MM 6-10 Flashcards
Translation
mRNA is translated into amino acid sequences.
Ribosome
The ribosome is a complex molecular machine found within all living cells, that serves as the site of biological protein synthesis. Ribosomes link amino acids together in the order specified by mRNA. Ribosomes consist of two major components: the small ribosomal subunit, which reads the RNA, and the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.
Codon
mRNA nucleotide triplets that specify which amino acid will be added during protein synthesis.
Stop codons
UAA
UGA
UAG
Start codon
AUG -methionine
mRNA structure
7-methyl guanosine cap-5’UTR-coding sequence-3’UTR-poly A tail.
Genetic mutation: Nonsense/stop
The introduction of a stop codon prematurely.
Frameshift mutation
A frameshift mutation is a genetic mutation caused by indels (insertions or deletions) of a nucleotide, resulting in a completely different translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein.
Trinucleotide repeat disorder
Trinucleotide repeat disorders are a set of genetic disorders caused by a mutation where trinucleotide repeats extend in the offspring, making a repeated section of DNA longer than it should be. Eg Huntington’s disease.
Translation: initiation
- Coming together: 2 ribosomal subunits come together with mRNA, tRNA bound to starting amino acid, GTP for energy, and initiation factors that aid in the recognition of start codon.
- tRNA recognizes start codon.
Ribosome sites
A: aminoacyl - entrance & acceptor site for next tRNA
P: peptidyl - contains the growing peptide chain
E: exit - harbors de acylated tRNA on its way out.
Translation: elongation
Involves the addition of amino acid chains to the carboxyl end of peptide chain. Unlike all other reading, mRNA is translated from 5’ –> 3’
tRNA enters A site. Peptide bond forms between adjacent amino acids with the growing chain held at A site. Unacylated tRNA in E site exits, allowing the growing chain to move to P site. A site is then free to accept another tRNA.
peptityltransferase
Enzyme involved in elongation of peptide sequence in translation.
Translation: termination
Occurs when UAA, UGA, UAG arrive at A site. Release factor recognizes stop codon and activates release.
Translation: trimming
A post post translational modification. Some proteins within a family differ by peptide length. Trimming or cleavage, provides for slightly different functions.
Ubiquitination
Protein is tagged with ubiquitin, thereby marking it for destruction by a proteasome.
Constitutive genes
Genes essential for life that are constantly expressed in all cells.
Inducible genes
Genes that are transcribed only as required. Determine tissue specificity.
What determines gene expression? simplistically.
Availability and accessibility of gene. And availability/accessibility of transcription factors.
Histone acetyltransferases (HATs)
Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group. DNA is wrapped around histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation increases gene expression by helping unwind gene rich euchromatin. Counteracted by HDAC (Histone deacetylases).
Histone deacetylases (HDAC)
Histone deacetylases are a class of enzymes that remove acetyl groups (O=C-CH3) from a lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. Plays a role in gene regulation. Counteracts HAT.
Transcription factors
Proteins that recognize and bind to a specific DNA promoter/enhancer region. Once bound they interact with RNA Pol II to promote transcription. Transcription factors are available at different abundances and have different rates of response, therefore helping regulate transcription. They can be inducible or constitutive.
Inducible transcription factors.
Present only when needed and are activated/inactivated by environmental cues.
miRNA
microRNA are small noncoding RNA molecule that effect protein regulation. miRNA sequences complementary to mRNA, and will hydrolyze it, preventing transcription and leading to degradation.
Aneuploidy
Aneuploidy is the presence of an abnormal number of chromosomes in a cell, for example a human cell having 45 or 47 chromosomes instead of the usual 46. Most cases of aneuploidy result in miscarriage.
Translocation
A translocation is a chromosome abnormality caused by rearrangement of parts between NONhomologous chromosomes. Translocations can be balanced (an even exchange of material with no genetic information extra or missing, and ideally full functionality) or unbalanced (where the exchange of chromosome material is unequal resulting in extra or missing genes).
Several forms of cancer are caused by translocations.
Copy number variation (CNVs)
Copy number variation (CNVs) is when large sections of the genome (>1000 base pairs) are repeated. The number of repeats in the genome varies between individuals causing necessary population variation. We all have CNVs, which can amplify certain gene expression.
