Topic 3: Voice of the Genome

Question 1

3.1.6) magnification formula

Answer 1

magnification = size of image/size of real object

Question 2

3.1.6)
a) An insect is 0.5mm long. In a book, a picture of the insect is 8cm long. Calculate the magnification of the insect.

b) An image from light microscope shows a human cheek cell at x100 magnification. The actual diameter of the cell is 59um. What is the diameter of the cell in the image?

Answer 2

a) magnification = image size/object size
80mm / 0.5mm = x160

b) image size = magnification x object size
100 x 0.059mm = 5.9mm

Question 3

converting um into mm

Answer 3

divide by 1000

Question 4

Prokaryotic cells

Answer 4

A prokaryotic cell is a single-celled organism that lacks a nucleus and other membrane-bound organelles. They are smaller and simpler in structure that eukaryotic cells, e.g. bacteria.

Question 5

Eukaryotic cells

Answer 5

Eukaryotic cells are cells that contain a nucleus and other membrane-bound organelles. Eukaryotic cells are complex and include all animal and plants cells.

Question 6

Organelles

Answer 6

Organelles compartments within the cell that perform a specific function. These compartments are usually isolated from the rest of the cytoplasm through intracellular membranes.

Question 7

List the features in the ultrastructure of eukaryotic cells

Answer 7

• nucleus
• nucleolus
• ribosomes
• rough and smooth endoplasmic reticulum
• mitochondria
• centrioles
• lysosomes
• Golgi apparatus

Question 8

Nucleus

Answer 8

Description:
- Large organelle
- Surrounded by a nuclear envelope (double membrane), which contains many pores.
- Contains DNA wrapped in histone proteins in a complex called chromatin, and a nucleolus.

Function:
- Controls the cell’s activities (by controlling the transcription of DNA)
- DNA contains instructions to make proteins.
- The pores allow substances to move between the nucleus and the cytoplasm.
- The nucleolus makes ribosomes.

Question 9

Lyosome

Answer 9

Description:
- A round organelle surrounded by a membrane, with no clear internal structure.

Functions:
- Contains digestive enzymes. These are kept seperate from the cytoplasm by the surrounding membrane, and can be used to digest invading cells or to break down worn out components of the cell.

Question 10

Ribosome

Answer 10

Description:
- A very small organelle that either** floats free** in the cytoplasm or is attatched to the rough endoplasmic reticulum.
- made up of protiens and RNA.
- Not surrounded by a membrane.

Function:
- The site of protein synthesis.

Question 11

Rough Endoplasmic Reticulum (RER)

Answer 11

Description:
- A system of membranes enclosing a fluid-filled space. The surface is covered with ribosomes.

Functions:
- Folds and processes proteins that have been made at the ribosome.
- proteins made in the RER are sent to the Golgi apparatus.

Question 12

Smooth Endoplasmic Reticulum (SER)

Answer 12

Description:
- Similar to RER, but with no ribosomes.

Function:
- Synthesises and processes lipids.

Question 13

Golgi Apparatus

Answer 13

Description:
- A group of fluid-filled, membrane-bound, flattened sacs. Often contains vesicles at the edges of the sacs.

Function:
- It processes and modifies proteins and lipids which have been made in the cell and packages them in vesicles to be transported out of the cell. It also makes lysosomes.

Question 14

Mitochondria

Answer 14

Description:
- Usually oval-shaped.
- Have a double membrane - the inner one is folded to form a structure called cristae.
- Inside is the matrix, which contains enzymes involved in respiration.

Function:
- The site of aerobic respiration, where ATP is produced.
- Found in large numbers in cells that are active and require a lot of energy.

Question 15

Centriole

Answer 15

Description:
- Small, hollow cylinders, made of microtubules (tiny protein cylinders). Found in animal cells but only some plant cells.

Function:
- Involved with the **seperation of chromosomes **during cell division.

Question 16

3.10) Mitosis

Answer 16

• In mitosis a parent cell divides to produce two genetically identical daughter cells.
• Needed for growth of multicellular organisms, for re[airing damaged tissues and for asexual reproduction.

Question 17

3.10) The cell cycle

Answer 17

Consists of interphase (a period of cell growth and DNA reapplication), mitosis (nuclear division), and cytokinesis (cell division).

Question 18

3.10) Interphase

Answer 18

Period off cell growth and DNA replication
consists of 3 stages:
- G1: cell grows and new organelles and proteins are made. Organelles replicated.
- S (synthesis) Phase: Cell replicates it’s DNA
- G2: Cell keeps growing and proteins needed for cell division are made.

