Cells Flashcards
What is Infantile onset encephalomyopathy mitochondrial DNA depletion syndrome (MDDS)?
Thymidine kinase, succinyl-coA synthase-nuclear genes imported into the mitochondria
What is the historical changes in the understanding of medicine?
What are haemophilia and agromegaly?
What are the differences between prokaryotes and eukaryotes?
Eukaryotes-highly diverse organisms. Most Eukaryotes have different types of cell are specialised for different functions. Most organs and tissues contain multiple specialised cell types that perform specific functions.
What scale is used in biology?
What is the central dogma of molecular biology?
What is ATP and what is it used for?
What is the role of enzymes in cells?
What are the macromolecules found in cells?
What is homeostasis?
the property of a system, especially a living organism, to regulate its internal environment so as to maintain a stable, constant condition
What does apoptosis come into play in cellular homeostasis?
What happens when cellular homeostasis fails?
What bonds are found in cells?
What does this image represent in terms of bonding?
GC bond stronger than AT bond
What is the difference between covalent and ionic bonding?
What is the geometry of covalent bonds?
The Novichok nerve uses which type of bonding?
What type of bonding is found in water and what are its properties?
What is the difference between a homopolymer and a heterpolymer?
Describe the main polymers found in cells?
What are monosaccharides?
What are the conformations possible in sugars?
What are disaccharides?
What are polysaccharides?
eg. cellulose and glycogen
What is glycogen?
What are the functions of glycoproteins?
What are the blood groups?
What are some important lipids found in cells?
Fatty acids are stored in the cytoplasm as triacylglcerol
Fatty Acids are metabolised to generate energy
What are some functions of nucleotides?
What is the amino acid structure?
What are a few polar amino acids?
What are a few nonpolar amino acids?
How can amino acids act as zwitterions?
What is a peptide bond?
How do amino acids form proteins structurally?
Give an example of a tertiary and a quarternary protein
Opioid receptor (tertiary, one protein)
Tubulin (quaternary, multi-protein)
What happens if protein assembly goes wrong?
What is the history of genetics?
Gregor mendel 1865 - foundation of genetics
X-ray diffraction R. Flankli 1952 determined structure
What is the structure of DNA?
Descirbe nucleic acid nomenclature
Describe the bases found in DNA and RNA
How are DNA sequences written?
Describe the packaging of DNA
Describe briefly the stages of DNA replication
What is meant by semi-conservative repication?
What are DNA replication forks?
How does PCR cause exponential expanion of DNA?
Describe the direction of DNA replication
How is DNA replication catalysed?
Why is DNA replication described as assymetrical?
What are okazaki fragments?
Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.
Decribe how DNA polymerase proofreading
What is sickle cell anaemia?
sickle-cell disease is caused by a single point mutation (a missense mutation) in the beta-hemoglobin gene that converts a GAG codon into GUG, which encodes the amino acid valine rather than glutamic acid.
Describe the central dogma of molecular biology
What is transcription?
Transcription is the first of several steps of DNA based gene expression (gene is a short part of DNA that encodes for a protein), in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase.
Copying DNA into mRNA to make complementrary RNA copy of DNA template. mRNA produced is edited and processed.
What are the key differences between DNA and RNA?
DNA contains the sugar deoxyribose, while RNA contains the sugar ribose. The only difference between ribose and deoxyribose is that ribose has one more -OH group than deoxyribose, which has -H attached to the second (2’) carbon in the ring.
DNA is a double-stranded molecule while RNA is a single-stranded molecule.
DNA is stable under alkaline conditions while RNA is not stable.
DNA and RNA perform different functions in humans. DNA is responsible for storing and transferring genetic information while RNA directly codes for amino acids and as acts as a messenger between DNA and ribosomes to make proteins.
DNA and RNA base pairing is slightly different since DNA uses the bases adenine, thymine, cytosine, and guanine; RNA uses adenine, uracil, cytosine, and guanine. Uracil differs from thymine in that it lacks a methyl group on its ring.
Describe some of the components of a gene
The gene is the basic physical and functional unit of heredity. It consists of a specific sequence of nucleotides at a given position on a given chromosome that codes for a specific protein (or, in some cases, an RNA molecule).
Genes consist of three types of nucleotide sequence:
coding regions, called exons, which specify a sequence of amino acids
non-coding regions, called introns, which do not specify amino acids
regulatory sequences, which play a role in determining when and where the protein is made (and how much is made)
Decribe the key components on a gene involved in transcription
Describe mRNA processing
Eukaryotic mRNA precursors are processed by 5′ capping, 3′ cleavage and polyadenylation, and RNA splicing to remove introns before being transported to the cytoplasm where they are translated by ribosomes
What is the alternative splicing of RNA
What is translation?
What is codon redundancy?
64 codons, 61 represent amino acids, and three are stop signals. Although each codon is specific for only one amino acid (or one stop signal), the genetic code is described as degenerate, or redundant, because a single amino acid may be coded for by more than one codon.
Describe the reading frames in translation
What are tRNAs?
