Cell Structure and Function: Gene to Protein Flashcards
What is a genotype?
An organisms hereditary information
What is a phenotype?
The observable or physiological traits of an organism
What is gene expression?
The process of going from DNA to a functional products (typically a protein)
What is DNA?
is the heritable material that is used to store and transmit information from generation to generation
What is RNA?
acts as a messenger to allow the information stored in the DNA to be used to make proteins
What is messenger RNA (mRNA)?
is a single-stranded RNA molecule that is complementary to one of the DNA strands of a gene
What is transfer RNA (tRNA)?
carry amino acids to the ribosome. They act as “bridges,” matching a codon in an mRNA with the amino acid it codes for. It’s the physical link between the mRNA and the amino acid sequence of proteins
What do proteins do?
Carry out cellular functions
What are the three stages of gene expression?
Transcription, processing and translation
Where does transcription occur?
In the nucleus
Where does processing occur?
In the nucleus
Where does translation occur?
In the cytoplasm
What is the gene expression regulation at transcription?
Transcription factors need to correctly assemble and DNA needs to be accessible
What is the gene expression regulation at RNA processing?
Capping, extending of polyadenylation, alternate splicing, producing an mRNA able to be translated
What is the gene expression regulation at translation?
regulatory proteins can block translation, variable mRNA life-spans
Why is controlling gene expression important?
Because it needs to achieve the right thing at the right time (temporal and spatial control)
What are housekeeping proteins?
Proteins continuously produced by DNA
Main features of housekeeping proteins?
Are the more commonly used proteins
Protein and mRNA are present in large quantities (e.g. tubulin)
Typically have long half life in cells
What causes the production of other proteins?
Cell signalling
Features of proteins produced by cell signalling as a response to stimuli?
They are short lived and carry out their required function
What is the 5’ end of DNA?
This is the beginning of the chain and the phosphate group of the first nucleotide sticks out
What is the 3’ end of DNA?
This is the end of the chain where the 3’ hydroxyl of the last nucleotide is exposed
What way are DNA sequences read?
From the 5’ end to the 3’ end
What is transcription?
Transcription is the first stage of gene expression. Genetic information encoded in the base-pair triplets of the DNA molecule is copied to RNA molecules
What are the three steps of transcription?
Initiation, elongation, termination
What is upstream?
The 5’ end of DNA (promotor)
What is downstream
The 3’ end of DNA (terminator)
What does RNA have instead of the T nucleotide?
U (Uracil)
What is RNA polymerase II?
is the main enzyme involved in transcription is RNA polymerase
What is the function of RNA polymerase II?
It uses a single-stranded DNA template to synthesise a complementary strand of RNA. Specifically, RNA polymerase builds an RNA strand in the 5’ to 3’ direction, adding each new nucleotide to the 3’ end of the strand
What is the first step of transcription?
Initiation
What are transcription factors (TFs)?
are proteins that bind to DNA so that the RNA polymerase can bind
What is a TATA box?
A promotor sequence of T and A
Where is the TATA box located?
25-35 base pairs upstream of the transcription starting site
What is the function of the TATA box?
It’s recognized by one of the general transcription factors, allowing other transcription factors and eventually RNA polymerase to bind
What are promoters?
are specific nucleotide sequences at the start of a gene (upstream) which signal the initiation of RNA synthesis by assembling a complex that includes RNA polymerase II and one or more transcription factors
What is the initiation process of transcription?
Assembly of several transcription factors is required including the TATA box binding protein (TBP).
Once these proteins have been assembled, RNA Polymerase II can bind to the sequence of DNA (as well as more transcription factors), known as the promoter, to form the transcription initiation complex.
This begins transcription
What is a transcription initiation complex?
RNA polymerase and various general transcription factors bound to the promoter region
What is the second step of transcription?
Elongation
What is the process of elongation?
One strand of the DNA (template strand) acts as a template for RNA polymerase II
As it reads the template strand of DNA, the enzyme builds an RNA molecule out of complementary nucleotides which are added to the growing 3’ end of the transcript
The DNA double helix shape reforms as the transcript leaves the template strand.
Transcription continues until terminated by a termination signal
How many nucleotides are exposed at once in elongation in transcription?
10-20 nucleotides are exposed at a time when unwound
Is the RNA transcript the same as the non-template strand of DNA?
Yes but T is replaced by U
What is the third step of transcription?
Termination
What is a terminator?
is a region of DNA downstream (3’ end) of a gene that causes the RNA polymerase II to detach
What is processing?
The second phase of gene expression which occurs in the nucleus. In this phase, mRNA molecules are processed before leaving the nucleus by modification at their ends and by RNA splicing
What is capping?
a modified G “cap” nucleotide is added to the 5’ end
What is tailing?
50-250 A (adenine) nucleotides “tail” are added to the 3’ end (also known as a Poly A tail). This means that the 3’ end becomes polyadenylated
What is the function of capping and tailing?
Capping and tailing are thought to facilitate export, confer stability, facilitate ribosome binding once in cytoplasm, protect RNA from degradation and enhance translation
What is an exon?
coding regions (including UTRs) - will be the expressed portions of the mRNA
What are introns?
non coding regions intervening exons on mRNA
What are UTR’s
untranslated regions at 5’ and 3’ ends
What is the spliceosome?
is a large complex of proteins and small RNAs and is located within the nucleus
What are the three steps of processing?
Capping, tailing and splicing
What is splicing?
Splicing is when introns are removed from the transcript and exons are spliced together/rejoined to form mature mRNA. The final mature mRNA transcript is then exported from the nucleus and used as a template during translation
Where does splicing take place?