Question 19

3.10) Stages of mitosis

Answer 19

1) Prophase: chromosomes condense. centrioles move to opposite ends of cell and form a network of spindle. Nuclear envelope breaks down
2) Metaphase: chromosomes line up along the middle of cell and become attached to the spindle by their centromere.
3) Anaphase: centromeres divide, separating each pair of sister chromatids. Spindles contract, pulling chromatids to opposite poles of the spindle.
4) Telophase: Chromatids reach opposite poles on the spindle. They uncoil - now called chromosomes again. Nuclear envelope forms around each group of chromosomes, so there are now two nuclei.

Question 20

3.10) Cytokinesis

Answer 20

cytoplasm divides and there are now two daughter cells that are genetically identical to the original cell.

Question 21

3.3) The role of the rough endoplasmic reticulum (RER) and the Golgi apparatus in protein transport

Answer 21

1) Proteins are made at the ribosomes.
2) The ribosomes on the rough endoplasmic reticulum make proteins that are excreted or attached to the cell membrane.
3) New proteins produced at the RER are folded and processed in the RER.
4) Then they’re transported to the Golgi apparatus in vesicles.
5) The Golgi apparatus further processes and modifies the proteins and sends them in vesicles to the plasma membrane.
6) The protein either attaches to the cell membrane or the vesicles fuse with the plasma membrane to secrete the finish protein product.

Question 22

3.9) Meiosis

Answer 22

• Meiosis is a type of cell division that happens in the reproductive organs to produce gametes
• Cells that divide by meiosis have the full number of chromosomes to start with (diploid), but the cells that are formed from meiosis have half the number (haploid).
• Meiosis produces four new daughter cells that are genetically different from each other. These are the gametes

Question 23

3.9) Why is miosis important?

Answer 23

It ensures genetic variation through the production of non-identical gametes as a consequence of independent assortment of chromosomes and crossing over of alleles between chromatids. Genetic variation is the differences between the individual’s genetic material in a population. This is important because it allows natural selection to occur and means if a disease were to spread across a population there is a higher chance of survival among the individuals.

Question 24

3.9) Explain how independent assortment leads to genetic variation

Answer 24

• Independent assortment is the production of different combinations of alleles in daughter cells due to the random alignment of homologous pairs along the equator of the spindle during metaphase I
• The combination of alleles that end up in each daughter cell depends on how the pairs of homologous chromosomes were lined up
• The different possible combinations of chromosomes in daughter cells increases genetic variation between gametes
  To work out the number of different possible chromosome combinations the formula 2n can be used, where n corresponds to the number of chromosomes in a haploid cell

Question 25

3.9) Explain what crossing over is and how it leads to genetic variation

Answer 25

Crossing over is a process that happens during meiosis when chromosomes of the same type are lined up and exchange genetic material. This results in new allelic combinations in the daughter cells and increases genetic diversity. Crossing over occurs between non-sister chromatids of homologous chromosomes, which are chromosomes that contain the same genes but may have different forms of the genes.

Question 26

3.11 i) Define what is meant by the term ‘stem cell’

Answer 26

Stem cells are unspecialised cells which have the ability to become specialised cells by the process of cell differentiation. Stem cells have an unlimited capacity to divide and can produce lots more stem cells by mitosis.

Question 27

3.11 i) Define what is meant by the term ‘pluripotency’

Answer 27

pluripotent stem cells can differentiate into any type of specialised cell except the extraembryonic cells (the cells that make up the placenta) .

Question 28

3.11 i) Define what is meant by the term ‘totipotency’

Answer 28

Totipotent cells have the ability to divide into any type of cell (including the extraembryonic cells which make up the placenta and umbilical cord).

Question 29

3.11 ii) Evaluate the use of stem cells in medicine

Answer 29

Benefits:
- could be used to replace damaged tissues in a range of diseases e.g. leukaemia.
- Could save lives - Stem cells could be used to grow organs for those awaiting transplants instead of relying on donars.
- Could improve the quality of lives - e.g. stem cells could be used to replace the damged cells in the eys of people who are blind.
- Adult stem cells can be obtained from bone marrow in a relatively simple operation with very little risk and donor can give consent.
- Embryonic stem cells can divide into any type of cell.

