Unit 2 Topic 3Ci Gene Expression Flashcards
Define gene expression
- undifferentiated stem cells undergo cell differentiation by differential gene expression
- hence, cells differentiate into different specialised cells
Outline the mechanism of cell differentiation by differential gene expression and eventually modify the function of the cell
- only certain genes are switched on in a cell under certain transcription factors, chemical stimuli, or other epigentic mechanisms
- other genes are switched off in the cell
- only the genes that are switched on are transcribed, forming mRNA
- mRNA translated to synthesis protein
- proteins produced permanently modify structures of the cells and control processes that can take plcae
- modify the function of cell
How are nucleosomes formed
wrapping DNA around histone proteins
Function of nucleosomes
- protect DNA and allow it to be packaged, allowing it to be supercoiled
How are histone proteins formed in an octamer arrangemnet
- histone proteins pack long DNA and coil to form nucleosomes
- as histone proteins are postiviely charged => interact with negatively charged phosphate group of DNA
- helped in an octamer arrangement
Formation of solenoid group
- H1 histoen binds with DNA
- form nucleosomal DNA => further condensation
- chromatin fibre as solenoid loop (30nm fibre)
What is the purpose of a solenoid group
- facilitate further packaging
Why do histone proteins and DNA associate well with each other
- histone proteins are positively-charged
- DNA is negatively-charged due to phosphate group
Comparison of closed chromatin and open chromatin
closed chromatin
- tightly held together
- associated with gene inactivity
- DNA is not readily exposed for transcription factors to bind
open chromatin
- less tightly held together
- associated with active gene expression
- one section is exposed ==> transcription factor is allowed to bind to DNA, promoting transcription
Define chromatin
a mixture of DNA and proteins that form the chromosomes found in the cells of humans and other higher organisms
What other factor also promote transcription in open chromatin
- polymerase 2
What is the most frequent method of gene regulation
- controlling transcription by transcription factor
How does single transcription factor control activity of several different genes?
- stimulating the expression of one gene
- and supressing the expression of another gene
How is it possible for several transcription facotrs to be involved in expression of single gene?
there are many levels of control
What are the functions of the non-coding regions of DNA
- affects transcription of protein-coding genes / modifying chromatin structure / modifying products of transcription
- regulate expression of protein-coding genes
What are non-coding regions of DNA
- RNA synthesised from transcription of DNA
- but not translated into proteins
- do not code for proteins
What is the promoter region of DNA
- region of DNA usually located near to the coding region of gene where transcription starts
Outline the process of how transcription is initiated
- transcription factors bind to promoter
- starting point of the transcription of the gene is identified
- enable binding of RNA polymerase to gene
- initiate transcription
What are the properties of promoter region
- usually found above the starting point of a gene (before start codon)
- attachment points for RNA polymerase and transcription factors adjacent to the gene
Is RNA polymerase a transcription factor
no
What is the enhancer region
- region of DNA located far from coding region of a gene which promotes transcription
How does the enhancer region promotes transcription
- when activator proteins (transcription factor) binds to enhancer sequences
- binding makes the structure of chromatin more open by causing chromatin to bend
- transcription is promoted
- rate of transcription of gene is greatly increased
How do eukaryotic cells become specialised
- when specific transcriptional factors move from the cytoplasm into the nucleus
- transcription of target genes can be stimulated or inhibited
- turn on / off genes ==> only certain proteins are produced in particular cell
- become specialised
What are transcriptional factors control protein creation
- molecules (proteins) from the cytoplasm enters the nucleus and binds to the DNA in the nucleus
- transcription occurs
- each one can bind to different base sequences on DNA
- enables RNA polymerase to bind
- initiate transcription of genes
- creates mRNA molecule for the gene
- translated into the cytoplasm ==> attach to ribosomes => create protein
What will happen without the binding of a transcriptional factor
- gene is inactive
- protein will not be made
What is Oestrogen
- steroid hormone (lipid-soluble) that can initiate transcription
How does oestrogen initiate transcription
- enters cytplasm through diffusion
- binds to a receptor site on the transcriptional factor (complementary in shape to part of the receptor of transcriptional factor)
- causes transcriptional factor to change shape ==> making it complementary
- activated transcriptional factor move through nuclear pores into nucleus ==> bind to DNA
- RNA polymerase attach ==> mRNA created
- initiate transcription
What is the implication of oestrogen being a steroid hormone
- lipid-soluble
- can transport through blood
- diffuse through cell membranes
Can transcription occur without the transcriptional factor
no
- RNA polymerase is a protein with unique 3D shape
- active site of the RNA polymerase is only complementary in shape to the DNA and the transcriptional factor together
- can only attach once transcriptional factor is attached
Properties of the enhancer region of DNA
- found far away from the gene being controlled
- DNA sequence that allows other transcription factors to bind
What is the silencer region of DNA
- region of DNA located far from coding region of a gene which inhibits transcription
How does the silencer region of DNA inhibits transcription
- when repressor proteins (transcription factors) binds to non-coding regions of DNA
- chromatin is less open / closed
- blocking or reducing the rate of transcription
Where do you find the silencer region of the DNA
- far away from the gene being controlled
Define lac operon
- cluster of genes which function together to make the enzymes for breaking down lactose
- contains lac Z / Y / A that work together to make enzymes that break down lactose
What is the function of lac I
- codes for the repressor protein
- which in the absence of lactose will bind the operator region
- hinder the binding of RNA polymerase at the promoter region
What happen with the lac operon regulation when lactose is absent
- repressor bound to silencer region of DNA
