Cellular Control - M6 Flashcards
Point / substitution Mutation
One base is replaced with another.
Addition / insertion / frameshift
Mutation
An extra base is added to the DNA molecule.
Deletion / frameshift
A base is removed from the DNA molecule.
Mutation causes no effect
no effect on phenotype of organism because normally functioning proteins are still synthesized
Damaging effects of mutations
phenotype of organisms is affected in a negative way because proteins are no longer synthesized or proteins synthesized are non-functional. Can interfere with one or more essential processes
Beneficial mutations
very rarely a protein synthesised that results in a new and useful characteristic in phenotype.
Genes can be regulated in 4 different ways:
Transcriptional – genes can be turned on or off
Post-transcriptional – mRNA can be modified which regulates translation
Translational: turning translation on/off
Post-translational – proteins can be modified after synthesis
Chromatin remodelling
Histones + DNA = chromatin
Heterochromatin is tightly wound DNA – visible during cell division
RNA polymerase can’t access gene so transcription can’t occur
Euchromatin – loosely wound DNA – present during interphase – this is when transcription can take place as RNA polymerase can bind
Histone modification
Histones are +ve and DNA is -ve
Histones can be modified to increase or decrease the level of packing
Acetylation or phosphorylation reduces +ve charge on histones causing it to coil less tightly allowing transcription
Methylation makes histones more hydrophobic so they bind closer together
RNA editing
Bases can be added, deleted or substituted
This increases the range of proteins that can be produced from a single gene
Translational control
Degradation of mRNA - The more resistant the molecule, the longer it will last in the cytoplasm, so more protein can be synthesised
Inhibitory proteins – bind to mRNA to stop it from binding to a ribosome
Activation of initiation factors which aid the binding of mRNA to ribosomes
Protein kinases
Catalyse addition of phosphate groups to proteins to change the tertiary structure and function
This usually activates enzymes so regulate cell activity
cAMP activates lots of protein kinases
Modification of proteins
Addition of non-protein groups
Modifying amino acids and the formation of bonds
Folding/shortening of proteins
Modification by cAMP – e.g. the lac operon cAMP binds to the cAMP receptor proteins increasing the rate of transcription of the structural genes
Control sites:
do NOT code for polypeptides
Promoter Region (P) DNA sequence where RNA polymerase binds
Operator Region (O) where repressor protein binds to
Structural genes
e.g:
:code for proteins not involved in gene regulation
Structural Gene (Z)
Structural Gene (Y)
Structural Gene (A)
Make
B- galactosidase
Lactose permease
Lactose transacetylase
Operon
A group of genes controlled by the same regulatory mechanism at the same time
An operon is a length of DNA made up of structural genes and control sites
The control sites regulate the expression of the structural genes
β-galactosidase in Gene regulation in Escherichia coli
hydrolyses lactose to glucose and galactose
Lactose permease in Gene regulation in Escherichia coli
enables the bacterium to take up lactose
β-galactosidase, Lactose permease enzymes are only produced in presence of …
These enzymes are only produced by the bacterium in the presence of lactose, indicating that there is a regulatory mechanism at work – the lac operon!
Describe how Genes Z and Y are switched on in bacteria that are moved to a nutrient medium which contains Lactose
lactose binds to repressor protein ;
changes , shape / structure (of protein) ;
removes it from / stops it binding to , operator ;
RNA polymerase binds to promoter ;
idea that (so that Z and Y) are , transcribed / mRNA made
Transcriptional control involves
Chromatin remodelling
Histone modification
Post-transcriptional/pre-translational control involves
RNA processing
RNA editing
Translational control involves
Degradation of mRNA
Inhibitory proteins
Activation of initiation factors which aid the binding of mRNA to ribosomes
Protein kinases
Post- translational control involves
Modifications of proteins
A homeobox is a DNA sequence that codes for a
protein transcription factor
homeodomain
This means they help to form the basic pattern of the body
For example, they control the………… of the organism (which end will develop into the head and which end will develop into the tail)
They also control the………… of organisms such as insects and mammals into distinct body parts and they control the development of body parts such as wings and limbs, as well as what …………. are present in each section of the body
polarity
segmentation
organs
!! DIFFERENCE BETWEEN Homeobox and homeobox gene
homeobox = DNA sequence that codes for a protein transcription factor- homeodomain
WHEREAS
a homeobox gene is any gene that contains a homeobox sequence
Why are homeobox genes similar between animals, fungi and plants
they all code for amino acid sequences that will form transcription factors, the DNA binding regions of which must have the same shape
why are homeobox gene sequences highly conserved
-genes very important
-mutation would have big efects - alter body plan
-Many other genes effected
-Mutations that cause variation in homeobox sequences can lead to organisms that are not viable (not properly developed) so are not favored by natural selection. Strong negative selection pressure
Homeobox genes summary
Regulatory genes
code for homeodomain (part of a protein)
Control body development
Regulate mitosis and apoptosis
180 bp
Homeobox genes are genes whose activity switches a whole set of other genes on or off, affecting an organism’s body plan (overall design of an organism’s body).
