Contents

1 Introduction 1

2 Suggested prior study 1

3 Course content 2

4 SAQs to test your understanding of key S377 concepts 3

4.1 Nuclear events: replication, cell cycle, RNA and protein synthesis 3

4.2 Cellular organization and processes 4

4.3 Proteins 5

4.4 Membranes 6

4.5 Mathematical skills 6

5 Other skills 7

5.1 Basic study skills 7

5.2 Writing skills 7

5.3 Information technology 7

Answers to SAQs 7

1 Introduction If you are intending to study S377, you should make sure that you have the

necessary background knowledge and skills to be able to enjoy the course fully

and to give yourself the best possible chance of completing it successfully.

Read through these notes carefully and work through the self-assessment

questions (SAQs) in Section 4. The notes cover the knowledge and skills you

should already possess to start the course, and the SAQs will provide a useful

exercise for all prospective students of S377.

If you understand the questions and can answer more than half of them, then it is

likely that you are well prepared to take on S377. However, if you do not

understand or are not confident in answering most of the SAQs, you should

consider doing some additional preparatory work before starting S377 or studying

one of the courses mentioned in Section 2 below. If you are still unsure whether

S377 is the right course for you, we advise you to seek further help and guidance

from your Regional Centre.

2 Suggested prior study S377 Molecular and cell biology is a Level 3 science course which makes

intellectual demands appropriate to the third year of a conventional degree. S377

Copyright © 2008 The Open University WEB 00204 2

2.1

S377 Molecular and cell biology

Are you ready for S377?

2

develops some of the subjects covered in Book 3 of the Level 2 course: S204

Uniformity and Diversity. It is therefore assumed that you will have studied S204

or that you have reached a level of biology that is commensurate with the level in

S204. If you have not studied S204 or an equivalent course, you are likely to find

S377 challenging and may have to do more background reading. We suggest that

S204 Book 3 The Core of Life, Volumes I and II would be appropriate for this

purpose.

3 Course content The following course description provides some detail about the content of the

course and the amount of study time associated with each of the books.

BOOK 1 From Molecules to Cells

Chapter 1 Evolution of the cell (2 study hours): The cell as the basic unit of life,

studying cells, their constituents, organization, processes and interactions.

Chapter 2 The foundations of life (14 study hours): Basic chemical principles

governing the structures and functions of biological macromolecules; molecular

modelling.

Chapter 3 Proteins (18 study hours): The three-dimensional structure of proteins

using molecular models of selected proteins to illustrate principles;

post-translational modifications; protein families and their structural evolution;

the relationship between protein structure and function; interactions of proteins

with other molecules; site-directed mutagenesis.

Chapter 4 Thermodynamics in biology (5 study hours): Principles of energy

transformation within a cell – how and why cells work.

Chapter 5 Nucleic acids and chromatin (20 study hours): A description of the

basic and higher-order structures of DNA within the cell nucleus and of different

types of RNA; ways in which DNA can be damaged.

Chapter 6 Membranes (6 study hours): The composition and structure of

membranes; specialized membranes of organelles; cellular architecture and

interactions between the plasma membrane and the cytoskeleton.

BOOK 2 The Dynamic Cell (Vol. 1)

Chapter 7 The dynamic cell (1 study hour): An introduction to Books 2 and 3.

Chapter 8 The cell cycle (11 study hours): An overview of the factors that

control progression through the cell cycle; events that occur during mitosis and

meiosis and the mechanisms by which cell division occurs.

Chapter 9 DNA replication (11 study hours): The mechanisms of DNA

replication; how DNA damage is repaired; the mechanisms of DNA

recombination.

Chapter 10 Gene expression (18 study hours): How gene expression is

controlled; the structures and functions of transcription factors and their

interaction with DNA; post-transcriptional events in RNA processing; RNA

export from the nucleus and the control of mRNA stability.

Chapter 11 Translation and protein turnover (11 study hours): A description

of how proteins are translated and directed towards appropriate compartments

within the cell; control of protein degradation by peptidases and the ubiquitin

pathway.

