Topic 3: Voice of Genome

Question 1

3.1 All living organisms are made of cells, sharing some common features. Outline the two types of cells, and which organisms they’re found in.

Answer 1

Prokaryotic organisms (such as bacteria) are prokaryotic cells (i.e. they’re single-celled organisms), whereas eukaryotic, multicellular organisms (such as animals and plants) are made up of eukaryotic cells. Eukaryotic cells are larger and more complex then prokaryotic cells.

Question 2

3.2 Explain the structure and function of a nucleus.

Answer 2

• The nucleus is a large organelle surrounded by a nuclear envelope (a double membrane), which contains many pores.
• It contains chromatin and a nucleolus.
  1. The pores allow substances to move between the nucleus and the cytoplasm.
  2. The nucleus controls the cell’s activities (by controlling the transcription of DNA).
  3. The nucleolus makes ribosomes.

Question 3

3.2 Explain the structure and function of a ribosome.

Answer 3

• A ribosome is a small organelle, either floating free in the cytoplasm, or attached to the rough endoplasmic reticulum.
• It’s made up of proteins and RNA.
• It does not have a membrane.
  1. It is the site of protein synthesis.

Question 4

3.2 Explain the structure and function of rough endoplasmic reticulum.

Answer 4

• A system of fluid-filled, flattened sacs.
• It is enclosed by a single membrane.
• The surface is covered with ribosomes.
  1. It folds and processes the proteins made of the attached ribosomes.

Question 5

3.2 Explain the structure and function of smooth endoplasmic reticulum.

Answer 5

• A system of fluid-filled, flattened sacs.
• It is enclosed by a single membrane.
  1. It synthesises and processes lipids.

Question 6

3.2 Explain the structure and function of a mitochondrion.

Answer 6

• Mitochondria have double membranes, where the inner membrane is folded to form structures called cristae.
• Inside is the matrix, which contained enzymes involved in respiration.
  1. It is the site of aerobic respiration, where ATP is produced.

Question 7

3.2 Explain the structure and function of the centrioles.

Answer 7

• They are small, hollow cylinders, made of microtubules.

1. They are involved in the separation of chromosomes during cell division.

Question 8

3.2 Explain the structure and function of lysosomes.

Answer 8

• A round organelle, containing digestive enzymes.
• The spherical sac has no clear internal structure, but is surrounded by a single membrane.
  1. They digest invading cells, or break down worn components of the cell.

Question 9

3.2 Explain the structure and function of a Golgi apparatus.

Answer 9

• A group of fluid-filled, flattened sacs.
• Surrounded by a single membrane.
• Vesicles are often seen at the edges of the sacs.
  1. They process and package new lipids and proteins.
  2. They also make lysosomes.

Question 10

3.3 How are proteins modified and transported within cells?

Answer 10

1. The new proteins enter the rough endoplasmic reticulum to be folded and processed, assuming a 3D shape as they move through it.
2. Vesicles pinched off the rough ER contain the proteins, and are transported to the Golgi apparatus, where the proteins are further modified.
3. The proteins enter more vesicles (pinched off the Golgi apparatus) to be transported around the surface of the cell.
4. These secretary vesicles fuse with the cell surface membrane, releasing the proteins (by exocytosis).
   [The ribosomes on the rough ER makes proteins that are excreted (such as extracellular enzymes) or attached to the membrane. The free ribosomes in the cytoplasm make proteins that stay in the cytoplasm.]

Question 11

3.4 Consider the ultrastructure of prokaryotic cells, explaining the function of 5 common components found in all prokaryotic cells.

Answer 11

Prokaryotic cells are extremely small, with a cytoplasm that contains no membrane bound organelles.

• The cell surface (or plasma) membrane controls the movement of substances into and out of the cell.
• Mesosomes are inward folds in the plasma membrane.
• A cell wall is always present in a prokaryotic cell (unlike in a eukaryotic cell). Surrounding the cell surface membrane, it provides support and prevents the cell from changing shape (keeping it rigid).
• While prokaryotic cells have ribosomes (the site of respiration), they are smaller than those in eukaryotic cells.
• A prokaryotic cell does not have a nucleus: instead, circular DNA lies free in the cytoplasm (as one long coiled strand) - it is not attached to any histone proteins either.

Question 12

3.4 Consider the ultrastructure of prokaryotic cells, explaining the function of 4 structures that aren’t always present in prokaryotic cells.

