Proteins

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Amino Acid Structure

Amino acids are the monomers of polypeptides; there are 20 amino acids common to all living organisms.
Each amino acid has a central carbon atom (α carbon) bonded to an amine group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and an R group.
The R group is the variable part that makes each amino acid different; it determines properties such as whether the amino acid is acidic or basic, or polar or non-polar.
The R group can be as simple as a hydrogen atom (glycine) or as complex as an aromatic ring (phenylalanine).
In a neutral environment, the carboxyl group donates a hydrogen ion (becoming negative) and the amine group accepts a hydrogen ion (becoming positive).

General structure of an amino acid

Peptide Bond Formation

A peptide bond forms between the carboxyl group of one amino acid and the amine group of another.
During peptide bond formation, a hydroxyl group (-OH) is lost from the carboxyl group and a hydrogen atom is lost from the amine group.
This is a condensation reaction, so water is released.
Dipeptides form from two amino acids; polypeptides form from three or more amino acids.
Hydrolysis breaks peptide bonds by adding water, splitting polypeptides back into amino acids.
The R group is not involved in peptide bond formation.

Forming a polypeptide

Dietary Requirements for Amino Acids

Humans can synthesise 11 non-essential amino acids from other amino acids.
The remaining 9 essential amino acids must be obtained from the diet.
A healthy, varied diet provides all essential amino acids; meat contains all nine, so vegetarian and vegan diets must be well balanced.
Diets that restrict certain foods may require supplementation to ensure all essential amino acids are consumed.

The Variety of Proteins

Protein diversity arises from the 20 amino acids, variation in polypeptide length (from a few to thousands), and differences in amino acid sequence.
The DNA base sequence determines the number and order of amino acids in a polypeptide.
For a polypeptide of 50 amino acids, there are 20⁵⁰ possible combinations (≈1.13 × 10⁶⁵); for an average protein of 300 amino acids, the number is effectively infinite.
Polypeptides are assembled at ribosomes by adding amino acids one by one; the mRNA codon determines which amino acid is added.
Proteins have many roles: enzymes (catalysis), blood clotting, structural fibres (collagen, keratin), transport (haemoglobin), cytoskeleton formation, cell adhesion, hormones, DNA compaction (histones), antibodies, membrane transport, and cell receptors.

Examples of Proteins

Rubisco (ribulose bisphosphate carboxylase) is a globular enzyme with 16 polypeptide chains that fixes CO₂ in photosynthesis; it is the most abundant enzyme on Earth.
Insulin is a short, globular hormone with 2 polypeptide chains, produced by β-cells in the pancreas; it binds to insulin receptors on liver, fat, and muscle cells to cause glucose absorption.
Immunoglobulins (antibodies) are globular proteins with a Y shape and highly variable binding sites, allowing them to bind millions of different antigens; they are the most diverse group of proteins.
Rhodopsin is a membrane protein in rod cells of the retina; it contains retinal (derived from vitamin A) and undergoes a conformational change when hit by a photon, sending a nerve impulse.
Collagen is a fibrous protein of three polypeptide chains forming a triple helix; it is the most abundant protein in the human body (~25%) and provides tensile strength in skin, blood vessels, and connective tissue.
Spider silk is a fibrous protein as strong as steel but lighter; it has rope-like and coiled parts, does not denature easily at extreme temperatures, and can be genetically engineered to be expressed in goats' milk.

Protein Structure: Effect of pH & Temperature

Protein structure is sensitive to temperature and pH because these factors affect the ionic interactions, hydrogen bonds, and other intermolecular forces that maintain the 3D shape.
Denaturation is the irreversible change of protein conformation; the bonds holding the shape are relatively weak and can be easily broken.
Denaturation alters the protein's shape, which may affect its function, physical state, and usefulness.
Each protein has an optimum pH at which its 3D structure is not denatured.
Denaturation is almost always irreversible, but small denaturations and renaturations can occur in some proteins (e.g., haemoglobin) in response to small pH fluctuations.
In egg white (albumin), heating causes hydrophobic amino acids to move to the edges, making the protein insoluble and forming a solid cooked layer.
In the stomach, low pH (pH 2) denatures dietary proteins; the enzyme pepsin has an optimum pH of 2.
Some extremophiles, such as Thermus aquaticus, have proteins stable at extreme temperatures (e.g., 80°C).

