Module 6 Section 1: Cellular Control

Question 1

3 types of mutation

Answer 1

Substitution
Deletion
Insertion
(Called point mutations)

Question 2

What is substitution

Answer 2

One or more bases are swapped for another
E.g. ATGCCT becomes ATTCCT

Question 3

What is deletion

Answer 3

One of more bases are removed
E.g. ATGCCT becomes ATCT

Question 4

What is insertion

Answer 4

One of more bases are added
E.g. ATGCCT becomes ATGACCG

Question 5

How may a mutation effect protein structures

Answer 5

The order of DNA bases in a gene determines the order of amino acids in a particular protein
If a mutation occurs in a gene, the primary structure (amino acid chain) of the protein it codes for could be altered
This could change final 3D shape of protein so it doesn’t work properly
E.g. active sites may not be formed properly

Question 6

Why may the mutation have a neutral effect on a proteins function

Answer 6

Genetic code is degenerate
Protein could be functionally redundant
Amino acids swapped are chemically similar

Question 7

Why does genetic code being degenerate result in mutations having a neutral effect

Answer 7

Some amino acids are coded for by more than one triplet
E.g. both TAT and TAC code for tyrosine
This means that if TAT is changed to TAC the amino acid will not change

Question 8

Why does the amino acids being functionally redundant result in mutations having a neutral effect

Answer 8

The mutated triplet codes for an amino acid which isn’t involved with the protein’s function
E.g. one located far from the enzymes active site so the protein works normally

Question 9

Why does the amino acids being chemically similar result in mutations having a neutral effect

Answer 9

The two amino acids may be different but they both function the same
E.g. if arginine is swapped for lysine
The mutation will have a neutral effect because the amino acids are chemically similar

Question 10

What is the result on the organism from a neutrally effected protein

Answer 10

A neutral effect on the protein won’t affect an organism at all
Also called silent mutation

Question 11

How may mutations result in proteins changing

Answer 11

Can make a protein more or less active
E.g. by changing the shape of an enzymes active site

Question 12

How can mutations have beneficial effects on proteins

Answer 12

Could increase chance of survival
E.g. bacteria having a mutated enzyme able to break down a wider range of antibiotics rather than just one kind

Question 13

How can mutations have negative effects on proteins

Answer 13

They may decrease the chances of survival
E.g. cystic fibrosis can be caused by a deletion which causes the CFTR protein to fold incorrectly so it’s broken down, leading to excess mucus production in the lungs

Question 14

How can mutations effect whether or not a protein is produced

Answer 14

Mutations can effect whether or not a protein is produced
A mutation can occur at the start of the gene so RNA polymerase can’t bind to it and begin transcription
This means that the protein coded for by the gene won’t be made
The loss of production of a protein can have harmful effects which can cause some genetic disorders

Question 15

What is a mutation

Answer 15

Random unpredictable changes in the DNA

Question 16

What is gene mutation compared to chromosome mutation

Answer 16

Gene mutation: change which affects one small part of a DNA molecule/ base sequence

Chromosome mutation: changes in large pieces of chromosomes or even the number of chromosomes present

Question 17

Types of chromosome mutations

Answer 17

Deletion: a section breaks off
Duplication: sections get duplicated
Translocation: a section breaks off and joins another chromosome
Inversion: a section breaks off, is reversed, and then joins back on

Question 18

Why do the structure and function of cells vary despite them having the same DNA

Answer 18

Not all the genes in the cell are expressed
This means they are not transcribed to make a functional protein
They are selectively switched on of off

Question 19

What does differing gene expression create

Answer 19

Means that different proteins are made which modify the cell
They determine cell structure and control cell processes
This includes the expression of more genes which produce more proteins

Question 20

At what stages can gene expression be controlled

Answer 20

Gene expression (and therefore protein synthesis) can be controlled at:
Transcriptional level
Post transcription level
Post translational level

Question 21

How can gene expression be controlled at a transcriptional level

Answer 21

Altering the rate of transcription of genes
This is controlled by transcription factors
These therefore affect the amount of mRNA and protein that is made

Question 22

How do transcription factors determine whether a gene is switched on or off

Answer 22

Transcription factors bind to DNA and switch genes on or off by increasing or decreasing the rate of transcription

Question 23

What determines whether a transcription factor can bind to DNA in prokaryotes and what can this mean

Answer 23

The shape of a transcription factor
This can be altered by the binding off some molecules
E.g. certain hormones and sugars

This means the amount of certain molecules in an environment or cell can control the synthesis of some proteins by affecting transcription factor binding