Pathogenic consequences result in autism, epilepsy, Huntington’s disease.
It is thought to occur during crossing over in meiotic recombination.
Single-nucleotide polymorphism (SNP)
An SNP is a variation in a single nucleotide that occurs at a specific position in the genome, including sense, missense, non-sense point mutations. Does not include insertions and deletions. We all carry about 3.5 million SNPs. Most are benign. Some are not; sickle cell anemia and cystic fibrosis.
Microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (2–5 base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within the genome, although most are in introns. They rarely cause disease. Used for paternity tests and in forensic identification.
Trisomy
Aneuploidy in which an extra chromosome is present due to nondisjunction. Can occur in meiosis 1 or 2. Eg trisomy of ch21 leads to down syndrome.
Patau syndrome
Trisomy of chromosome 13. 80% die within first year. Mental and muscular development issues. Polydactyly, microchephaly, and many other side effects.
Edwards syndrome
Trisomy of chromosome 18. Babies born small with heart defects. 50% die in first week.
Turners Syndrome
Monosomy of the X chromosome. Typically infertile, do not develop breast or menstruate, have a thick webbed neck, develop heart issues and have a shorter life expectancy.
Point mutation
A point mutation is a type of single nucleotide polymorphism that causes a single nucleotide base substitution, insertion, or deletion of the genetic material, DNA or RNA.
Includes synonymous (silent), and nonsynonymous [nonsense (premature stop codon), and missense (different codon)].
Considered small-scale pathogenic mutations.
Silent mutation
A genetic mutation that does not alter the phenotype of an organism. When within the exon of a gene, silent mutations are generally synonymous mutations, coding for the same amino acid
Synonymous mutation:
A point mutation that codes for the same amino acid due to the degeneracy of the genetic code. Synonymous mutations are silent point mutations.
Nonsense mutation
A nonsense mutation is a non-synonymous point mutation in which a codon is prematurely made into a stop codon. This causes the protein to be shortened because of the stop codon interrupting its normal code. How much of the protein is lost determines whether or not the protein is still functional.
Missense mutation
A missense mutation is a non-synonymous point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. Depending on the location, missence mutations can be conservative (properties of protein remain the same) or nonconservative (protein function changes). E.g sickle cell anemia.
Non-synonymous mutation
A point mutation that alters the amino acid sequence of a protein. It is contrasted with synonymous substitution which do not alter amino acid sequences. Includes missense and nonsense mutations.
Frameshift mutation
A point mutation in which an amino acids is inserted or deleted.
Small-scale pathogenic mutation
Includes point mutations and aberrant splicing. Compared to large-scale pathogenic mutations.
Aberrant splicing
Mutation caused by the skipping or introduction of an exon during splicing.
Large-scale pathogenic mutation
Includes aneuploidy, translocations, and copy number variation. Compared to small-scale mutations.
Genomic instability
Considered a characterization of cancer. One genetic mutation causes a cellular change, which in turn causes more mutations within the cell, sometimes allowing for rapid growth, the bypassing of safety mechanisms, rapid division, resistance to apoptosis and then metastasis.
Driver mutation
A driver mutation increases genomic instability and can lead to cancer. Driver mutations often increase the occurrence of other mutations. Eg, a mutation that bypasses safety mechanisms or speeds cell growth/division.
Mosaicism
2 lineages that can occur from chromosomal aberration.
Robertsonian translocation
When two acrocentric chromosomes merge together, rather than swapping. There is one fewer chromosome but not necessarily lost DNA. 50% chance that offspring is viable, and another 50% that it has down syndrome (if 14-21 translocation).
Clinical indications for prenatal cytogenetics
History of miscarriages
Chromosomal abnormality
Age of mother
Abnormal ultrasound
Clinical indications for postnatal cytogenetics
dysmorphic features
developmental delay
Clinical signs specific to chromosomal disorder.
Infertility, many miscarriages
Family history of heritable chromosomal abnormality.
Imprinting
Genomic imprinting is the phenomenon by which certain genes are expressed in a parent-of-origin-specific manner (randomly determined). If the allele inherited from the father is imprinted, it is thereby silenced, and only the allele from the mother is expressed. The process involves DNA methylation and histone methylation without altering the genetic sequence.
