DP Biology SL B1.2 Proteins

DP Biology SL B1.2 Proteins - Full notes

RevisionPrep

DP Biology SL | B1.2 Proteins

DP BIOLOGY · THEME B: FORM AND FUNCTION

B1.2

Proteins

Full notes for SL · IB-style

Contents

1	Amino acids: the monomers of proteins
2	Peptide bonds and polypeptides
3	Essential amino acids and diet
4	The diversity of proteins
5	Denaturation
6	Amino acid structure
7	Peptide bonds and polypeptides
8	Essential and non-essential amino acids
9	The diversity of proteins
10	Primary and secondary structure
11	Tertiary structure
12	Quaternary structure and conjugated proteins
13	Globular and fibrous proteins
14	Denaturation
15	Protein functions
16	Proteomes
17	Effect of R groups on protein properties
18	Sickle cell anaemia: one change, big effects
19	Mixed review: worked problems
20	Additional exam-style practice
21	Practical: testing for proteins
22	Proteins in industry and medicine
23	Protein folding and disease
24	Common misconceptions and links
25	Exam-style question with markscheme
26	Check your understanding
27	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
draw the generalized structure of an amino acid
explain how peptide bonds form by condensation
explain the dietary requirement for essential amino acids
explain why there is an almost unlimited variety of polypeptides
explain the effects of heat and pH on protein structure

This booklet covers the SL content of this subtopic. Additional Higher Level material is not included.

Guiding questions

How can just 20 amino acids produce the enormous variety of proteins in living things? How does a protein's shape determine its function?

How this topic is examined

B1.2 is tested through amino acid and peptide bond diagrams, calculations of possible sequences, and denaturation.

Always connect the sequence of amino acids to the shape of the protein, and the shape to its function.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 Amino acids: the monomers of proteins

Twenty amino acids, one common plan.

Think about it

All proteins in your body are built from the same 20 building blocks. How could so few building blocks make thousands of different proteins?

Proteins are polymers of amino acids. Every amino acid has the same basic structure: a central carbon atom bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and a variable side chain called the R group.

There are 20 different amino acids commonly found in proteins, each with a different R group. R groups vary in size, charge and polarity: some are hydrophobic, some hydrophilic, some positively or negatively charged, some contain sulfur. These differences give each amino acid its chemical properties, and they determine how a protein folds and functions.

Figure 1. The generalized structure of an amino acid.

Quick check

1. Name the four groups attached to the central carbon of an amino acid.

2. How many amino acids are commonly found in proteins?

Answers: 1. amino group, carboxyl group, hydrogen, R group 2. 20

2 Peptide bonds and polypeptides

Amino acids are joined by condensation.

Two amino acids join by a condensation reaction between the carboxyl group of one and the amino group of the other, releasing a molecule of water. The bond formed (–CO–NH–) is a peptide bond. Two amino acids form a dipeptide; many form a polypeptide. A protein consists of one or more polypeptides.

Peptide bonds are formed on ribosomes during translation (D1.2). Polypeptides have an amino group at one end (the N-terminus) and a carboxyl group at the other (the C-terminus). Polypeptides can be broken down by hydrolysis, catalysed by protease enzymes during digestion.

Polypeptides vary enormously in length: the hormone insulin has 51 amino acids in two chains; the muscle protein titin has more than 34 000.

Common mistake

Drawing the peptide bond between two R groups. The peptide bond forms between the carboxyl group of one amino acid and the amino group of the next.

Quick check

1. Name the bond between amino acids.

2. Which groups react to form it?

3. Where are peptide bonds formed in cells?

Answers: 1. peptide bond 2. carboxyl of one and amino of the next 3. ribosomes

3 Essential amino acids and diet

Some amino acids must come from food.

Plants can synthesize all the amino acids they need. Animals, including humans, can make some amino acids from others, but not all. Essential amino acids cannot be synthesized in the body and must be obtained from the diet; humans need nine. Non-essential amino acids can be made from other compounds.