Describe the stages of translation
Translation is a process by which the genetic code contained within an mRNA molecule is decoded to produce the specific sequence of amino acids in a polypeptide chain.
What are ribosomes?
A ribosome is a cell organelle. It functions as a micro-machine for making proteins. Ribosomes are composed of special proteins and rRNA. Ribosomes are found ‘free’ in the cytoplasm or bound to the endoplasmic reticulum (ER) to form rough ER.
Describe processing that happens after translation
How do antibiotics target protein synthesis?
Describe how DNA expression varies between cells
Describe how the expression of genes changes in disease
Describe the different level of control of gene expression
Describe the regulation of trancription
Many levels of regulation, transcription is the first, key step. The chromatin structure (histones) determine accessibility of the DNA for transcription. It can be modified by acetylation or deacetylation. Transcription is regulated by the binding of specific transcription factors to the promoter region of the gene. The presence/absence of these factors determine whether a gene is transcribed into RNA.
Alternative splicing can change the properties of the protein. MicroRNAs can cause a messenger RNA to be degraded or prevent its translation into a protein.The spatial association between genomic DNA and histone proteins within chromatin plays a key role in the regulation of gene expression and is largely governed by post-translational modifications to histone proteins, particularly H3 and H4. These modifications include phosphorylation, acetylation, and mono-, di-, and tri-methylation, and while some are associated with transcriptional repression, acetylation of lysine residues within H3 generally correlates with transcriptional activation. Histone acetylation is regulated by the balance between the activities of histone acetyl transferase (HAT) and histone deacetylase (HDAC).
What are transcription factors?
Transcription factors are important in medicine because they are the target of many drugs. (mediate transcription. (Proteins folded specific way – transcription factors unique)
Glucocorticoids bind to and activate a cytoplasmic glucocorticoid receptor. The activated glucocorticoid receptor translocates into the nucleus and binds to specific response elements in the promoter regions of anti-inflammatory genes. The glucocorticoid receptor also acts through other transcription factors, notably nuclear factor-kappaB (NF-kappaB) and activator protein-1 (AP-1), that mediate the expression of inflammatory genes.
Hormones like oestrogen can switch on a gene and start transcription by binding to the Oestrogen receptor which can then act as a transcription factor and bind to DNA, promoting transcription.
Decribe how transcription factors create conditions for transcription
Describe how transcription factor mutations cause disease?
Describe the multilevel control of gene expression
What is alternative splicing?
Describe VEGFA splicing
How do miRNAs regulate mRNA activity
What are miRNAs?
Describe what RISC is and what it does
Describe what is meant by miRNA reguaiton of protein coding genes
What is the association between miRNAs and disease?
How can miRNAs function as biomarkers?
Can miRNA be used in mlecular profiling of cancer of unknown origin?
Describe what PCR is
A simple idea that revolutionised molecular biology – clinical genetic testing
• Exponential amplification of target DNA • Kary Mullis, 1985.
Kary Mullis invented the polymerase chain reaction (PCR).
Received Nobel Prize in chemistry in 1993
Almost all clinical genetic testing involves PCR and most other modern molecular biology techniques
Method to make millions of copies of a short piece of DNA of interest.
20 nanograms (ng) of genomic DNA 0.00001% of this is the piece we want to ‘amplify’. 2 hrs later - \>
Micrograms of specific product (plus original 20 ng of genomic DNA)
>99.99% of the total is now our product of interest. PCR enables you to study just the small piece of DNA that is of interest, for example a specific ‘disease-associated’ mutation
Describe the process of PCR
The critical concept is that there is an excess of oligonucleotide ‘primers’ which hybridise to the complementary sequence in the target DNA. Firstly everything is separated or denatured at 95C, then during the annealing step at 55C the primers bind to opposite strands (their sequences are designed to do this).In the extension phase (72C) the primers are extended towards each other at the 3’ -OH group, to which nucleotides complementary to the template are attached by DNA polymerase. In each cycle the primers are incorporated into the products. In the next cycle both the products and the original templates are available to be copied again (exponential increase) in a reaction primed by more of the primers, which are available in excess.
What are the components of the PCR reaction?
Because the process involves incubation at high temperatures it is necessary to use an enzyme that can work under these conditions (most proteins in our bodies would be denatured by heating to 950C!). This problem was solved by isolating the DNA polymerase from bacteria which live in hot springs and are therefore adapted to high temperatures. The ‘Taq’ polymerase comes from the bacterium Thermus aquatic.
Describe how PCR can be used in diagnostics
What is sanger sequencing?
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. Developed by Frederick Sanger and colleagues in 1977, it was the most widely used sequencing method for approximately 40 years.
What is Next Generation Sequencing?
Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing.
Process hundreds of millions of sequencing reads in parallel
Common concept is the analysis of millions of sequences associated with a solid surface (or in wells)
Paradigm shift – generation of so many reads opens up new possibilities Generating millions of DNA sequence in a single experiment
Describe some of the applications of NGS
How can NGS have an impact in the field of medicine?