Limitations:
- Obtaining stem cells from embryos created by IVF raises ethical issues because the procedure results in the destruction of an embryo that’s viable.
- Adult stem cells can’t develop into all the specialised cell types that embryonic stem cells can.
- If patient cannot use their own adult stem cells in a transplant there is a risk of rejection.
- Many ppl believe that at the moment of fertilisation a genetically unique individual is formed that has the right to life.
- Risks of infections and cancers with lab cultured stem cells.

Question 30

3.11 ii) Give three ways in which regulatory authorities help society to consider the benefits and ethical issues of embryonic stem cells in research.

Answer 30

1) Looking at proposals for research and deciding if they should be allowed considering the ethical issues - this ensures there is a good reason for stem cell research and that it won’t need to be repeated.
2) Licensing and monitoring centres involved in embryonic stem cell research ensures fully trained staff who are aware of implications and won’t waste resources e.g embryos. Helps avoid unregulated research.
3) Producing guidelines and codes of practice - ensuring scientist work in a similar manner for comparison , using acceptable sources and methods to make it as ethical as possible.
4) Monitoring developments in research - keeps guidelines up to date
5) Providing Info and advice to governments and professionals - improves society’s understanding of what’s involved in stem cell research and why it is important.

Question 31

3.12) Explain how differential gene expression allows cells to become specialised

Answer 31

1) A stimulus acts on unspecialised cells
2) Activator and repressor molecules can bind to promotor regions on the DNA sequence. Some genes become switched on and are active whereas other genes are switched off.
3) The active genes are transcribed to produce MRNA
4) mRNA is then translated on ribosomes and used to produce protein.
5) The protein has the ability to change the structure and function of cells

Question 32

Transcription Factors

Answer 32

Transcription factors control the expression of genes
They are Proteins that bind to DNA and activate or deactivate genes by increasing or decreasing the rate of transcription:
- Activators are transcription factors that increase the rate of transcription by helping RNA polymerase bind to the DNA and begin transcription.
- Repressors are transcription factors that decease the rate of transcription by preventing RNA polymerase from binding and so stopping transcription.

Question 33

3.12) What is an operon?

Answer 33

An operon is a section of DNA that contains a cluster of:
- structural genes (which code for useful proteins) that are transcribed together.
- control elements, including a promotor (A DNA sequence that RNA polymerase binds to) and an operator (A DNA sequence that transcription factors bind to).
- A regulatory gene that codes for an activator or repressor.

Question 34

3.12) Lac operon

Answer 34

The lac operon is found in E.coli and contains the genes that produce enzymes needed to respire lactose for when glucose isn’t available.

The LO as 3 structural genes - lacZ, lacY and lacA, which produce proteins that help the bacteria digest lactose.

When Lactose is NOT present:
The regulatory gene (lacI) produces the lac repressor, which binds to the operator site and blocks transcription because RNA polymerase can’t bind to the promoter.

When lactose is present:
It binds to the repressor, changing the repressor’s shape so that it can no longer bind to the operator site. RNA polymerase can now begin transcription of the structure genes.

Question 35

3.14i) Phenotype

Answer 35

The expressed characteristics of an organism, which results from the interactions of the genes of the organism with the environment in which it lives.

Question 36

3.14i) Continuous vs discontinuous variations in phenotype

Answer 36

• Continuous variation: When the individuals within a population vary within a range - there are no distinct categories. E.g. height, mass, skin colour.
• Discontinuous variation: When there are two or more distinct categories - each individual falls into only one of thee categories. E.g. blood group

Question 37

3.14i) Monogenic characteristics

Answer 37

Characteristics that are controlled by only one gene. They tend to show discontinuous variation e.g. blood group.

Question 38

3.14i) Polygenic characteristics

Answer 38

Characteristics that are controlled by a number of genes at different loci. They usually show continuous variation, e.g. height.

Question 39

3.14ii) Epigenetics

Answer 39

Epigenetics refers to changes in DNA that alter the expression of genes without changing the base sequence of DNA itself. These changes can be caused by environmental factors and are heritable.
Two examples of epigenetic modification are DNA methylation and histone modification.

Question 40

3.14ii) DNA methylation

Answer 40

When a methyl group (-CH3) is attached to the DNA coding for a gene at a CpG site. Increased methylation changes the DNA structure, making chromatin more condensed so that the proteins and enzymes needed for transcription can’t bind to the gene so it inhibits transcription and the gene is not expressed - it’s repressed.