Animal proteins (meat, fish, eggs, dairy) contain all the essential amino acids in good proportions. Many single plant foods are low in one or more: cereals are low in lysine, legumes in methionine. A vegan diet can provide all essential amino acids by combining different plant protein sources, such as rice with lentils or beans with maize. Lack of protein or essential amino acids causes protein deficiency diseases such as kwashiorkor, which causes swelling, poor growth and weakened immunity.

Quick check

1. Define essential amino acid.

2. How can vegans obtain all essential amino acids?

Answers: 1. one that cannot be synthesized and must be obtained from food 2. by combining complementary plant proteins

4 The diversity of proteins

Twenty to the power of the chain length.

Amino acids can be linked in any sequence. With 20 possible amino acids at each position, a polypeptide of n amino acids can have 20ⁿ possible sequences. A short chain of just 5 amino acids has 3.2 million possibilities; a typical protein of 300 amino acids has a number of possible sequences far larger than the number of atoms in the universe.

The sequence of amino acids is determined by the base sequence of a gene (D1.2). The sequence determines how the polypeptide folds into a precise three-dimensional shape, and the shape determines the function. Proteins have a vast range of functions: enzymes (catalysis), hormones (insulin), transport (haemoglobin), structure (collagen, keratin), defence (antibodies), movement (actin, myosin), receptors and channels in membranes.

The full set of proteins produced by a cell or organism is its proteome. Unlike the genome, which is the same in every cell, the proteome differs between cell types and changes over time, because different genes are expressed.

WORKED EXAMPLE 1 Possible sequences

Calculate the number of possible tripeptides and the number of possible polypeptides 4 amino acids long.

Solution

Tripeptides: 20³ = 8 000A1

4 amino acids: 20⁴ = 160 000A1

Protein	Function
Rubisco	enzyme that fixes carbon dioxide in photosynthesis
Insulin	hormone that lowers blood glucose
Immunoglobulins (antibodies)	bind to specific antigens
Rhodopsin	pigment in rod cells that absorbs light
Collagen	structural protein giving strength to skin, tendons and bones
Spider silk	strong, elastic fibres for webs

Quick check

1. How many possible sequences are there for a polypeptide 3 amino acids long?

2. Define proteome.

3. Why is the proteome of a liver cell different from that of a muscle cell?

Answers: 1. 8 000 2. all the proteins produced by a cell or organism 3. different genes are expressed

5 Denaturation

Shape is everything, and shape can be destroyed.

Denaturation is a change in the three-dimensional shape of a protein that causes it to lose its function. The bonds that hold the folded shape (hydrogen bonds, ionic bonds and others between R groups) are broken, but the peptide bonds, and so the amino acid sequence, are not.

Heat increases the kinetic energy of the molecule, causing vibrations that break hydrogen bonds and other weak interactions. Most human proteins begin to denature above about 40 to 45 °C; cooking an egg white turns the soluble protein albumin into an insoluble white solid. Some organisms, such as bacteria in hot springs, have proteins stable at much higher temperatures.

Extremes of pH change the charges on R groups (adding or removing H⁺), disrupting ionic bonds and hydrogen bonds between them. Each protein has an optimum pH; pepsin works best in the strongly acidic stomach, while most enzymes work best near neutral pH.

Denaturation is usually irreversible. It is important for enzymes, which only work if their active site has the correct shape (C1.1).

Figure 2. The activity of an enzyme rises with temperature and then falls sharply as the protein denatures.

Key point

Denaturation breaks the bonds holding the 3D shape, not the peptide bonds. The sequence stays the same, but the shape and function are lost.

Quick check

1. Define denaturation.

2. Which bonds are broken in denaturation?

3. Why do extremes of pH denature proteins?

Answers: 1. change in 3D shape causing loss of function 2. hydrogen, ionic and other bonds between R groups (not peptide bonds) 3. alter charges on R groups, breaking ionic and hydrogen bonds

6 Amino acid structure

A common pattern.