- RNA polymerase cannot bind to DNA sequence
- RNA polymerase is prevented from transcribing the genes for synthesising lactase (because there isnt any)
- inhibition of lactose metabolism increases concentration of undigested lactose
What happen with the lac operon regulation when lactose is present
- lactose binds to the repressor protein
- inhibits the repressor protein from binding the DNA
- repressor can no longer bind to the silencer region
- RNA polymerase bind to the promotor
- genes coding for lactase are transcribed
What happen with the lac operon regulation when translation of lactase occurs
- lactase (enzyme) causes break down of lactose molecules
- concentration of lactose decreases
- less lactose available to bind to repressor
- repressor binds to silencer again
- preventing RNA polymerase from binding to the promoter
What are exons
- coding sections of the gene
What are introns
- non-coding DNA
- removed then broken down back into nucleotides ready for use
What are spliceosome
- enzyme complex assembled from small nuclear RNA and proteins
- form and causes introns to form loops, allowing exons to be joined together in a process
Define RNA splicing
- catalyses the removal of introns from pre-mRNA
- removing introns from the gene to splice exons together
- translated to become polypeptide
What are the differences between pre-mRNA and mature-mRNA
pre-mRNA: contains exons and introns
mature-mRNA: contains only exons, leave nucleus to be translated into polypeptides
Define alternative splicing
- different versions of mature mRNA with different codon sequences can be produced from the same gene
What can different versions of mature mRNA cause phenotype
- same gene can produce different versions of mature mRNA with different codon sequences
- different versions of mature mRNA translated to polypeptides of different amino acid sequences
- different bondings between R groups ==> different shapes and functions of the protein produced
- varies in its’ biological function
- causes variations in phenotypes
What is the advantage of alternative splicing
- results in more variety in the phenotype than is comedy for directly in the genotype
- single gene can give rise to more protein
- one gene can perform many different functions under different conditions
- single genotype can produce various genotypes
Where do post-translational control occurs
Golgi apparatus
How does modification of protein leads to cell differentiation
- modifed after protein synthesis by translation
- change in the function of the protein in the cell
- change in the structure and function of the cell
- cell differentiation
Outline the process of cell differentiation
- chemical stimulus (demethylation) / transcription factors
- certain genes are activated / switched on
- mRNA produced from active genes
- translation of mRNA to form polypeptide / protein
- permanent modification of the cell
What is epigenetics
- study of control of gene expression by factors other than changed in the DNA sequence
What is epigenetic modifications
- heritable changes in the gene expression that do not involve changes in the DNA sequence
What is DNA methylation
- adding methyl group (-CH3) by DNA methyltransferase enzyme to the cytosine base next to a guanine base in DNA
- always inhibits transcription
What is the consequences of DNA methylation
- causes DNA to bind more tightly to the histone proteins
- heterochromatin is formed
- DNA less accessible to transcription factors
What is DNA demethylation
- removal of methhyl groups from DNA
- enabling genes to become active for transportation as the genes are switched on
What are the applications of the DNA methylation
controlling gene expression
1. embryonic development
2. X-chromosome inactivation
How does DNA methylation help with cancer
- genetic predisposition for a genetic disease
- DNA methylation ensures that human cancers can stay silent in the genes
What is histone acetylation
- adding acetyl group (-COCH3) to one of the lysines in the histone structure
- promotes transcription
Consequences of histone acetylation
- causes heterochromatin structure to open up
- activates chromatin to be come euchromatin
- DNA more loosely bound to histones
- DNA more accessible to transcription factors
- genes in the area can be transcribed
What is the mechanism of histone acetylation
- lysine has positively charged R groups => form ionic bonds with negative charged phosphate backbone of DNA
- acetyl group added (negative charge) => histone overal has no charge
- histone = less associated with the negatively charged DNA
What is histone methylation
- adding methyl group to one of the lysines in the histone structure
- may cause inactivation of DNA or activation of a region
- usually linked to silencing of a gene / whole chromosome
What is moulting
insects sheeding exoskeleton by histone modification
How is moulting controlled by hormones
- controlled by two hormones (ecdysone, juvenile hormones)
ecdysone
- steroid hormone
- controls the events of moulting (whether the insects should undergo moulting)
juvenile hormones
- controls which kind of moulting occurs
- level of juvenile hormones decrease = more adult characteristics occur
What are examples of how cells change due to internal stimuli
- sex hormones produced at puberty stage cause certain cells to change by DNA methylation
How is the polypeptide chains different between adult and fetal haemoglobin
adult haemoglobin: two alpha, two beta globin polypeptide chains
fetal haemoglobin: two alpha, two gamma globin polypeptide chains ==> stronger affinity for oxygen than human haemoglobin
How is epigenetic control showed in the differences of fetal and adult haemoglobin
- different versions of globin genes are swithced on and off during human development (embryo to baby)
- genes for fetal gamma globin are expressed during fetal development due to histone acetylation
- histone and dna methylation silence the fetal gamma globin just before and after birth (ncRNA are involved asw)
- adult beta globin genes activated just before birth in the bone marrow
How do we measure the differentiation between cells
- compare the proteins contained in cells
- find out which genes have been expressed or repressed
- certain proteins are only produced in certain cells for performing specific functions
What are examples of certain proteins are only produced in certain cells for performing specific functions
- enzymes needed to produce insulin hormone to convert glucose to glycogen is only produced by the islet of Langherans cells in the pancreas
- smooth muscle cells only express housekeeping proteins
- cerebral cortex of the brain has 318 extra proteins
- human testes have the greatest variety of extra proteins on top of normal housekeeping proteins