Question 24

How do transcription factors work in eukaryotes

Answer 24

Transcription factors are proteins that bind to specific DNA sequences (e.g. enhancer or promoter regions).
The right complex of transcription factors is required for transcription to begin
By increasing/decreasing the production of specific transcription factors, transcription of other genes can be controlled

Question 25

How do transcription factors work in prokaryotes

Answer 25

Control of genes expression involves transcription factors binding to operons Factors that increase rate are activators Factors that decrease rate are repressors

Question 26

What is an operon

Answer 26

This is a section of DNA that contains a cluster of structural genes that are transcribed together Efficient way of saving resources as if certain gene products are not needed, then all of the genes involved in their production can be switched off Contain structural genes (transcribed together), control elements and regulatory gene

Question 27

Function of structural genes

Answer 27

Structural genes code for useful proteins, such as enzymes

Question 28

What is the lac operon

Answer 28

E.coli bacterium respires glucose but can use lactose if glucose isn’t available The structural genes that produce the enzymes needed to respire lactose are: lacZ, lacY and lacA These include beta-galactosidase and lactose permease Regulatory gene lacl is located nearby and codes for repressor which prevents transcription of structural genes in absence of lactose

Question 29

What happens in the lac operon if lactose is not present

Answer 29

Regulatory gene (lacl) produces the lac repressor This is a transcription factor that binds to the operator site when there’s no lactose present This blocks transcription because RNA polymerase can’t bind to the promoter Called down regulation

Question 30

What happens in the lac operon when lactose is present

Answer 30

When lactose is present, it binds to the repressor, changing the repressors shape, so that it can no longer bind to the operator site RNA polymerase can now begin transcription of the structural genes

Question 31

Where are control elements found and what is the function of the different parts

Answer 31

Control elements include a promoter and an operator Promoter: a DNA sequence located before the structural genes that RNA polymerase binds to Operator: a DNA sequence that transcription factors (e.g. repressor) bind to

Question 32

Function of regulatory genes

Answer 32

Regulatory gene codes for an activator or repressor

Question 33

Role of cAMP in lac operon

Answer 33

cAMP binds to CRP (cAMP receptor protein) which bind to CAP, this helps it to bind to DNA This helps RNA polymerase to bind to the DNA which increases the rate of transcription when more enzymes are needed to be produced to metabolise lactose efficiently

Question 34

What are the post transcriptional/ pre-translational control mechanisms affecting gene expression

Answer 34

The product of transcription is a precursor molecule (pre-mRNA) This is then modified to form mature mRNA before bind to ribosome for translation This is done by adding a cap (modified nucleotide) to 5’ end and tail (long chain of adenine nucleotides) to the 3’ end Splicing then occurs where RNA is cut to remove introns Exons are joined together Occurs within nucleus

Question 35

Role of cap and tail in post transcriptional/ pre-translational control mechanisms

Answer 35

Help to stabilise mRNA and delay degradation in the cytoplasm Cap acts as aid to binding of mRNA to ribosomes Also called telomeres

Question 36

What are exons and introns

Answer 36

Exons: EXpressed regiONs (coding DNA) Introns: INTRagenic regiON (non coding DNA)

Question 37

What is RNA editing

Answer 37

Nucleotide sequence of some mRNA molecules can be changed Done through base addition, deletion or substitution Have same effect as point mutations and results in the synthesis of different proteins that can have different functions This increases the range of proteins that can be produced from a single mRNA molecules or gene

Question 38

Methods of translational control

Answer 38

Degradation of mRNA: the more resistant the molecule the longer it will last in the cytoplasm meaning a greater quantity of protein synthesised Binding of inhibitory proteins to mRNA prevents it binding to ribosomes and synthesis of proteins is slowed Activation of initiation factors which aid the binding of mRNA to ribosomes

Question 39

What are protein kinases and how do they work

Answer 39

Enzymes which catalyse the addition of phosphate groups to proteins These are activated by the secondary messenger cAMP Addition of phosphate group changes tertiary structure and therefore the function of a protein Regulators of cell activity

Question 40

Mechanisms of post-translational control

Answer 40

Addition of non protein groups such as carbohydrate chains, lipids or phosphates Modifying amino acids and the formation of bonds such as disulfide bridges Folding or shortening of proteins Modification by cAMP (e.g. in the lac operon cAMP binds to the cAMP receptor protein increasing the rate of transcription of the structural genes)

Question 41

How is gene expression controlled at a transcriptional level in eukaryotes

Answer 41

Histone modification DNA coils around histones because they are positively charged and DNA is negatively charged Histones can be modified to increase or decrease the degree of packing