Question 41

3.14ii) Histone Modification

Answer 41

Include the addition or removal of acetyl groups (COCH3)
1) When histones are acetylated, the chromatin is less condensed and the genes are activated.
2) When acetyl groups are removed from the histones, the chromatin becomes highly condensed and the genes are repressed. Removal of acetyl groups increases the positive charge on histone proteins. This increases the attraction to phosphate groups on DNA and chromatin becomes more condensed.

Question 42

3.14ii) How does the structure of chromatin affect transcription?

Answer 42

• Histones are proteins that DNA wraps around to form chromatin which makes up chromosomes
  Chromatin can be highly condensed or less condensed. How condensed it is affects the accessibility of DNA and whether or not the proteins and enzymes needed for transcription can bind to it.

Question 43

3.14i) Give an example of a characteristic that is influenced by both genotype and the environment

Answer 43

1) Height - is a polygenic characteristic. However, height can be limited due to environmental factors like nutrition
- Cancer is the uncontrolled cell division that leads to the growth of tumours. The risk of developing cancer is affected by genes, but environmental factors such as diet and smoking can also influence the risk.

Question 44

3.13) How are the cells of multicellular organisms organised into tissues, tissues into organs and organs into systems?

Answer 44

The cells in complex multicellular organisms like people are organized into tissues, groups of similar cells that work together on a specific task. Organs are structures made up of two or more tissues organized to carry out a particular function, and groups of organs with related functions make up the different organ systems.

Question 45

3.8 i) what is meant by Locus?

Answer 45

The position of a gene on a chromosome is called a locus (plural: loci).

Question 46

3.8 ii) Gene Linkage

Answer 46

Genes with loci on the same chromosome are linked because genes on the same chromosome will stay together during independent assortment and their alleles will be passed onto offspring together.
The only reason this won’t happen is if crossing over occurs.

Question 47

3.8 ii) Sex-Linked characteristics

Answer 47

A characteristic is said to be sex-linked when the locus of the allele that codes for it is on a sex-chromosome.
Females = XX
Males = XY
Y chromosome is smaller and so carries fewer genes. Most genes on the sex chromosomes are only carried on the X chromosome. As males only have one X chromosome, they often only have one allele for sex-linked genes, therefore they express the characteristic of this allele even if it’s recessive. This makes males more likely to to show recessive phenotypes for genes that are sex-linked. Therefore they are much likely to show sex-linked recessive conditions such as colour blindness. These are know as x-linked disorders.

Question 48

3.14 iii) Understand how epigenetic changes can be passed on following cell division

Answer 48

The epigenome is heritable (i.e. when a cell divides and replicates, epigenetic changes affecting the expression of genes in the DNA of that cell may be passed on to daughter cells).

During gamete production, DNA in the parent cell usually undergoes de-methylation but often methyl groups are not removed and therefore are present in the DNA in the sperm or egg cells.

A potential explanation for why this occurs is that if an epigenetic change occurs in response to an environmental factor, it may be beneficial for this epigenetic change to also occur in daughter cells so that they are also better adapted for the environmental factor (in the same way the original cell was)

Question 49

3.4) List the ultrastructure of prokaryotic cells

Answer 49

Always Present:
- Cell wall
- Cell surface membrane
- Cytoplasm (no membrane-bound organelles)
- Circular DNA
- Ribosomes (70S, smaller than in eukaryotes)

Sometimes Present:
- Flagellum
- Capsule
- Mesosomes
- Plasmid
- Pili

Question 50

3.4) Cell wall in prokaryotic cells

Answer 50

Strengthens and Supports the cell and prevents it from changing shape.
Made of peptidoglycan.

Question 51

3.4) Capsule

Answer 51

A final layer surrounding some prokaryotic cells (e.g. bacteria) made up of secreted slime. helps to protect bacteria from attack by cells of the immune system.

Helps cell to retain moisture and adhere to surfaces.

Question 52

3.4) Plasmid

Answer 52

Small loops of DNA that are separate from the main circular DNA molecule. They contain genes that can be passed between prokaryotes.
(E.g. genes for antibiotic resistance)

Question 53

3.4) Flagellum

Answer 53

Long, hair like structure that rotates to make the prokaryotic cell move.

Question 54

3.4) Pili

Answer 54

Short hair-like structures which help prokaryotes stick to other cells and can be used in the transfer of genetic material between cells.