Levels of Protein Structure

Primary structure is the sequence of amino acids in a polypeptide; the DNA determines this sequence, and the precise position of each amino acid determines the final 3D shape.
Secondary structure arises from coiling or pleating of the amino acid chain, held together by hydrogen bonds between carbonyl (C=O) and amine (N-H) groups on parallel strands.
Secondary structure includes α (α) helices and β (β)-pleated sheets.
Tertiary structure is the complex 3D shape formed by folding of the secondary structure; it is determined by interactions between R groups.
Interactions in tertiary structure include hydrogen bonds between polar R groups, hydrophobic interactions between non-polar R groups and water, disulfide bridges between cysteine R groups, and ionic bonds between charged R groups.
Quaternary structure occurs when a protein consists of multiple polypeptide chains (subunits) functioning together; proteins with only one chain do not have quaternary structure.
Quaternary proteins can be conjugated (containing non-protein prosthetic groups) or non-conjugated (no non-protein components).
Haemoglobin is a conjugated protein with four polypeptide subunits, each containing a haem prosthetic group with an iron ion (Fe²⁺).
Insulin (two subunits joined by disulfide bridges) and collagen (three subunits wound into a helix) are non-conjugated proteins with quaternary structure.

Globular & Fibrous Proteins

Globular proteins are compact, roughly spherical, and soluble in water; they have hydrophobic R groups towards the centre and hydrophilic R groups on the outside.
The solubility of globular proteins allows them to be transported and to function in metabolic reactions; their specific shapes enable roles such as enzymes and immunoglobulins.
Some globular proteins are conjugated, e.g., haemoglobin contains the prosthetic group haem.
Fibrous proteins are long strands of polypeptide chains with cross-linkages from hydrogen bonds; they have little or no tertiary structure.
Fibrous proteins are insoluble in water due to a large number of hydrophobic R groups.
Fibrous proteins have a highly repetitive amino acid sequence, creating strong, organised structures suitable for structural roles (e.g., keratin in hair and nails, collagen in connective tissue).
Collagen is formed from three polypeptide chains held by hydrogen bonds into a triple helix, giving great tensile strength; covalent cross-links between R groups hold triple helices together to form fibrils.
Collagen fibres are aligned with the forces they withstand; they are found in tendons, cartilage, ligaments, bones, teeth, skin, blood vessel walls, and the cornea.

Protein Imaging Technology

Cryogenic electron microscopy (cryo-EM) rapidly freezes protein solutions and exposes them to electrons to produce images.
Cryo-EM allows reconstruction of the 3D shape of proteins and visualisation of their interactions with other molecules.
Unlike X-ray crystallography, cryo-EM does not require crystallisation, which can be time-consuming, may fail for some proteins, and removes contextual information by visualising proteins outside the cell.

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練習問題

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1.Which of the following is the monomer of a polypeptide?
Easy
- AAmino acid
- BNucleotide
- CMonosaccharide
- DGlycerol
2.The following diagram of a dipeptide has four parts numbered 1 to 4. Part 1 is the group -NH2, part 2 is the group -COOH, part 3 is the bond joining the two amino acids, and part 4 is the variable side chain. Which row of the table correctly identifies each labelled part?
Easy
- A1 = Amino group, 2 = Carboxyl group, 3 = Peptide bond, 4 = R-group
- B1 = Carboxyl group, 2 = Peptide bond, 3 = R-group, 4 = Amino group
- C1 = R-group, 2 = Amino group, 3 = Peptide bond, 4 = Carboxyl group
- D1 = Amino group, 2 = Peptide bond, 3 = R-group, 4 = Carboxyl group
3.Which of the following is not a function of proteins?
Easy
- AActing as a store of chemical potential energy in cells
- BForming the cytoskeleton within a cell that facilitates chromosome movement
- CActing as chemical messengers that are secreted by glands and act on different parts of the body
- DSpeeding up chemical reactions within a cell
4.A simple tetrapeptide consists of four amino acids. How many different combinations of amino acids would be possible for this peptide?
Medium
- A160 000
- B16 000
- C1 600 000
- D16 000 000
5.Which of the following are all examples of proteins?
Medium
- ARhodopsin, immunoglobulins, rubisco
- BRubisco, collagen, amylopectin
- CAmylopectin, collagen, guanine
- DInsulin, amylose, spider silk
6.Which of the following is involved in the secondary structure of a protein? I. Double helix II. β-pleated sheets III. Hydrogen bonds IV. Hydrophobic interactions
Medium
- AII and III
- BI and II
- CI, II and III
- DII, III and IV
7.Amino acids consist of oxygen, hydrogen, carbon and nitrogen atoms. Using bond-length data, the approximate length of one amino acid is 0.7 nm. What would be the approximate length of a dipeptide of this amino acid after a condensation reaction has occurred?
Medium
- A1.2 nm
- B1.0 nm
- C1.4 nm
- D1.6 nm
8.Which of the following chemical groups does not bond directly with the central carbon of an amino acid?
Medium
- A-OH
- B-NH2
- C-COOH
- D-H

