digestive enzyme
Egg albumin - egg white
Serum albumin - found in blood
Urease - hydrolyses urea
β-Lactoglobulin - protein in cow/sheep’s milk
Name the functions of the following proteins.
Haemoglobin Myoglobin Chymotrypsinogen Cytochrome c Lysozyme
Haemoglobin - transports oxygen in blood
Myoglobin - iron/oxygen binding in muscle tissue
Chymotrypsinogen - inactive precursor of chymotrypsin (digestive enzyme)
Cytochrome c - haem protein
Lysozyme - glycoside hydrolase, breaks down cell walls in peptidoglycans
Why do proteins have different isoelectric points?
It depends on the amino acid residues that make them up, as all side chains have a certain pK value so will contribute to this.
i.e. basic proteins have lots of basic amino acids e.g. lysines, arginines
acidic proteins have lots of acidic amino acids e.g. glutamate, aspartate
What does a pI > 7 mean?
Basic proteins
Contain many positively charged (basic) amino acids (accepted a proton)
What does a pI < 7 mean?
Acidic proteins
Contain many negatively charged (acidic) amino acids (donated a proton)
What are most protein’s pI?
~5-8, but certain ones will be much higher or much lower.
Why do proteins have different pI points?
Due to the function of the protein in the cell.
e.g. a protein that’s positively charged will want to interact with something negatively charged
Amino acids contribute to what in the protein?
Structure - chemical bonding
Function - due to electrical properties (pI) and what it can then interact with.
If pH < pI protein is _________
protonated
If pH > pI protein is _________
deprotonated
If pH ___ pI protein is protonated
If pH ___ pI protein is deprotonated
>
What is the average size of a protein?
Biologically active peptides and proteins come in a varying range of sizes,
(When we’re talking about proteins <100 AA residues, we call them peptides)
Define peptide/oligopeptide
A few amino acids in length, generally <100 amino acid residues
Define polypeptide/protein
Many amino acids, generally >100 amino acid residues
What is the word(s) for a small protein?
Peptide/oligopeptide
What is the word(s) for a protein sequence longer than >100 amino acid residues?
Polypeptide/protein
Give an example of an important small peptide in the body.
Angiotensin II (8 amino acids)
What is angiotensin II derived from?
Angiotensinogen (~425 amino acids)
What is angiotensin II?
A potent vasoconstrictor molecule which binds strongly to angiotensin receptors, regulating blood pressure
Why is angiotensin II important clinically?
Angiotensin receptor blockers can be made which mimic the structure of angiotensin II, getting in the way of it binding to the receptors and its vasoconstriction.
This will lower the blood pressure and thus can be important in hypertension.
What is angiotensin II structure be used to treat?
Hypertension
How can angiotensin II structure be used to lower blood pressure?
Angiotensin receptor blockers can be made which mimic the structure of angiotensin II, getting in the way of it binding to the receptors and its vasoconstriction.
This will lower the blood pressure and thus can be important in hypertension.
What is the amino acid sequence of angiotensin II?
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe
What is the function of cytochrome c important in?
The electron transport chain
What is a Dalton?
A measure of molecule weight in a ratio related to the weight of a hydrogen atom.
What is the function of Apolipoprotein B?
Important in transport of dietary lipids around body
What do protein sizes range from?
e.g.
Molecular weight/number of residues/number of polypeptide chains
Cytochrome c = 13,000/104/1
Apolipoprotein B = 513,000/4,536/1
Table 22
Label the proteins listed that are found in humans
Cytochrome c
Haemoglobin
Serum albumin
Apolipoprotein B
Table 22
Label the proteins listed that are found in animals
Ribonuclease A (bovine pancreas) Lysozyme (chicken egg white) Myoglobin (equine heart) Chymotrypsin (bovine pancreas) Chymotrypsinogen (bovine)
Table 22
Label the proteins listed that are found in bacteria/yeast.
Hexokinase (yesat) RNA polymerase (E. coli) Glutamine synthetase (E. coli)
Table 22
Name the molecular weight ranges from humans, animals and bacteria/yeast
Human - 13,000 - 513,000
Animal - 13,700 - 22,000
Yeast/bacteria - 102,000 - 619,000
Table 22
Name the number of residues ranges from humans, animals and bacteria/yeast
Human - 104 - 4,536
Animal - 124 - 245
Yeast/bacteria - 972 - 5,628
Table 22
Name the proteins with no quaternary structure
= 1 polypeptide chain
Cytochrome c Ribonuclease A Lysozyme Myoglobin Chymotrypsinogen Serum albumin Apolipoprotein B
Table 22
Name the proteins with a quaternary structure
= >1 polypeptide chain
Hexokinase (2) Chymotrypsin (3) Haemoglobin (4) RNA polymerase (5) Glutamine synthetase (12)
How many residues does cytochrome c contain and what is its molecular weight?
(small)
104 residues
13,000 Daltons
(small)
How many residues does apolipoprotein B contain and what is its molecular weight?
(large)
4,536 residues
513,000 Daltons
(large)
What is the molecular weight of the largest known protein and how many amino acids does it contain?
Hint: we know glutamine synthetase has 619,000 amino acid residues
Hint: we know glutamine synthetase has 619,000 amino acid residues
Titin
Molecular weight = 2,993,000
1 polypeptide chain
What is the function of titin?
It is an aptly named giant protein that is part of the sarcomeric apparatus in cardiac myocytes. It has 1 polypeptide chain
(almost 3 million Daltons in molecular weight/~27,000 amino acid residues)
How many amino acid residues does titin contain?
Average Mw of 1 amino acid = 110
So approximately 27,000 amino acid residues
What is the average molecular weight of 1 amino acid?
110 Da
Protein sizes can range, give 2 examples
Cytochrome c - 104 amino acids
Titin - 27,000 amino acids
What is a conjugated protein?
A protein that is covalently linked to chemical components in addition to amino acids.
What do we call a protein that is covalently attached to other things?
Conjugated proteins
What are lipoproteins attached to, and give an example.
Lipids
B1-Lipoprotein of blood
What are glycoproteins attached to, and give an example.
Carbohydrates
Immunoglobulin G
What are phosphoproteins attached to, and give an example.
Phosphate groups
Casein of milk
What are hemoproteins attached to, and give an example.
Haem (iron porphyrin)
Haemoglobin
What are flavoproteins attached to, and give an example.
Flavin nucleotides
Succinate dehydrogenase
Give examples of prosthetic groups metalloproteins can be attached to.
Iron Zinc Calcium Molybdenum Copper
Give an example of an iron metalloprotein.
Ferritin
Give an example of a zinc metalloprotein.
Alcohol dehydrogenase
Give an example of a calcium metalloprotein.
Calmodulin
Give an example of a molybdenum metalloprotein.
Dinitrogenase
Give an example of a copper metalloprotein.
Plastocyanin
What do lipo- and glycoproteins get attached to?
Important metabolic constituents
glyco- –> sugars
lipo- –> lipids
What is the function of phosphoproteins?
These add phosphate groups
- some of these are natural
- other proteins, this is used as a key regulatory mechanism, where you can control many enzymes and proteins by phosphorylation status.
What type of conjugate protein is often used to control enzymes and proteins?
Phosphoproteins - as they can be controlled by phosphorylation status.
What is succinate dehydrogenase?
A flavoprotein (adds flavin nucleotides as a synthetic group) that is a glycolytic enzyme
What do phospho- and flavoproteins have in common?
They contain synthetic groups which is important for the protein to be active.
What is the significance of metal ions and proteins?
You can add a whole range of metal ions to some proteins that are important clinically.