3

BOOK 3 The Dynamic Cell (Vol. 2)

Chapter 12 Transport and compartmentalization (18 study hours):

Intracellular vesicles and how molecules are moved around a cell; exocytosis and

endocytosis; the role of the cytoskeleton in cellular architecture and functional

organization of the cell.

Chapter 13 Signal transduction (12 study hours): How cells receive and

transduce signals from outside; receptors and second messenger systems; the

links between signalling pathways and gene transcription.

Chapter 14 Cell death (6 study hours): How and why cells die; the pathways

that lead to cell death by apoptosis.

BOOK 4 The Interactive Cell

Chapter 15 Cellular interaction (1 study hour): An introduction to Book 4.

Chapter 16 Migration and adhesion (12 study hours): How cells position

themselves within their environment or within a multicellular organism; cell

migration as a process in development, tissue reorganisation or repair; how

leukocytes move around the body.

Chapter 17 Differentiation (12 study hours): How cells differentiate into

distinct lineages; asymmetric division; control of differentiation, including the

roles of Hox genes, signalling molecules and extracellular matrices;

differentiation during development; plasticity and the role of stem cells in mature

tissues.

Chapter 18 Cell ageing and senescence (12 study hours): Theories of cellular

ageing; replicative senescence of cells; factors that control longevity of an

organism.

Chapter 19 Tumourigenesis (11 study hours): How cells become malignant;

checkpoints on malignancy; invasion and metastasis of tumours; anti-tumour

therapies.

4 SAQs to test your understanding of key S377 concepts

4.1 Nuclear events: replication, cell cycle, RNA and protein synthesis

SAQ1

Briefly list and describe the stages of the cell cycle. What do we call stages at

which the cell cycle can be halted and what role do these play? How are cells that

have exited the cycle described?

SAQ2

During the first growth phase of a cell, are there (a) more, (b) fewer, (c) about the

same number, or (d) exactly the same number of chromosomes as molecules of

DNA in the nucleus?

4

SAQ3

Are the DNA molecules (a) shorter, (b) longer, (c) about the same length, or (d)

exactly the same length during mitosis as they are in interphase?

SAQ4

Briefly list the key differences and similarities in the replication of the two

strands of a double-stranded DNA molecule within a cell.

SAQ5

Fill in the blanks in the following paragraph about RNA synthesis.

The enzyme …………….. copies stretches of DNA into RNA in a process called

………… . This process is initiated at the gene ……….. and the growing mRNA

molecule is copied using the ……….. strand of the DNA as a template. The other

DNA strand is known as the ………. strand.

SAQ6

Fill in the blanks in the following paragraph about protein synthesis.

The transfer of information from the mRNA base sequence to the amino acid

sequence of the polypeptide is known as……………… . This occurs on a cellular

component called the ………. .

4.2 Cellular organization and processes

SAQ7

Look at the list of proteins 1–13 below, and match each of them to the part(s) of

the eukaryotic cell or the organelles, in which they are located, using the bulleted

list immediately following. (Some of them are localized in more than one part of

the cell, and some move between compartments.) Also note down the functions

of each of these proteins.

Proteins

1 Na+/K

+ ATPase

2 cadherin

3 clathrin

4 hexokinase

5 DNA polymerase

6 tubulin

7 actin

8 calcium ATPase

9 MAP kinase

10 glutamate dehydrogenase

11 inositol triphosphate (IP3) receptor

12 insulin

13 glucose transporter;

5

Parts of eukaryotic cell/organelles

• nucleus

• mitochondrion

• cytoplasm

• endoplasmic reticulum

• endocytic vesicle

• secretory vesicle

• plasma membrane

• anchoring (intercellular) junction

• cytoskeleton

• microtubules.

4.3 Proteins

SAQ8

There are many different proteins and a wide range of protein functions. List

some of the functions of proteins.

SAQ9

Proteins are formed by polymerization of what kind of molecule?

SAQ10

What do you understand by the following terms as applied to proteins?

� primary structure

� secondary structure

� tertiary structure

� quaternary structure.

SAQ11

By means of a diagram, describe the generalized structure of an amino acid.

SAQ12

What is a peptide bond and how is it formed? Use a diagram in your answer.

SAQ13

What is meant by the ‘active site’ of an enzyme?