Question 55

3.4) Mesosomes

Answer 55

Inward folds in the plasma membrane. Their function is debated with many scientists believing that they are just artefacts from the preparation process of microscopy, which others believe they contain enzymes required for respiration

Question 56

3.4) Circular DNA in prokaryotes

Answer 56

No nucleus, DNA floats free in cytoplasm. Circular DNA = one long coiled up strand. it’s not attached to any histone proteins.

Question 57

3.6) How is the ovum (egg cell) specialised for it’s function.

Answer 57

• Zona pellucida = a protecting coating which the sperm has to penetrate in order for fertilisation to occur, it then hardens after they have entered. The main purpose of the ZP is to prevent polyspermy.
• Haploid nucleus so that a full set of chromosomes is restored at fertilisation.
• Cortical granules release substances which cause the zona pellucida to harden.
• Follicle cells from a protective coating around the egg.

Question 58

3.6) How are spermatozoa (sperm cells) specialised for it’s function?

Answer 58

• Contain lots of mitochondria to provide energy for rotation of the flagellum which enables cell to move.
• Acrosomes contain digestive enzymes which break down the zona pellucida and allow sperm to penetrate egg.
• haploid nucleus

Question 59

3.7) Describe the process of fertilisation

Answer 59

1) The sperm head meets the protective jelly layer around the egg cell called the zona pellucida and the acrosome reaction occurs - enzymes digest the zona pellucida.
2) The sperm head fuses with the cell membrane of the egg cell thus allowing the sperm nucleus to enter the egg cell.
3) The cortical reaction occurs - the egg cell releases chemicals from cortical granules which thicken the zona pellucida making it impenetrable to other sperm. (prevents polyspermy)
4) The nuclei fuse and a full set of chromosomes is restored, thus forming a zygote.

Question 60

Core Practical 5: Prepare and Stain a root tip squash to observe the stages of mitosis

Answer 60

Method:
1) Using a scalpel cut 1cm from the tip of the growing root (the tip is the growing region therefore mitosis should be occurring there).
2) Place root tip into test tube of Hydrochloric acid (HCL), which softens a loosens the root tissues, and then into water bath as 60 degrees for 10 mins.
3) Using pipette rinse root tip with cold water and leave to dry on paper towel.
4) Cut approx. 2mm off the tip and place onto microscope slide (use filter paper to absorb any excess water)
5) Use mounted needle to break tip open and spread cells out thinly.
6) Add drop of stain (toluidine blue) to make chromosomes easier to see under a microscope.
6) Gently lower cover slip over cells using mounted needle to prevent air bubbles forming.
7) Push down firmly to squash tissue to make the tissue thinner and allow light to pass through when viewing under microscope.
8) Can now look at stages of mitosis under a light microscope.
9) Calculate the mitotic index using: mitotic index = number of cells with visible chromosomes / total number of cells observed

Risk Assessment
Hazard: Scapel Risk: Cut yourself Prevention: Cut away from your body, cut on white tile to prevent slipping
Hazard: hydrochloric acid Risk: Irritant (corrosive depending on conc.) Prevention: wear googles, wash hands if spills

Question 61

Light microscopes

Answer 61

Use light to form an image
max. resolution of around 0.2um. Max usefull magnification = x1500

Question 62

Electron microscopes

Answer 62

Use electrons to form an image
higher resolution that light microscopes so give more detailed images
max magnification= about x1500000

Transmission electron microscopes (TEMs)
- uses electromagnets to focus a beam of electrons through the specimen. Denser parts of the specimen absorb more electrons, which makes them look darker on the image you end up with. Give high resolution images but can only be used on thin specimens.

Scanning electron microscopes (SEMs)
Scan a beam of electrons across the specimen. This knocks off electrons from the specimen which are in a cathode ray tube to form an image. Shows the surface of the specimen and can be 3D. Can be used on thick specimens but have lower resolution images than TEMs

Question 63

Core Practical: Mitosis root tip squash
Why do you only use the first 5mm from the tip of the onion root?

Answer 63

This is where you will find cells that are undergoing mitosis (it is where there is meristem tissue).

Question 64

Core Practical: Mitosis root tip squash
Why do you press down firmly on the cover slip?

Answer 64

To get a thin layer of cells so that light can pass through.

Question 65

Core practical: root tip squash
Why was a stain used? What stain can be used?

Answer 65

To stain the chromosomes to make them visible
Can be either toluidine blue or acetic orcein

Question 66

Core Practical: root tip squash
when counting the cells to calculate the mitotic index, what should you do to ensure that your count is accurate?

Answer 66

1. Examine large number of fields of view / many cells;
2. to ensure representative sample