Answer 12

1. Plasmids are small loops of DNA that aren’t part of the main circular DNA. They contain genes for things like antibiotic resistance, and can be passed between prokaryotes.
2. Pili are short hair-like structures that help prokaryotes adhere to surfaces - they help them stick to other cells, and can be used in the transfer of genetic material between cells.
3. Slime capsules (made up of secreted slime) help protect the bacteria from attack by cells of the immune system. They can also prevent dehydration.
4. The flagellum is a long, hair-like structure that rotates to make the prokaryotic cell move (some cells can have more than one flagellum).

Question 13

3.5 What is the equation used to calculate magnification?
Convert:
m to cm, to mm, to μm, to nm.

Answer 13

Magnification = Image size/Actual size
1m = 100cm
1cm = 10mm
1mm = 1000μm
1μm = 1000nm

Question 14

3.6 How is the egg cell, a mammalian gamete, specialised for its function?

Answer 14

While the egg cell has all the same organelles as other eukaryotic cells, it is further specialised for its function:

1. It contains a haploid nucleus.
2. It carries huge food reserves to nourish the developing embryo (with the cytoplasm containing lysosomes and liquid droplets).
3. The zona pellucida forms a protective glycoprotein layer - the sperm have to penetrate this.
4. Follicle cells from the ovary form a protective coating.

Question 15

3.6 How is the sperm cell, a mammalian gamete, specialised for its function?

Answer 15

While the sperm cell has all the same organelles as other eukaryotic cells, it is further specialised for its function:

1. The flagellum allows the sperm to swim towards the egg cell.
2. The numerous mitochondria provide energy for tail movement.
3. The acrosome contains digestive enzymes to break down the egg cell’s zona pellucida, and enable the sperm to penetrate the egg cell.

Question 16

3.7 Explain the process of fertilisation in mammals.

Answer 16

1. The acrosome reaction:
   - The sperm cells, attracted to the chemicals released by the ovum, swim towards it.
   - When a sperm head makes contact with the zona pellucida, the acrosome swells and fuses with the sperm cell membrane.
   - The acrosome releases digestive enzymes, breaking down the zona pellucida and allowing the sperm to move towards the egg cell membrane.
2. The cortical reaction:
   - When the sperm head fuses with the cell membrane of the egg cell, the ovum releases cortical granules from vesicles.
   - The chemicals from the cortical granules thicken the zona pellucida, making it impenetrable to other sperm [this allows only one sperm to fertilise the egg cell].
3. Fertilisation:
   - The sperm nucleus enters the egg cell (with a discarded tail), fusing with the nucleus of the ovum.
   - The two haploid nuclei create a diploid zygote.

Question 17

3.8 i) What is a locus (or loci)?

Answer 17

Locus (loci): the location of genes on a chromosome.

Question 18

3.8 ii) Explain the linkage of genes on a chromosome, and what implication this has for inheriting certain characteristics together.

Answer 18

Independent assortment means that genes with loci on different chromosomes end up randomly distributed in the gametes - they are not necessarily inherited together.
Genes with loci on the same chromosome are linked: they will stay together during independent assortment, and tend to be passed on to the offspring together. Therefore, some characteristics, and certain alleles for different genes, tend to be inherited together.
However, genes with loci on the same chromosome can still be separated into different gametes, should crossing over split them.
The closer together the loci of two genes on a chromosome are, the more closely they are said to be linked. This is because crossing over is less likely to split them up.

Question 19

3.8 ii) Explain the effect of sex linkage.

Answer 19

A characteristic is said to be sex-linked when the locus of the allele that codes for it is on a sex chromosome.
In mammals, females have XX sex chromosomes, and males XY sex chromosomes.
The Y chromosome is smaller than the X chromosome, and carries fewer genes. So males, having only one X chromosome, often have only one allele for sex-linked genes.
Because they only have one copy, they express the characteristic of this allele even if it’s recessive. This makes males more likely than females to show recessive phenotypes for genes that are sex-linked.

Question 20

3.9 How does meiosis ensure genetic variation?

Answer 20

Meiosis takes place in the reproductive organs, and ensures genetic variation by producing non-identical gametes. The initial diploid cell is a combination of 23 maternal chromosomes, and 23 paternal chromosomes, but this is replicated to produce four gametes.