もっと問題

9.All life (except a few primitive prokaryotic species) uses the same 20 amino acids joined into polypeptides. Which of the following is not a possible hypothesis for why all life uses the same 20 amino acids?
Medium
- APolypeptide chains join together to increase the range of possible functions that they can carry out
- BOnly the 20 amino acids existed when life began, so all life now uses them
- CAll organisms share a common ancestor, so the link between the genetic code and amino acid sequences is already fixed
- D20 amino acids is more than enough to give a huge, almost infinite range of characteristics for all life
10.Which of the following causes fibrous polypeptides to be insoluble?
Medium
- ATheir surface has nonpolar amino acids
- BThey are very long
- CThey are usually structural
- DThey have more than one polypeptide chain
11.Which row of the table best classifies common proteins with differing numbers of polypeptide chains?
Medium
- AOne chain = Lysozyme, Two chains = Insulin, Three chains = Collagen
- BOne chain = Collagen, Two chains = Insulin, Three chains = Haemoglobin
- COne chain = Lysozyme, Two chains = Haemoglobin, Three chains = Insulin
- DOne chain = Haemoglobin, Two chains = Lysozyme, Three chains = Collagen
12.Which of the following words best describes the structure of a large macromolecule such as a protein and its final 3-D shape?
Medium
- AConformation
- BPresentation
- CStructure
- DConfirmation
13.When using molecular visualisation software to represent large biological molecules, which aspect of a macromolecule would not necessarily be distinguishable?
Medium
- AThe flexing of a molecule when in aqueous solution
- BThe surface topography (e.g. of a cell-surface receptor)
- CThe location of the active site of an enzyme
- DThe presence of a cavity to show an ion channel through a membrane protein
14.Which interactions or features differentiate tertiary structure from secondary structure in proteins? I. Hydrogen bonds II. Disulphide bridges III. Hydrophobic interactions IV. α-helices V. Interactions between R-groups of amino acids
Hard
- AII, III and V
- BI and II
- CII and V
- DII, III and IV
15.The formation of the 3D shape of a globular protein relies on hydrophobic and hydrophilic interactions. Which statement correctly describes this process?
Hard
- AHydrophobic R groups of amino acids are repelled by the water surrounding the protein, forcing them into the centre of the protein away from the water, and the hydrophilic R groups get pulled to the outside
- BWhen peptide bonds form, the condensation reaction releases water, which forms hydrogen bonds with the hydrophilic R groups of the amino acids
- CCertain hydrophilic amino acid R groups are able to form hydrogen bonds with other hydrophilic amino acid R groups on different proteins
- DHydrophilic R groups are repelled by the water and are forced away into the centre of the 3D structure, causing the shape to be distorted
16.Human insulin is a peptide hormone consisting of 51 amino acids. Which of the following would represent the minimum number of bases that the gene coding for insulin would consist of?
Hard
- A153
- B26
- C51
- D102
17.Trypsin is a digestive enzyme found in pancreatic juices that breaks down proteins into polypeptides in the small intestine. Which of the following would be the most accurate description of the conformation of trypsin?
Hard
- AIt is a functional protein that is folded into a specific shape which is held in position by bonds between the R-groups of neighbouring amino acids, with hydrophilic R-groups facing towards the outside of the molecule
- BIt is a functional protein that is folded into a specific shape which is held in position by bonds between the R-groups of neighbouring amino acids, with hydrophobic R-groups facing towards the outside of the molecule
- CIt is a structural protein that is folded into a specific shape which is held in position by bonds between the R-groups of repeating amino acids
- DIt is a functional protein that is folded into a specific shape which is held in position by bonds between the R-groups of neighbouring amino acids, with hydrophilic R-groups facing towards the inside of the molecule