A small proportion (<1%) of genes are imprinted, meaning that gene expression occurs from only one allele.
Human diseases involving genomic imprinting include Angelman syndrome and Prader–Willi syndrome.
Chromosomal microarray
the gold standard for future testing. Same resolution as FISH, but genome wide detection. Should be applied to all cases of developmental daly, intellectual disability, autism or congenital anomalies.
G band Karyotyping
Used to detest chromosomal abnormalities and other large scale genetic disorders.
FISH
Used for insertions or deletion disorders when cause is suspected.
Transcription factor domains:
DNA-binding domain-the sequence specific binding domain.
Trans-activating domain (TAD) contains binding sites for other proteins such as transcription coregulators.
Optional signal sensing domain (SSD) is a ligand binding domain), which senses external signals and, in response, transmits these signals to the rest of the transcription complex,
3’ Polyadenylation
The 3’ outermost segment is cleaved by an endonuclease. The Poly A polymerase adds adenosine 40-250 residues. Slows degradation by exonucleases in cytosol. The longer the tail, the longer the lifespan of RNA.
Differential splicing
Different exons of a gene may be included or excluded from the final, processed messenger RNA (mRNA) produced from that gene. Consequently, the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions. Regulation is done with splicing activators that promote the usage of a particular splice site, and splicing repressors that reduce the usage of a particular site.
5’ capping
The addition of 7 methylguanosine residue, to which proteins bind, protecting RNA from nuclease attack. It also allows for nuclear export of RNA; the caps are recognized by the nuclear pore complex for export into the cytoplasm.
miRNA
micro RNA are small noncoding strands of RNA that regulate expression. They are complementary to a particular mRNA and will bind to it, downregulating expression by preventing translation.
rRNA
rRNA; Ribosomal RNA, accounts for 80-90% of RNA in cells. It is produced by transcription but not translated. It plays a structural and enzymatic role in ribosomes.
tRNA
tRNA; Transfer RNA, transcribed but not translated. Covalently bind Amino acids and transports them to ribosome.
mRNA
mRNA; Messenger RNA, translated and contains instructions for protein synthesis.
RNA polymerase: Several types make different types of RNA. Do not require primer. Reads 3-5 and builds from 5-3.
RNA editing
Editing events may include the insertion, deletion, and base substitution of nucleotides within the edited RNA molecule. Whan codons are introduced at various places protein structure changes, generating protein diversity.
Factors that contribute to gene diversity
Differential splicing
RNA editing
Multiple promoters and multiple polyadenylation sites.
Activators
Activators are transcription factors that enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene.
They can recruit chromatin modifiers to loosen DNA (which will neutralize lysine tails on histamine).
Enhancers are sites on the DNA helix that are bound by activators.
Silencers
Transcription factors can also prevent transcription and removal will initiate transcription. Silencers are regions of DNA sequences that, when bound by particular transcription factors, can silence expression of the gene.
Transcription factor
A protein that binds to DNA and regulates gene expression by promoting or suppressing transcription.
Transcriptional regulation
Controlling the rate of gene transcription for example by helping or hindering RNA polymerase binding to DNA
Terms for increasing the rate of gene transcription
upregulation, activation, or promotion –
Terms for decreasing the rate of gene transcription
downregulation, repression, or suppression
Coactivator
A protein that works with transcription factors to increase the rate of gene transcription.
Corepressor
A protein that works with transcription factors to decrease the rate of gene transcription.
Response element
A specific sequence of DNA that a transcription factor binds to.
Response element
A specific sequence of DNA that a transcription factor binds to.
How can we regulate protein activity?
Ligand binding De/Phosphorylation Expression-levels and location Cofactors Proteolytic cleavage
How is tight regulation of proteins maintained
Rapid protein turnover ensures that protein levels are appropriate as needs change.
Lysosomal degradation
Degrades proteins that are imported into the cell
Proteasomal degradation
Degrades cytosolic proteins marked for destruction
Lysosomes
Membrane organelles within the cell that degrade proteins, nucleic acids, carbs and lipids. They arise from the endoplasmic reticulum. They have proton pumps that produce a low pH within (pH 4). They also have acid hydolases.
They receive contents by fusing with membranes from autophagosomes, phag/pino/endocytosis.