1. During meiosis, the independent assortment of chromatids as they line up, before dividing, is random, and therefore a source of genetic variation: the four gametes formed from meiosis each has a different combination of maternal and paternal chromosomes.
2. During the first meiotic division, the homologous chromosomes come together as pairs, and all four chromatids come into contact. At these contact points (chiasmata), the chromatids break and rejoin, exchanging sections of DNA between non-sister chromatids. Crossing over produces genetically variable chromosomes that contain different combination of alleles, from both parents. This means that each of the four gametes contains chromosomes with different alleles. [There is no crossing over between sex chromosomes during meiosis]

Question 21

3.10 What is the role of mitosis and the cell cycle?

Answer 21

Mitosis and the cell cycle produces genetically identical daughter cell (this is achieved by DNA replication, and the arrangement of chromosomes by the spindle). It is vital for cell growth (to repair or replace damaged cells) and for asexual reproduction (where offspring are genetically identical to each other and their parent).

Question 22

3.10 Outline the first stage of mitosis.

Answer 22

Prophase:

• The chromosomes condense, becoming shorter and thicker, with the replicated copies forming sister chromatids.
• The centrioles move to opposite ends of the cell, forming a network of protein fibres called spindle.
• The nuclear envelope breaks down

Question 23

3.10 Outline the second stage of mitosis.

Answer 23

Metaphase:

• The chromosomes (each as two chromatids) line up along the middle of the cell
• They attach to the spindle by their centromere

Question 24

3.10 Outline the third stage of mitosis.

Answer 24

Anaphase:

• The centromeres divide, separating the sister chromatids.
• The spindle fibres contract, pulling the chromatids to opposite poles of the cells
• The spindle breaks down.

Question 25

3.10 Outline the fourth stage of mitosis.

Answer 25

Telophase:
- The chromatids unravel, forming chromosomes again.
- A nuclear envelope reforms, enclosing the two sets of genetic material in two separate nuclei.
Cytoplasmic division (cytokinesis): the cytoplasm divides to form two identical daughter cells.
- In animal cells, the cell surface membrane constricts around the centre of the cell, dividing into two new cells.
- In plant cells, a cell plate is synthesised between the two new cells.

Question 26

3.11 i) Explain what stem cells are. What is potency?

Answer 26

Stem cells are unspecialised cells, having the ability to develop into different types of cells (and become specialised), through the process of differentiation. The ability of stem cells to differentiate into specialised cells is called potency.

Question 27

3.11 i) Explain the types of potency.

Answer 27

Totipotency: the ability of a stem cell to produce all types of cells. [Totipotent stem cells are only present in mammals, in the first few cell divisions of an embryo. After this point, the embryonic stem cells become pluripotent.]
Pluripotency: the ability of a stem cell to produce all types of cells, with the exception of extraembryonic cells (which are cells of the placenta and umbilical cord).

Question 28

3.11 ii) Discuss the ethical considerations of using stem cells in medical therapies.

Answer 28

Stem cells can be used in regeneration medicine, where diseased or damaged cells can be replaced, engineered or regenerated for normal function.
+ This could save lives.
+ This could also improve the quality of life for many people.
Adult stem cells:
- An operation is required to obtain adult stem cells: while relatively simple and low risk, it certainly provides discomfort (and is invasive).
- Adult stem cells aren’t as flexible as embryonic stem cells: they only specialise to a limited number of cells.
- There is a risk of rejection by the person’s immune system.
+ However, there’s less risk of rejection if a patient’s own adult stem cells are used for a stem cell transplant.
Embryonic stem cells:
+ Embryonic stem cells can develop into all types of specialised cells.
- However, some people object to the destruction of embryonic stem cells, claiming they have a right to life.

Question 29

3.11 ii) Discuss the way society uses scientific knowledge to make decisions about the use of stem cells in medical therapies.

Answer 29

1. Take ethical issues into consideration and ensure that embryos are involved for a good reason.
2. License and monitor centres, so that only fully trained staff are employed and unregulated research is avoided.
3. Produce guidelines and codes of practice.

Question 30

3.12 Explain how cells become specialised.

Answer 30

Stem cells become specialised through differential gene expression, where some genes are switched on (and become active), while others are switched off (and become inactive) - under the right conditions, of course.
mRNA is only transcribed from active genes, and is then translated into proteins. These proteins modify the cell: they determine the cell structure or control cell processes, allowing the cell to become specialised.