18.Rituximab is a therapeutic protein used to treat certain cancers and autoimmune diseases. It is very sensitive to temperature and pH changes and is typically injected into the bloodstream. Which statements explain why therapeutic proteins such as rituximab cannot be taken orally? I. The molecule would vibrate so fast once in the stomach that the intermolecular bonds would break II. The conformation of the protein will change once in the stomach and it may become non-functional III. The protein may become insoluble once in the stomach and form a precipitate due to the breakage of ionic bonds IV. Conditions in the stomach will cause the hydrophobic R-groups of the protein to be exposed to the outside of the molecule
Hard
- AII, III and IV
- BI and IV
- CI, II and III
- DII and III
19.Denaturation of a protein is almost always irreversible.
Easy
True or false?
20.The R-group of an amino acid is involved in the formation of the peptide bond.
Easy
True or false?
21.Hydrogen bonds in the secondary structure of a protein form between R-groups, whereas hydrogen bonds in the tertiary structure form between amine and carbonile groups.
Medium
True or false?
22.Proteins with only one polypeptide chain do not have a quaternary structure.
Easy
True or false?
23.Fibrous proteins have a large number of hydrophobic R-groups, which makes them insoluble in water.
Medium
True or false?
24.Which of the following are functions of proteins? (select all that apply)
Medium
- ACatalysing cellular reactions as enzymes
- BTransporting oxygen as haemoglobin
- CCarrying the genetic code in the nucleus
- DForming the cytoskeleton that moves chromosomes during the cell cycle
- EActing as chemical messengers secreted by glands
25.Which of the following statements about collagen are correct? (select all that apply)
Medium
- AIt is a fibrous protein made of three polypeptide chains
- BThe chains are held together by hydrogen bonds to form a triple helix
- CIt is the most abundant protein in the human body, making up about 25%
- DIt is a globular protein that is soluble in water
- EEach polypeptide chain contains about 1000 amino acids
26.Which of the following interactions determine the tertiary structure of a protein? (select all that apply)
Medium
- AHydrogen bonds between polar R-groups
- BHydrophobic interactions between non-polar R-groups and water
- CDisulfide bridges between cysteine R-groups
- DIonic bonds between positively and negatively charged R-groups
- EPeptide bonds between amino acids
27.Match each protein with its correct description.
Medium
- Rubisco
- Insulin
- Immunoglobulins
- Rhodopsin
- Enzyme that fixes CO2 from the atmosphere during photosynthesis, composed of 16 polypeptide chains
- Hormone produced by β-cells in the pancreas that causes absorption of glucose from the blood
- Antibodies with a generic 'Y' shape and highly variable binding sites
- Light-sensitive pigment in the retina of the eye that contains retinal derived from Vitamin A
28.Match each level of protein structure with its correct description.
Medium
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
- The sequence of amino acids in a polypeptide
- Coiling into α-helices or folding into β-pleated sheets held by hydrogen bonds
- The complex three-dimensional shape formed by interactions between R-groups
- Multiple polypeptide chains functioning together as a single protein
29.Place the levels of protein structure in order from the simplest to the most complex.
Medium
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
30.Place the steps of peptide bond formation between two amino acids in the correct order.
Medium
- A hydroxyl group is lost from the carboxyl group of one amino acid
- A hydrogen atom is lost from the amine group of the other amino acid
- The remaining carbon atom of the first amino acid bonds to the nitrogen atom of the second amino acid
- Water is released as a product of the condensation reaction
31.How many polypeptide subunits make up a haemoglobin molecule?
Medium
- AFour
- BTwo
- CThree
- DOne
32.Haemoglobin is a conjugated protein because each subunit contains a non-protein prosthetic group.
Medium
True or false?
33.Which statement best explains why the rate of reaction decreases at temperatures well above the optimum?
Medium
- AThe bonds holding the tertiary structure break, so the active site changes shape and the enzyme is denatured
- BThe peptide bonds holding the amino acids in sequence break, so the enzyme falls apart
- CThe enzyme molecules move more slowly and collide less often
- DThe substrate molecules are used up more quickly at high temperatures
34.Denaturation of a protein by extremes of pH is caused by breaking the peptide bonds between amino acids.
Medium
True or false?
35.Match each type of protein with an example from the list.
Medium
- Enzyme
- Hormone
- Transport protein