Autophagosome
An autophagosome is a spherical structure with double layer membranes. After formation in the ER, autophagosomes deliver cytoplasmic components to the lysosomes. The outer membrane of an autophagosome fuses with a lysosome to form an autolysosome. The lysosome’s hydrolases degrade the autophagosome-delivered contents and its inner membrane.[
Autophagy
Proteins and organelles are packed into autophasomes, which then fuse with lysosomes for degradation.
Lysosomal storage diseases
LSDs are a group of metabolic disorders that result from defects in lysosome or autophagasome function, which require many critical enzymes. If one of these enzymes is defective the large molecules accumulate within the cell, eventually killing it.
Ubiquitination (brief)
The process by which proteins are marked and targeted for destruction by proteosomes.
Ubiquitin chains are added to lysine residues to mark destruction
Ubiquitin
Small proteins that are added in chains to lysine residues. Poly-ubiwuitin chains are biomarkers for proteosomal degradation.
Proteosome
Proteasomes are large, barrel shaped protein complexes located in the nucleus and the cytoplasm. They are composed of at least 7 alpha and 7 beta subunits.
They degrade unneeded or damaged proteins by proteolysis and are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins.
Targeted proteins enter the complex and are proteolyzed by proteases (trypsin, chymotrypsin).
The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins.
Proteins are tagged for degradation by ubiquitin chains, which bind to the proteasome, allowing it to degrade the tagged protein.
Ubiquitin ligases
A ubiquitin ligase (E3) assists in the transfer of ubiquitin to the lysine reside of a protein substrate. There are hundreds of different E3s, providing substrate specificity.
Mutations can cause disease.
Ubiquitination steps
Ubiquitin is activated by ubiquitin activating enzyme (E1)
Ubiquitin is then conjugated by ubiquitin conjugating enzyme (E2).
Ubiquitin is transferred to the target protein by ubiquitin ligase (E3), which recognizes the target substrate
Parkin
Parkin is a protein that is a component of a multiprotein E3 ubiquitin ligase complex, thereby assisting in protein degradation. Mutations in this gene cause Parkinson’s disease.
MDM2
MDM2 is a protein involved in an E3 ubiquitin ligase that targets p53 (which is a tumor suppressor). Upregulation of MDM2 is seen in many cancers.
Post-translational modifications
- Ligand bonding
- Cleavage (zymogens -> enzyme)
- Phosphorylation
- Ubiquitination
- Fatty acid modification
- Glycosylation
Protein phosphorylation
- Activates
- Deavtivates
- Conformational change
- Promotes interactions
Fatty acid modification of proteins -purpose
Allows protein to attach to membranes and other proteins.
Phosphorylase vs Phosphatase. Which does what?
Phosphorylase adds phosphate (kinase).
Phosphatase removes phosphate (dephosphorylation by hydrolyses)
Prader–Willi syndrome
Prader–Willi syndrome is a genetic disorder due to loss of function of specific genes on chromosome 15. Symptoms include weak muscles, poor feeding, and slow development, often accompanied by obesity and type 2 diabetes.
Occurs due to a deletion on the father’s chromosome 15. Due to imprinting, the maternally inherited copies of these genes are virtually silent, and only the paternal copies of the genes are expressed.
Deletion on the same gene but on the mother’s side results in Angelman syndrome (AS).
Angelman syndrome (AS)
Angelman syndrome (AS) is a neurodevelopmental disorder characterized by severe intellectual and developmental disability, sleep disturbance, seizures, jerky movements (especially hand-flapping), frequent laughter or smiling, and usually a happy demeanor.
AS is a classic example of genomic imprinting in that it is caused by deletion or inactivation of genes on the maternally inherited chromosome 15 while the paternal copy, which may be of normal sequence, is imprinted and therefore silenced.
TATA box
TATA box is a DNA sequence found in the promoter region of some genes. It is the binding site of either general transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase.
During the process of transcription, the TATA binding protein (TBP) normally binds to the TATA-box sequence, which unwinds the DNA and bends it through 80°. The AT-rich sequence of the TATA-box facilitates easy unwinding, due to weaker base-pairing interactions between A and T bases, as compared to between G and C.
The TATA box is usually found at the binding site of RNA polymerase II.