They are found in clusters called hox clusters
Most animals have very similar homeobox genes.
Genes are highly conserved (have not evolved much)
Code for production of transcription factors. These can bind to certain sections of DNA and cause it to be transcribed.
Hox genes
a very important subset of homeobox genes
One group of Homeobox genes only present in animals
determine the identity of embryonic body regions along the anterior-posterior axis (i.e. the head-tail axis)
They are responsible for correct positioning of body parts.
In animals, they are found in gene clusters, mammals have 4 on different chromosomes.
The order in which they appear along the chromosome is the order in which their affects are expressed in the organisms.
Humans have 39 Hox genes.
Diploblastic animals have
Diploblastic animals have two primary tissue layers (jellyfish, corals, anemones)
Triploblastic animals have
Triploblastic animals have three primary tissue layers (arthropods and vertebrates)
Hox genes in the head control
Hox genes in the head control the development of mouthparts,
Hox genes in the thorax control
Hox genes in the thorax control the development of wings, limbs or ribs.
Individual vertebrae and structures develop from segments in the embryo called _______. They are directed by ____ ______ to develop in a particular way depending on their _______.
somites.
Hox genes.
position.
A homeobox is a DNA sequence that codes for a protein transcription factor
The transcription factors (that homeobox sequences code for) attach to DNA at specific locations and regulate the transcription of genes (e.g. genes that control the early development of eukaryotic organisms) by turning various different genes on and off in the correct order
A homeobox is a DNA sequence that codes for a protein transcription factor
The transcription factors (that homeobox sequences code for) attach to DNA at specific locations and regulate the transcription of genes (e.g. genes that control the early development of eukaryotic organisms) by turning various different genes on and off in the correct order
Radial body shape
Radial – no left or right, only top and bottom. Jellyfish are an example
Bilateral body shape
Bilateral – left and right, head and tail. Most animals are an example.
Asymmetry body shape
Asymmetry – no lines of symmetry. Sponges are an example.
How do Homeobox genes work
The proteins produced act as transcription factors
- molecular switches which mRNA production ON or OFF
- they do this by binding to specific DNA sequences called regulatory elements
All homeotic genes share the same ___ base sequence encoding_____ ______sequence of amino acids
180
The same
HOMEOBOX sequence binds
This section of the protein binds to the groove in the DNA double helix
What is apoptosis
Programmed cell death
Cyclins act as ……….
CDKs act as …….. (once activated by cyclins)
regulators
catalysts
Process of apoptosis
-The DNA of the cell becoming denser and more tightly packed
-The nuclear envelope of the cell’s nucleus breaking down and chromatin condensing
-Vesicles forming that contain hydrolytic enzymes
-Phagocytes engulfing and digesting the cell via phagocytosis
Mitosis and apoptosis
Both are essential in shaping organisms
Mitosis increases the number of cells available for growth.
Apoptosis helps to shape body parts by removing cells and tissues.
Cells undergoing apoptosis can release chemical signals which stimulate mitosis and cell proliferation, leading to remodelling of tissues.
Hox genes regulate both mitosis and apoptosis.
Example of External stimulus of genes regulating cell cycle
External e.g: stress caused by lack of nutrient availability, could result in gene expression which prevents cells from undergoing mitosis
Example of External stimulus of genes regulating apoptosis
gene expression which leads to apoptosis being triggered can be caused by attack by a pathogen
Example of internal stimulus of genes regulating apoptosis and cell cycle
DNA damage. if DNA damage is detected during cell cycle, can result in expression of genes which cause cell cycle to pause and then even apoptosis
Mitosis is controlled by various different genes that are categorised into two distinct groups:
……..-………are genes that stimulate cell division
……..-………. genes are genes that reduce cell division
Proto-oncogenes
Tumour-suppressor
Tumour-suppressor genes can also…………. …………… in cells with damaged DNA that cannot be repaired
stimulate apoptosis
Clusters of homeobox genes are called
hox clusters.
Larger organisms have ______ hox clusters
more
The regulation of the pattern of anatomical development is called ________
morphogenesis.
DNA is _____ charged due to ______ _______ groups.
While histones are ________ charged
This way they can bind together
Negatively
Negative phosphate
Positively
Regulatory genes
Proteins involved in DNA regulation
E.g repressor protein
(lac I)
Epigenetics is
term used to describe the control of gene expression by the modification of DNA.
sometimes used to include all of the different ways in which gene expression is regulated
why is the genetic code degenerate
, because a single amino acid may be coded for by more than one codon.