- Structural protein
- Immunoprotein
- Rubisco
- Insulin
- Haemoglobin
- Collagen
- Immunoglobulins
36.Match each bond or interaction with the level of protein structure in which it is primarily involved.
Medium
- Peptide bonds
- Hydrogen bonds between amine and carbonile groups
- Disulfide bridges
- Ionic bonds
- Hydrophobic interactions
- Primary structure
- Secondary structure
- Tertiary structure
37.Place the following stages of protein structure formation in order from first to last.
Medium
- Amino acids are joined by peptide bonds into a sequence
- The chain coils into α helices or folds into β-pleated sheets
- The secondary structure folds into a complex three-dimensional shape
- Multiple polypeptide subunits assemble into a functional protein
38.Which of the following statements about the R-group of an amino acid are correct? (select all that apply)
Medium
- AIt determines whether the amino acid is acidic or basic.
- BIt is involved in the formation of the peptide bond.
- CIt can be as simple as a single hydrogen atom.
- DIt determines whether the amino acid is polar or non-polar.
- EIt is the same in all 20 amino acids.
39.Which of the following are roles of proteins in cells or organisms? (select all that apply)
Hard
- ACatalysing metabolic reactions
- BTransporting oxygen in the blood
- CStoring genetic information
- DForming the cytoskeleton
- EActing as hormones
40.Which of the following interactions contribute to the tertiary structure of a protein? (select all that apply)
Hard
- AHydrogen bonds between R-groups
- BHydrophobic interactions
- CDisulfide bridges
- DPeptide bonds
- EIonic bonds
41.Complete the sentence about the elements found in proteins.
Easy
Proteins contain the elements carbon, hydrogen, oxygen and ____.
42.Name the two types of secondary structure formed when a polypeptide coils or folds.
Medium
The two types of secondary structure are the ____ and the ____.
43.Complete the sentence about the bonds that hold a protein's shape together.
Medium
The covalent bonds that form between the R-groups of cysteine amino acids in the tertiary structure are called ____.
44.Human insulin consists of two polypeptide chains: chain A has 21 amino acid residues and chain B has 30 amino acid residues. What is the total number of amino acid residues in one insulin molecule?
Medium
45.How many essential amino acids must humans obtain from their diet, out of the 20 naturally occurring amino acids?
Medium
46.Name the type of reaction by which two amino acids are joined together to form a dipeptide.
Medium
47.Give the name of the bond that forms between the carboxyl group of one amino acid and the amine group of another.
Medium
48.Name the prosthetic group found in each subunit of haemoglobin.
Medium
49.Pepsin has an optimum pH of 2 in the stomach. How many times more acidic is this than a solution of pH 6?
Medium
50.Complete the sentence about the structure of amino acids.
Medium
Amino acids have a central carbon atom bonded to an amine group, a carboxyl group, a hydrogen atom and a variable group known as the ____.
51.Complete the sentence about protein structure.
Medium
The sequence of amino acids in a polypeptide is known as the ____ structure of a protein.
52.Human insulin consists of two polypeptide chains: chain A has 21 amino acid residues and chain B has 30 amino acid residues. How many peptide bonds are present in the entire insulin molecule?
Medium
53.Explain why the precise sequence of amino acids in a polypeptide determines the three-dimensional shape and function of a protein.
Hard
54.Human insulin consists of two polypeptide chains: chain A has 21 amino acid residues and chain B has 30 amino acid residues. What is the total number of amino acid residues in one insulin molecule?
Medium
- A61 amino acids
- B56 amino acids
- C46 amino acids
- D51 amino acids
55.How many essential amino acids must humans obtain from their diet, out of the 20 naturally occurring amino acids?
Medium
- A9 amino acids
- B11 amino acids
- C10 amino acids
- D8 amino acids
56.Pepsin has an optimum pH of 2 in the stomach. How many times more acidic is this than a solution of pH 6?
Medium
- A12000 times
- B11000 times
- C9000 times
- D10000 times
57.Human insulin consists of two polypeptide chains: chain A has 21 amino acid residues and chain B has 30 amino acid residues. How many peptide bonds are present in the entire insulin molecule?
Medium
- A59 peptide bonds
- B49 peptide bonds
- C44 peptide bonds
- D54 peptide bonds

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