6

SAQ14

For an enzyme-catalysed reaction, the relationship between the initial reaction

rate (υ) and initial substrate concentration ([S]) is given by the Michaelis–Menten

equation:

[ ]

[ ]max

S

SK

υ

υ

Μ

=

+

Draw a graph of υ against [S], indicating υmax and KM. What do the terms υmax and

KM signify?

SAQ15

What is meant by the term ‘allosteric regulation’?

4.4 Membranes

SAQ16

List the molecular components of biological membranes.

SAQ17

What are the main features of the fluid-mosaic model of membrane structure?

SAQ18

How do integral and peripheral membrane proteins differ in terms of their

association with a membrane?

SAQ19

What distinguishes saturated from unsaturated fatty acids?

SAQ20

How do cis unsaturated chains affect membrane fluidity?

4.5 Mathematical skills

Probability

If you have trouble with this question, we recommend that you consider studying

the relevant section of the short course S151 Maths for Science prior to tackling

S377.

SAQ21

A bag contains equal numbers of blue, green, red and yellow marbles. Marbles

are drawn out one at a time, then each is immediately replaced in the bag. What is

the probability of drawing the sequence yellow, red, red, yellow?

7

Concentration and molarity

If you have trouble with this question, you may need to study the relevant

sections of S103 Discovering Science or S104 Exploring Science.

SAQ22

Concentration is the amount of substance present per unit volume of solution, i.e.

amount of substanceconcentration

volume of solution=

Concentration may be expressed as mass per unit volume (e.g. g l−1

, mass

concentration) or moles per unit volume (e.g. mol l−1

, molar concentration).

How many grams of sodium chloride, NaCl, are dissolved in 10 cm3 of a

0.5 molar solution? (The relative molecular mass of NaCl is 58.44.)

5 Other skills

5.1 Basic study skills

You should have the ability to organise time for study; to pace study; to interpret

figures and graphs and to make effective notes on the material you study. You

should be able to use information from a variety of sources (journals, books,

DVD-ROMs, the internet) and distinguish between relevant and irrelevant

information.

5.2 Writing skills

You should have the ability to write clearly and unambiguously, concisely and

coherently, presenting your arguments in a logical way and using clear and

appropriate diagrams.

5.3 Information technology

S377 will make use of a DVD and the internet. You should be reasonably

conversant with the use of the internet for searching and information retrieval.

Answers to SAQs

SAQ1

The cell cycle is divided into four phases: G1, during which cell growth occurs; S

phase, in which DNA synthesis occurs; followed by G2, which is a further period

of growth, and finally by M phase or mitosis, during which the cell division

actually happens. The cycle is punctuated in several places by molecular

checkpoints which serve to check that all preceding processes are satisfactorily

completed before allowing progression to the next stage. Cells that have exited

from active cell cycling are described as G0 or quiescent.

8

SAQ2

The correct answer is (d) – each DNA molecule forms one chromosome, so there

are exactly the same number.

SAQ3

The correct answer is (d) – each DNA molecule remains exactly the same length.

Prior to mitosis, it is in a more condensed form due to coiling into the

chromosome.

SAQ4

Key differences: The leading strand is replicated by continual synthesis, whilst the

lagging strand is replicated discontinuously in the form of short DNA segments

termed Okazaki fragments, which are then joined together.

Key similarities: For both strands, synthesis occurs by the incorporation of

nucleotides, polymerised in a 5′ to 3′ direction, and involves processing by DNA

polymerase and helicase proteins.

SAQ5

The enzyme RNA polymerase copies stretches of DNA into RNA in a process

called transcription. This process is initiated at the gene promoter and the

growing mRNA molecule is copied using the antisense strand of the DNA as a

template. The other DNA strand is known as the sense strand.

SAQ6

The transfer of information from the mRNA base sequence to the amino acid

sequence of the polypeptide is known as translation. This occurs on a cellular

component called the ribosome.