Every amino acid has a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom and a variable R group. The 20 different R groups give amino acids different properties: non-polar, polar, acidic or basic.

WORKED EXAMPLE 2 Drawing (basic)

Draw the general structure of an amino acid.

Solution

Central C with H, NH2, COOH and RA2

Quick check

1. Which part of an amino acid varies?

2. Name the simplest amino acid.

Answers: 1. the R group 2. glycine (R = H)

7 Peptide bonds and polypeptides

Condensation of amino acids.

A peptide bond forms by condensation between the carboxyl group of one amino acid and the amino group of the next, releasing water. A chain of amino acids is a polypeptide, with an N-terminus and a C-terminus.

WORKED EXAMPLE 3 Counting (standard)

How many peptide bonds and water molecules are involved in forming a polypeptide of 150 amino acids?

Solution

149 peptide bonds; 149 water moleculesA1

Quick check

1. How many different tripeptides can be made from 20 amino acids?

Answers: 1. 203 = 8000

8 Essential and non-essential amino acids

Dietary needs.

Essential amino acids cannot be synthesized by the body and must come from the diet; non-essential amino acids can be made from other compounds. Animal proteins usually contain all essential amino acids; vegans must combine plant proteins (e.g. legumes and grains).

WORKED EXAMPLE 4 Vegan diet (standard)

Explain why vegans eat a variety of plant protein sources.

Solution

Individual plant proteins may lack some essential amino acidsR1

Combining sources provides all essential amino acidsR1

9 The diversity of proteins

Sequence determines shape.

With 20 amino acids and chains of hundreds of residues, the number of possible polypeptides is astronomically large. The amino acid sequence, coded by genes, determines how the polypeptide folds and therefore its function.

WORKED EXAMPLE 5 Possibilities (standard)

How many sequences are possible for a polypeptide of 100 amino acids?

Solution

20100A1

≈ 1.3 × 10130A1

10 Primary and secondary structure

Sequence and local folding.

Primary structure is the amino acid sequence. Secondary structure is regular folding into α-helices and β-pleated sheets, stabilized by hydrogen bonds between the C=O and N–H groups of the backbone (not the R groups).

WORKED EXAMPLE 6 Secondary structure (standard)

Identify the bonds stabilizing an α-helix.

Solution

Hydrogen bonds between C=O and N–H of the backboneA1

11 Tertiary structure

The 3D shape of a polypeptide.

Tertiary structure is the overall 3D folding, stabilized by interactions between R groups: hydrogen bonds, ionic bonds between charged R groups, disulfide bridges (covalent, between cysteines), and hydrophobic interactions (non-polar R groups clustered inside).

Interaction	Between	Strength
hydrogen bond	polar R groups	weak
ionic bond	acidic and basic R groups	moderate; sensitive to pH
disulfide bridge	two cysteine R groups	strong (covalent)
hydrophobic interaction	non-polar R groups	weak, collectively important

WORKED EXAMPLE 7 Folding (exam level)

Explain why non-polar amino acids are usually found inside globular proteins.

Solution

Hydrophobic R groups are excluded from waterR1

Polar R groups face outwards, making the protein solubleR1

12 Quaternary structure and conjugated proteins

More than one chain.

Quaternary structure is the arrangement of two or more polypeptides. Haemoglobin has four polypeptides (two α, two β), each with a haem group (a prosthetic group): it is a conjugated protein. Insulin has two chains joined by disulfide bridges.

WORKED EXAMPLE 8 Haemoglobin (standard)

Why is haemoglobin described as a conjugated protein?

Solution

Contains a non-protein prosthetic group (haem) in addition to polypeptidesR1

13 Globular and fibrous proteins

Shape and function.

Feature	Globular	Fibrous
shape	compact, spherical	long, narrow
solubility	usually soluble	insoluble
role	metabolic (enzymes, hormones, transport)	structural
examples	insulin, haemoglobin, enzymes	collagen, keratin

WORKED EXAMPLE 9 Collagen (exam level)

Explain how the structure of collagen relates to its function.