Question 31

3.12 What are transcription factors? What are the two types?

Answer 31

Transcription factors initiate and regulate the transcription of genes. There are two types:
- Activators: helping RNA polymerase bind to DNA and begin transcription.
- Repressors: prevent RNA polymerase from binding to DNA and inhibit transcription.
[Gene expression can be controlled by altering the rate of transcription of genes - increased transcription produces more mRNA, which can be used to make more protein. Activators increase the rate of reaction, while repressors decrease the rate of reaction].

Question 32

3.12 Explain the requirements for gene expression, including the prevention of gene expression, in eukaryotic cells.

Answer 32

In eukaryotic cells, genes are first uncoiled, allowing accessible regions of the DNA to be transcribed into mRNA. The enzyme RNA polymerase needs to bind to the promoter region (a section of DNA adjacent to the gene being transcribed) for transcription to take place - without this, the gene remains switched off. The attachment of a regulatory protein (a type of transcription factor, otherwise known as an activator) is usually also required to start transcription.
Transcription of a gene can be prevented by a repressor molecule (a type of transcription factor, otherwise known as a repressor): it attaches to the promoter region, preventing RNA polymerase from reaching the attachment site. In addition, protein repressor molecules can attach to regulatory proteins, preventing them from binding to the attachment site.

Question 33

3.12 Explain the lac operon model as an example of gene expression.

Answer 33

E. coli is a bacterium that uses lactose to respire when glucose isn’t available. Lactose is broken down by the enzyme β-galactosidase.
However, when lactose is absent, the gene for β-galactosidase is normally switched off: a repressor molecule (a type of transcription factor) binds to the operator gene (a DNA sequence that transcription factors bind to). This prevents RNA polymerase from binding to the promoter region, which prevents the structural gene (for β-galactosidase) from being transcribed.
When lactose is present in the environment, it binds to the repressor molecule - this changes the shape of the repressor molecule, preventing it from binding to the operator site. The RNA polymerase can now transcribe the structural gene, producing β-galactosidase (to break down lactose).

Question 34

3.13 How are cells in multicellular organisms organised?

Answer 34

In multicellular organisms, cells are specialised for a specific function.
Tissues are groups of specialised cells working together to carry out a particular function.
An organ is a group of tissues working together to carry out a particular function.
An organ system is a group of organs working together to carry out a particular function.

Question 35

3.14 ii) How can epigenetic changes modify the activation of certain genes?

Answer 35

Epigenetic changes can occur in response to changes in the environment. The epigenome determines which genes are expressed and transcribed, thus altering the phenotype. This doesn’t alter the base sequence of DNA, but instead attaches and removes chemical group to and from the DNA.

1. Methylation of DNA: a methyl group is attached to the DNA coding for a gene, changing the DNA structure so that RNA polymerase and transcription factors can’t bind to the gene. This prevents mRNA from being transcribed, and the gene is not expressed.
2. Histone modification: [histones are proteins that DNA wraps around to form chromatin, which makes up chromosomes]
   - When histones are acetylated (acetyl groups are added), the chromatin is less condensed. The DNA isn’t wrapped as tightly around the histones, allowing gene expression to take place: proteins can bind to the DNA, enabling transcription to take place.
   - When acetyl groups are removed from the histones, the chromatin becomes highly condensed. The DNA is wrapped more tightly around the histones, preventing proteins from binding to the DNA and inhibiting transcription of genes.

Question 36

3.14 iii) How can epigentic changes be passed on following cell division?

Answer 36

Epigenetic changes are usually removed from the DNA during the production of gametes, but some escape the removal process and end up in the sperm or egg cell.
If these epigenetic changes are passed on, then certain activated or deactivated genes in the original cell will be the same for the daughter cells (if an epigenetic change occurred in response to a change in the environment, then the daughter cells may be equipped to deal with the changed environment in the same way as the original cell was).

Question 37

3.15 Explain how phenotypes are affected by variation in genotype as well as the environment.

Answer 37

Some phenotypes are determined by genes at a single locus (monohybrid inheritance), and often fall into discrete groups with no overlap - this is called discontinuous variation.
Many phenotypes are affected by multiple alleles for the same gene at many loci (polygenic inheritance), and often fall within a range, with no distinct categories - this is called continuous variation.
While some phenotypes are only influenced by genotype, most are influenced by both genotype and the environment.