Meaning a point mutation may have no effect, allowing the same protein to be made for normal functioning
what is a point mutation
If only one amino acid is affected by substitution, insertion or deletion
Frameshift mutation
e.g: insertion and deletion
Disrupts triplet code reading
Codon
A sequence of three bases which codes for a particular amino acid
Mutations can occur _____, often during ______ ____________, but the rate of mutations is increased by ________
spontaneously
DNA replication
mutagens
Physical mutagens
e.g
how
ionizing radiation such as X-rays
break one or both DNA strands. Some breaks can be repaired, but mutations can occur in the process
Chemical mutagens
e.g:
How
Deaminating agents
chemically alter bases in DNA such as converting cytosine to uracil in DNA, changing the base sequence
3 types of biological mutagens
alkylating agents
base analogs
viruses
alkylating agents in mutation
methyl or ethyl are attached to bases resulting in the incorrect pairing of bases during replication
base analogs in mutation
incorporated into DNA in place of the usual base during replication, change base sequence
Viruses in mutation
viral DNA may insert itself into a genome, changing the base sequence
reasons for a silent mutation
-mutation occur in non-coding region of DNA (introns)
-code for same amino acid due to degenerate nature of the genetic code
-may result in changes to the primary structure that do or effect the overall structure or function of proteins synthesised
Nonsense mutations
result in a codon becoming a stop codon. Result in a shortened protein being synthesised which is normally non-functional. Normally have negative effects on phenotypes
Missense mutations
result in incorporation of an incorrect amino acid(s) into the primary structure when the protein is synthesised. Result depends on the role the amino acid plays in the structure and .: function of the protein synthesised
Chromosome mutations
effect the whole chromosome or number of chromosomes within a cell
Can be caused by mutagens or normally in meiosis
changes in chromosome structure during chromosome mutations =
-Deletion
-Duplication
-Translocation
-Inversion
Deletion in chromosome mutations
section of chromosome breaks off and is lost within cell
translocation chromosome mutations
section of one chromosome breaks off and joins another non-homologous chromosome
Inversion chromosome mutations
section of chromosome breaks off, is reversed and then joins back onto chromosome
modifying mRNA - 4 steps
1) RNA splicing. remove introns
2)Add cap (modified nucleotide) to 5’
3)Add tail of adenine to stabalise mRNA, prevent degredation
4)mRNA editing . make different versions of mRNA to make different proteins
Two ways to decrease Translation
A) Degrade mRNA
B)Inhibitory proteins bind to mRNA so that it can’t bind to a ribosome
How to increase Translation
Activate initiation factors
-allowing mRNA to bind to Ribosome
-by phosphorylation of proteins to activate them which is done by Protein kinases
-Protein kinases can be activated by cAMP
Post-translational gene control 4 ways
A) add non-protein groups
B)Modify amino acids to make bonds
C)Protein folding (tertiary and quaternary)
D) Modification by cAMP (activation)
2 example of Post-translational gene control
Modification by cAMP (activation)
1) cAMP + CRP binds to RNA polymerase to upregulate its activity
2) cAMP activates kinases
Kinases then go onto phosphorylate and activate other enzymes and proteins
Lac operon In presence of glucose or Lactose process
1) when glucose is present, lac I is expressed to make repressor protein.
Binds to operator, blocks Promoter (RNA binding site)
2) RNA polymerase can’t bind to Promoter due to blockage, no transcription of 3 structural genes
3)when Lactose is present, it binds to repressor protein, causing a conformational gene. Hence the repressor can no longer bind to the operator, unblocking the Promoter
4)RNA polymerase then binds to the Promoter to start transcription
5)CRP can bind to cAMP and the whole complex can bind to RNA polymerase to upregulate its activity
6) Glucose decreases cAMP concentration inside cell. Hence the CRP-CAMP-RNA polymerase complex will dissociate, down regulating transcription
7)Lactose is released from the repressor protein. The repressor protein binds to the operator once more, preventing RNA polymerase from binding to the promotor to start transcription again
does lack O (operator gene) code for a protein
no
is cyclic AMP made of protein
nein
remember, made from ATP
what stage of meiosis does independant assortment accour
Metaphase I and Metaphase II
what stage of meiosis does independant assortment accour
Metaphase I and Metaphase II
outline roles of PCR in sequencing a genome
amplify DNA
different lengths of fragments/ chain termination
outline roles of electrophoresis in sequencing a genome
tp put DNA in size order
to read base sequence
outline roles of digestion of DNA by restriction enzymes in sequencing a genome
to cut (genome DNA) into smaller (750 bp) fragments
to cut vectors / BACs / plasmids (for gene library)
why genome has to be fragmented before sequencing
-genome too big/ very large
-accuracy better/fewer errors
-divide job ober time/ different labs
where does repressor protein bind
operator region