Question 42

What do acetyl and phosphate groups do in histone modification

Answer 42

The addition of acetyl groups (acetylation) or phosphate groups (phosphorylation) reduces the positive charge on histones (makes them more negative) Higher negativity causes DNA to coil less tightly allowing certain genes to be transcribed

Question 43

What do methyl groups do in histone modification

Answer 43

Addition of methyl groups (methylation) makes the histones more hydrophobic so they bind more tightly to eachother to cause DNA to coil more tightly and preventing transcription of genes

Question 44

What is epigenetics

Answer 44

Used to describe how the modification of DNA controls gene expression Used sometimes to include all the different ways in which gene expression is regulated

Question 45

What is morphogenesis

Answer 45

The regulation of the pattern of anatomical development is called morphogenesis Morphogenesis is controlled by regulatory genes called homeobox genes

Question 46

What is a body plan

Answer 46

The general structure of an organism E.g. a fruit fly has body parts (head, abdomen) that are arranged in a particular way

Question 47

What are homeobox genes

Answer 47

Highly conserved regions of DNA found in animals, plants and fungi 180 base pairs long Code for homeodomains - protein segments (60 amino acids long) that act as transcription factors Able to switch genes on and off - they are regulatory genes Control the development of the body plan Highly conserved because any mutation would be fatal

Question 48

What are Hox genes

Answer 48

Hox genes are one specific group of homeobox genes only found in animals Responsible for the positioning of body parts Highly conserved across great evolutionary distances

Question 49

Where are Hox genes found

Answer 49

Hox genes are found in gene clusters Mammals have 4 clusters on each chromosome

Question 50

How do Hox genes control development

Answer 50

Homeobox sequences code for a part of the protein called the homeodomain The homeodomain binds to specific sites on DNA enabling the protein to work as a transcription factor The proteins bind to DNA at the start of developmental genes, activating or repressing transcription and so altering the production of proteins involved in the development of the body plan

Question 51

With do body plans work in relation to the layout of an organism

Answer 51

Tend to exhibit colinearity which means that the order they appear along the chromosome is the order in which their effects are expressed in the organism Means that in segmented animals (vertebrae in humans or sections of worms) Hox genes in the head control development on mouthparts and Hox genes in the thorax control development of wings, limbs or ribs

Question 52

How can the development of structures associated with the vertebrae of an organism be determined

Answer 52

Individual vertebrae and associated structures have all developed from segments in the embryo called somites Somites are directed by Hox genes to develop in a particular way depending on their position in the sequence

Question 53

Different types of symmetry in body plans

Answer 53

Radial symmetry: organisms have a top and bottom, but no left or right side Bilateral symmetry: organisms have a left, right side and head and tail end Asymmetry: organisms have no lines of symmetry

Question 54

What is apoptosis

Answer 54

Apoptosis is highly controlled process involving programmed cell death

Question 55

Process of how apoptosis helps to shape the layout of an organism

Answer 55

Enzymes inside the cell break down important cell components such as proteins in the cytoplasm and DNA in the nucleus As the cell’s contents are broken down it begins to shrink and break up into fragments (apoptotic bodies) The cell fragments are engulfed by phagocytes and digested

Question 56

How do mitosis and apoptosis work together in body plans

Answer 56

Mitosis and differentiation create the bulk of body parts and then apoptosis refines them by removing the unwanted structures E.g. tadpoles develop into frogs and their tails are removed by apoptosis During development, genes that control apoptosis and genes that control mitosis are switched on and off in appropriate cells This means that some cells die while some new cells are produced and the correct body plan develops

Question 57

What can genes that regulate apoptosis and mitosis respond to

Answer 57

Genes that regulate apoptosis and progression through the cell cycle can respond to both internal and external stimuli

Question 58

Example of internal stimuli that can influence mitosis and apoptosis

Answer 58

An internal stimuli could be DNA damage If DNA damage is detected during the cell cycle, this can result in the expression of genes which cause the cycle to be paused and can trigger apoptosis

Question 59

Example of external stimuli that can influence mitosis and apoptosis

Answer 59

External stimulus such as stress caused by a lack of nutrient availability could result in gene expression that prevents cells from undergoing mitosis Gene expression which leads to apoptosis being triggered can also be caused by an external stimulus such as attack by a pathogen

Question 60

What can stress be defined as here

Answer 60

The condition produced when the homeostatic balance within an organism is upset

Question 61

What can stress be caused by

Answer 61

A change in temperature or intensity of light (external) Release of hormones of psychological stress (internal) These have a greater impact during growth and development of an organism