SAQ7

Protein Location Functions

1 Na+/K

+ ATPase plasma membrane pumps K

+ into the cell and Na

+ out

using energy from ATP

2 cadherin plasma membrane,

anchoring junction

adhesion molecule

3 clathrin endocytic vesicle,

cytoplasm

forms clathrin-coated pits and

vesicles

4 hexokinase cytoplasm phosphorylates glucose (glycolysis

pathway)

5 DNA polymerase nucleus, mitochondrion replicates DNA

6 tubulin microtubules,

cytoplasm

polymerizes to form structural

element of cell

7 actin cytoskeleton,

cytoplasm

role in cell movement and muscle

contraction

9

8 calcium ATPase plasma membrane,

mitochondrion,

endoplasmic reticulum

pumps Ca2+

out of the cytoplasm

using energy from ATP

9 MAP kinase cytoplasm, nucleus activates transcription factors

10 glutamate

dehydrogenase

mitochondrion converts glutamate into α-keto-

glutarate, which feeds into the TCA

cycle

11 IP3 receptor endoplasmic reticulum linked to Ca2+

channels

12 insulin secretory vesicles a hormone produced in the pancreas

13 glucose transporter plasma membrane facilitates glucose diffusion into the

cell

SAQ8

Examples of protein functions include enzymes, receptors, recognition,

mechanical support, transport, storage of nutrients, adhesion, generation of

movement.

SAQ9

Proteins are formed by polymerization of amino acids (a chain of amino acids is

called a polypeptide).

SAQ10

The primary structure of a protein is the linear sequence of amino acids of which

it is composed; secondary structure refers to the conformation of the polypeptide

backbone in the folded polypeptide; the tertiary structure of a protein describes

the overall three-dimensional arrangement of the polypeptide; and quaternary

structure refers to the assembly of two or more polypeptides (subunits) in a

protein.

SAQ11

H

αH N

H

R

C C OH

O

Figure 1 Generalized structure of an amino acid. R is the variable side-chain.

The Cα carbon is linked to an amino group, a carboxylic acid group and a

side-chain.

10

SAQ12

A peptide bond is the bond formed between two amino acids residues in a

polypeptide (Figure 2). It is formed by the elimination of a water molecule

between the amino group of one amino acid and the carboxyl group of another.

H

NH

H

R1

C C

O

N

H

R2

C C OH

O

H

peptide group

peptidebond

Figure 2 A peptide bond between two amino acids. (The atoms within the box

comprise the peptide group.)

SAQ13

The active site of an enzyme is the site at which the substrate binds and

undergoes chemical modification.

SAQ14

v

[S]0

vmax

��

v�����

Figure 3 Plot of initial reaction rate (υ) against initial substrate concentration

([S]) for an enzyme-catalysed reaction.

υmax is the maximal rate of the enzyme-catalysed reaction; KM is the concentration

of substrate at which the rate of reaction is half the maximal rate (i.e. υmax/2).

SAQ15

The term ‘allosteric regulation’ describes the phenomenon by which binding of a

regulator at one site on a protein can affect the conformation of the protein at a

remote binding site for a second ligand.

SAQ16

Membranes contain phospholipids, proteins, glycoproteins, proteoglycans,

glycolipids and cholesterol.

11

SAQ17

The fluid-mosaic model of membrane structure describes a fluid lipid bilayer

with embedded or attached membrane proteins moving freely in the plane of the

bilayer.

SAQ18

Integral membrane proteins span the lipid bilayer, whereas peripheral membrane

proteins are associated with only one side of the bilayer.

SAQ19

Unsaturated fatty acids contain one or more carbon-carbon double bonds (C=C).

Saturated fatty acids have no carbon-carbon double bonds.

SAQ20

Cis unsaturated chains are bent. They therefore prevent tight packing of the fatty

acyl chains in the bilayer and increase membrane fluidity.

SAQ21

1 : 256.

The probability of drawing a yellow marble is 1 in 4; and the probability for each

of the other three colours is also 1/4. So the probability of drawing them in this

sequence of four is

1 1 1 1 1.

4 4 4 4 256× × × =

SAQ22

0.29 g.

Mass concentration = molar concentration × relative atomic mass

= 0.5 × 58.44 g 1−1

So in 10 cm3 (= 0.01 litre), the mass of NaCl = 0.5 × 58.44 × 0.01 g

= 0.2922 g = 0.29 g (2 sig figs).