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S377 Molecular and cell biology
Are you ready for S377?
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
1
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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.
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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
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.
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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.
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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?
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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;
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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?
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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:
υ=
υmax [S]
K Μ + [S]
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?
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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.
concentration =
amount of substance
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.)
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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.
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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
8
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-ketoglutarate, 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
H
O
N
Cα
C
H
R
OH
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.
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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.
peptide
bond
H
H
O
N
C
C
H
R1
H
O
N
C
C
H
R2
OH
peptide group
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
vmax
vmax/2
KM
0
[S]
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.
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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).
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