Solution

Three polypeptides wound in a triple helix, cross-linkedR1

High tensile strength for tendons, skin and boneR1

14 Denaturation

Losing shape.

Denaturation is a change in the 3D shape of a protein (tertiary and quaternary structure) caused by high temperature, extreme pH, or some chemicals. Bonds between R groups break; the protein loses its function. Denaturation is usually irreversible.

WORKED EXAMPLE 10 Heat (standard)

Explain why boiling an egg turns the white solid.

Solution

Heat breaks hydrogen and other bonds in albuminR1

Proteins unfold and aggregate (denatured)R1

Common mistake

Saying denaturation breaks peptide bonds. It disrupts the bonds that hold the 3D shape; the primary structure usually remains.

Quick check

1. Why does extreme pH denature proteins?

Answers: 1. changes the charges on R groups, breaking ionic and hydrogen bonds

15 Protein functions

A wide range of roles.

Function	Example
catalysis	enzymes such as amylase
transport	haemoglobin (oxygen)
hormones	insulin
defence	antibodies
structure	collagen, keratin
movement	actin and myosin
receptors	rhodopsin (light)

16 Proteomes

All the proteins of a cell.

The proteome is the complete set of proteins produced by a cell, tissue or organism at a particular time. It varies between cell types and over time because different genes are expressed, even though the genome is the same.

WORKED EXAMPLE 11 Proteome (exam level)

Explain why liver and muscle cells have different proteomes although they have the same genome.

Solution

Different genes are expressed in different cell typesR1

Proteome depends on gene expression, not just the genomeR1

17 Effect of R groups on protein properties

Polarity and charge.

The R groups exposed on the surface determine solubility and interactions with other molecules. Membrane proteins have hydrophobic R groups in the region that crosses the bilayer and hydrophilic ones exposed to the aqueous environment.

WORKED EXAMPLE 12 Membrane protein (standard)

Predict the R groups in the part of a channel protein that spans the membrane.

Solution

Hydrophobic (non-polar)A1

Interact with the fatty acid tails of phospholipidsR1

18 Sickle cell anaemia: one change, big effects

From DNA to disease.

A single base substitution changes the sixth amino acid in the β-chain of haemoglobin from glutamic acid (polar) to valine (non-polar). Haemoglobin molecules stick together at low oxygen, distorting red blood cells into sickle shapes that block capillaries.

WORKED EXAMPLE 13 Effect (exam level)

Explain how one amino acid change causes sickle-shaped cells.

Solution

Valine is non-polar; creates hydrophobic patchR1

Haemoglobin molecules aggregate into fibres at low oxygen, distorting cellsR1

19 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 14 Mixed problem (exam level)

Describe the four levels of protein structure using haemoglobin as an example.

Solution

Primary: sequence of amino acids in each chainR1

Secondary: α-helices; tertiary: folded chain around haemR1

Quaternary: four polypeptides combinedR1

20 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 15 Paper 1 question (standard)

Which bond is covalent and helps stabilize tertiary structure? A. hydrogen bond B. ionic bond C. disulfide bridge D. hydrophobic interaction

Solution

CA1

WORKED EXAMPLE 16 Paper 2 question (exam level)

Explain how temperature affects protein structure.

Solution

Increased kinetic energy causes vibrationsR1

Hydrogen and ionic bonds break; protein unfolds (denatures)R1

21 Practical: testing for proteins

Biuret test.

Add biuret reagent (copper(II) sulfate in alkaline solution) to a sample: a colour change from blue to purple indicates peptide bonds. A colorimeter can make the test semi-quantitative.

WORKED EXAMPLE 17 Controls (standard)

Why is water tested alongside the samples?

Solution

Negative control: shows the colour without proteinR1

Try this

Test egg white, milk, glucose solution and water with biuret reagent. Which contain protein?

22 Proteins in industry and medicine

Enzymes and biologics.