This is carried out through the spliceosome within the nucleus
What is alternative splicing?
is a process by which
different combinations of exons are joined together. This results in the production of multiple forms of mRNA from a single pre-mRNA
What is a triplet codon?
3 nucleotides on the base sequence that code for a particular amino acid
What is an anti-codon?
nucleotide sequence complementary to that of a corresponding codon in a messenger RNA (mRNA) sequence. An anticodon is found at one end of a transfer RNA (tRNA) molecule.
What does protein sequence determine?
Protein final structure
What does the final structure of a protein determine?
The function of the protein
What is translation?
The final stage of gene expression that occurs in the cytoplasm
What are the three steps of translation?
Initiation, elongation, termination
What is the mRNA binding site?
place where mRNA binds to a small subunit
What is the A site?
where the “next in line” tRNA is held
What is the P site?
Where the tRNA carrying the growing polypeptide is held
What is the E site?
Where tRNA’s exit from
What is the first step of translation?
Initiation
What is initiator mRNA?
Is the tRNA carrying methionine
What is the process of initiation in translation?
Small ribosomal subunit with initiator tRNA (already bound), binds to the 5’ cap of mRNA
Small ribosomal subunit scans downstream to find the translation start site (AUG)
Hydrogen bonds form between initiator anticodon and mRNA
Large ribosomal subunit then binds completing the initiation complex
What type of energy is required for initiation in translation?
GTP
What is the second step of translation?
Elongation
What is the process of elongation in translation?
Codon recognition: mRNA bases pair with complementary anticodon. GTP is invested to increase accuracy / efficiency
Peptide bond formation: A large subunit rRNA catalyses peptide bond formation. Removes it from tRNA in P site
Translocation: moves tRNA from A to P site tRNA in P site moves to E where the tRNA is released. Energy is required (GTP
What is the function of aminoacyl-tRNA synthetases?
It is an enzyme that adds amino acids to tRNA in the cytoplasm
What is the third stage of translation?
Termination
What is the process of termination in translation?
The appearance of a mRNA stop codon results in the A site being bound by a release factor
Bond between p-site tRNA and last amino acid is hydrolysed releasing the nascent (growing) polypeptide
Hydrolysis of two GTP is required
Ribosome components are disassembled and recycled
The protein assumes its three-dimensional conformation either spontaneously as it emerges from the ribosome or with the help of chaperones.
What determines the properties of amino acids?
Its side chain (R group)
What is the primary structure?
A single polypeptide chain that has a specific sequence/order of amino acids
What is the N terminus
is the end of a polypeptide that has a free amino acid group
What is the C terminus
is the end of a polypeptide that has a free carboxyl group
How is a polypeptide read?
From the 5’ end to the 3’ end
What type of bonds are inbetween amino acids?
Covalent bonds (relatively strong)
What is the secondary structure?
The single chain/sequence of amino acids becomes folded or twisted due to weak hydrogen bonds forming between the amino acids in the chain
What are the two types of secondary structures?
There are 2 common kinds: alpha (α ) helix and beta (β) pleated sheet
What is the tertiary structure?
Sulphide bonds between the folded secondary structures form the tertiary structure, which is irregular and specific for each protein because it depends on the amino acid sequence. Its 3D shape is stabilized by side chain interactions
What is the quaternary structure?
Multiple proteins associate together to form a functional protein (not all proteins do this)
Many Globular proteins consist of 2 or more polypeptide chains held loosely together
What is a signal peptide?
is at the N terminus of the protein (20 amino acids at the/near the leading end of the polypeptide) that targets it to the endoplasmic reticulum
What are signal recognition particles (SRP)?
A protein-RNA complex that recognizes a signal peptide as it emerges from the ribosome. If a signal peptide is at the N terminus the a SRP recognises that the ribosome needs to go to the rough endoplasmic reticulum
Process of polypeptide synthesis
Polypeptide synthesis begins
SRP binds to signal peptide
SRP binds to receptor protein on endoplasmic reticulum membrane
SRP detaches and polypeptide synthesis resumes
Signal cleaving enzyme cuts off signal peptide
Completed polypeptide folds into final conformation. A secretory protein (Such as insulin) is solubilised in lumen while a membrane protein remains anchored to the membrane. Both then go to the Golgi apparatus from the RER via vesicles for further maturation.
Where do proteins in vesicles go after they leave the endoplasmic reticulum?
The trans-face of the Golgi apparatus
What is phosphorylation?
a post-translational modification where there is an addition of a phosphate group
What can post-translation modifications do?
Can confer activity
Ability to interact with other molecules
Direct to particular locations
What are mutations?
A permanent and random change to the base sequence of DNA
What is the germ line and how can mutations effect it?
is that lineage of cells that eventually forms the eggs and sperm in the adult. Mutations in the germ line can effect many cells and can be catastrophic
What is local cells and how can mutations effect them?
Local mutations occur during cell division not in the whole body and have local effects
What is a point mutation?
a mutation affecting only one or very few nucleotides in a gene sequence
What is a substitution mutation?
A point mutation where one base is replaced by another - can have minimal or major effect
What is an insertion/deletion mutation?
A point mutation which can cause a frameshift due to adding/removing nucleotides and can have major effect if within coding sequence
What is a silent mutation?
is a change in the sequence of nucleotide bases which constitutes DNA, without a subsequent change in the amino acid or the function of the overall protein
What is a frameshift?
is a genetic mutation caused by a deletion or insertion in a DNA sequence that shifts the way the sequence is read
What is on the 5’ end of protein?
phosphate
What is on the 3’ end of protein?
carboxyl group