Proteins are used as biological detergents (proteases and lipases), in food production (rennet in cheese), and as medicines (insulin, monoclonal antibodies). Protein engineering changes amino acid sequences to improve stability.

Quick check

1. Why must biological detergents be used at moderate temperatures?

Answers: 1. enzymes denature at high temperatures

23 Protein folding and disease

When folding goes wrong.

Misfolded proteins can aggregate and cause disease: amyloid plaques in Alzheimer's disease, prions in Creutzfeldt–Jakob disease (misfolded prion proteins cause normal ones to misfold). Chaperone proteins help other proteins fold correctly.

In the real world

AlphaFold, an AI system, can predict protein 3D structures from amino acid sequences with high accuracy, transforming research into protein function and drug design.

Quick check

1. What is the role of chaperone proteins?

Answers: 1. help polypeptides fold into the correct 3D shape

24 Common misconceptions and links

Students often think…	Actually…
denaturation breaks peptide bonds	it breaks the bonds holding 3D shape
all amino acids can be made by the body	nine essential amino acids must be eaten
the genome and proteome are the same	the proteome varies between cells and over time

How B1.2 connects to the rest of the course

Topic	Connection
B1.1 Condensation	the same reaction type forms peptide bonds
D1.2 Protein synthesis	genes determine amino acid sequence
C1.1 Enzymes	active sites and denaturation
B3.1 Gas exchange	haemoglobin
C3.2 Defence	antibodies

25 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 3. Effect of temperature on enzyme activity.

(a) Draw the general structure of an amino acid. [2]

(b) Explain how two amino acids form a dipeptide. [2]

(d) Using the graph, explain the effect of temperature above 40 °C on the enzyme. [3]

Markscheme

Part	Answer	Marks
(a)	central C with H, NH₂, COOH	A1
	R group labelled	A1
(b)	condensation between carboxyl and amino groups	R1
	water released; peptide bond	R1
(c)	20⁵ = 3 200 000	A1
(d)	rate falls	A1
	heat breaks hydrogen / ionic bonds	R1
	active site changes shape: denaturation	R1

Examiner's comments. In (d), weaker answers said the enzyme was 'killed'. Enzymes are not alive; they are denatured.

26 Check your understanding

Section A: multiple choice

1. The bond between two amino acids is a

A. peptide bond B. glycosidic bond C. ester bond D. phosphodiester bond

2. The number of possible tripeptides is

A. 60 B. 400 C. 8 000 D. 3

3. Essential amino acids

A. are made in the liver B. must be obtained from food C. are not needed D. are only in plants

4. Denaturation

A. breaks peptide bonds B. changes the amino acid sequence C. is always reversible D. changes the 3D shape of a protein

5. The variable part of an amino acid is the

A. amino group B. R group C. carboxyl group D. central carbon

6. The proteome is

A. all the proteins made by a cell or organism B. all the genes C. all the amino acids D. one protein

Section B: structured

7. Explain why there is an almost unlimited variety of proteins. [3]

8. Explain the effect of extreme pH on proteins. [3]

9. Outline four functions of proteins with examples. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A

7. 20 amino acids in any order; 20ⁿ sequences; different shapes and functions.

8. Changes charges on R groups; breaks ionic and hydrogen bonds; shape and function lost.

9. Enzymes (rubisco), hormones (insulin), transport (haemoglobin), structure (collagen), defence (antibodies).

27 Summary and topic map

Idea	Remember
Amino acid	amino, carboxyl, H, R group; 20 types
Peptide bond	condensation between carboxyl and amino groups
Essential amino acids	from diet; combining plant proteins
Diversity	20ⁿ sequences; proteome
Denaturation	heat and pH break bonds; loss of shape and function

Before the exam, make sure you…

•draw amino acids and peptide bonds accurately
•link sequence to shape to function
•say proteins are denatured, not killed
•calculate 20ⁿ correctly

Proteins on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 4. Topic map for Proteins.

revisionprep.comIB-style notes · question bank · mock papers