Flashcards
Week 8
Cards in this deck (74)
- 1Describe the structure of DNA and RNADNA:
-double-stranded (2 phosphodiester backbones)
-high molecular weight
RNA:
-single stranded (1 phosphodiester backbone). Contains intra-molecular base-pairing
-Heterogeneous in size - 2Differences between RNA and DNA in terms of their structureRNA has an OH group at ribose C2 while DNA has a H
RNA uses uracil (missing a methyl group) where DNA uses thymine - 3Is RNA/DNA stable?DNA is stable
RNA is not. If left in aq conditions, the OH attacks the phosphate group on an adjacent nucleotide fragmenting the strand - 4Describe the hydrogen bonds between basesThey are weak interactions that can be easily disrupted (so that DNA can be copied). Although weak, there are lots of them so the molecule is stable
- 5Which bases are the purines and pyrimidines?Purines- A+G
Pyrimidines- T+C - 6What are gene regulatory elements?Sequences of DNA that regulate switching on/off of genes.
Promoter elements are upstream (close to the gene)
Enhancer elements are downstream (can be scattered in the DNA) - 7What are: exons introns? How are the introns removed/exons put together?Exons are coding DNA. Introns are non-coding DNA.
They are removed from primary DNA by splicing. The exons are forcibly ligated together. - 8Describe the repeat elements present in DNA-Derived from viruses
-Most common repeats are the LINE and SINE families. They are used to detect polymorphisms
-Repeat elements create stability in chromosomes - 9What are the basic building blocks for DNA synthesis?Deoxynucleoside triphosphates (dNTPs) eg. dGTP
- 10What direction does DNA synthesis proceed in? What enzyme does it involve?5' to 3' direction.
DNA polymerase - 11How does DNA polymerase work?-It catalyses the extension of DNA in the 5' to 3' direction. It is dependent on the hydrogen bonds formed between complementary bases
-Requires dNTPs
-It must have a template and an RNA primer
-It has an editing activity - 12Purpose of the RNA primer?-Section of RNA that recognises the sequence. It is later removed and replaced with DNA
-It provides a free 3' end which receives incoming dNTPs - 13Describe the replication fork-DNA polymerase moves along the leading strand synthesising DNA in a 5' to 3' direction
-On the lagging strand, Okazaki fragments are created
-This is because as the fork widens, DNA polymerase jumps back to the newly exposed DNA - 14How is a whole chromosome replicated? (in a way that doesn't take forever)-Replication bubbles are created at several points in the genome where the DNA strands have been ripped apart (at the origin of replication)
-Replication forks form in opposite directions from the point of origin
-These origins eventually meet up - 15How does proof reading occur in DNA replication?-DNA polymerase adds a base and them moves back to check it
-If it is wrong the base is excised, and DNA polymerase moves on
-DNA polymerase detects incorrect bases by checking for unusual shapes or folding of the DNA - 16Describe the key features of transcription-Uses RNA polymerase to synthesise RNA with DNA as a template
-CTP, UTP, GTP and ATP (nucleoside triphosphates) are used as building blocks
-RNA is synthesised in the 5' to 3' direction
-Only 1 strand is copied - 17What is the co-trancriptional process?-The primary RNA transcript created, is an exact copy of the DNA present (incl. introns)
-As the bubble moves along the DNA, the RNA chain extends
-A spliceosome attaches onto RNA immediately and splices the introns out.
-Splicing and transcription occur at the same time hence the name - 18What are ribosomes?Complexes made up of structural rRNA and proteins that assemble polypeptides (proteins) as instructed by the mRNA sequence
- 19What is the structure of ribosomes?-Made up of a large/small subunit
-Has a P-site and an A-site where p-tRNA and a-tRNA bind respectively
-2 sites on the ribosome expose codons of mRNA for tRNA to join to
-p-tRNA carries the polypeptide chain while a-tRNA brings another aa where a peptide bond is formed - 20Describe the structure of tRNAs-3 stem loop structures
-Stabilised by base pairing
-Distinct functional regions
-Specific tRNA for each aa - 21How are proteins translated quickly?-More than 1 ribosome attaches to a single mRNA forming a polysome
-1 transcript can lead to multiple proteins - 22Stop codons? Start codon?UAA
UGA
UAG
Where translation stops. There is no tRNA with the correct anticodon
AUG - 23How many possible reading frames are there?3
- 24How many chromosomes are present in humans? Is all the entire genome present in the nucleus?22 autosome pairs
1 pair of sex chromosomes (eg. XX in F, XY in M)
No. A small amount is present in the mitochondria - 25Define: transcriptome proteomeComplete set of RNA transcripts
Complete set of proteins produced
They are dynamic and vary at different points of time and between different cell types - 26How can the human genome be messy?-Protein coding genes vary in size and internal organisation
-Genes are unevenly distributed between and within chromosomes
-Several mRNAs can be transcribed from some genes
-Genes can made functional non-protein coding RNA
-Genes can overlap - 27Why is not all RNA translated into proteins?-Some genes encode for untranslated RNAs such as rRNA or tRNA
-Some RNA molecules modify other RNA molecules such as snRNA or snoRNA
-miRNA binds to 3'UTR and inhibits translation - 28Define: satellite DNA tandem repeatsBlocks of tandem repeats. Often found at the centromere
Sequence of DNA copied multiple times. - 29What are: mini satellites micro satellites?Mini- highly polymorphic and found at telomeres
Micro- small arrays of simple sequence repeats and usually in intergenic/intronic DNA - 30What is the role of: 1) Telomeres 2) Centromeres 3) Mini satellites?1) Allows replication to the tip of the chromosome. Adds stability to the telomere as it's fragile
2) Essential for segregation during cell division. Proteins involved in cell division bind to centromeric sequences
3) Has no know purpose. However can cause mispairing during cell division to give large scale duplication/deletion (between homologous) or translocation of DNA (between non-homologous). - 31How is DNA packaged?-DNA wraps around histones forming chromatin (eg. a nucleosome)
-Nucleosomes are packed together to form a solenoid
-Solenoids packed to form a chromosome - 32What are the 2 forms chromatin can exist in? Describe themEuchromatin (active areas):
-extended state throughout the nucleus (always open)
-the genes expressed reflect the function of the cell
Heterochromatin (transcriptionally silent):
-Exist in active (decondensed) or inactive (condensed) - 33Purpose of mitosis?-Cell division/organised growth
-Genetically identical products - 34What happens in prophase? Prometaphase?-Chromosomes condense
-Spindle assembles outside nucleus
-Spindle microtubules bind to chromosomes
-Kinetochores face in opposite directions - 35What happens in metaphase? Anaphase?-Spindle gathers chromosomes to equator
-Tension forms on kinetochores at centromeres
-When chromosomes are at spindle poles, kinetochore microtubules begin to disappear
-Polar microtubules elongate to push poles apart - 36What happens in telophase? Cytokinesis?-Nuclear membrane beings to reform around chromosomes
Nucleoli reappear and plasma membrane cleavage is initiated
-A contractile ring of actin and myosin filaments in the cleave furrow forming 2 daughter cells - 37What happens when an error is found in the checkpoints in the cell cycle?-Cell attempts to repair the mistake
-Apoptosis if serious - 38Function of meiosis?-Reduction division
-Re-assortment of genes by independent segregation of chromosomes and crossing over (recombination) - 39Mechanism of meiosis?-Each homologue replicates to give 2 chromatids
-Homologues pair
-Exchange of material between non-sister chromatids occurs
-The chiasmata is the physical manifestation of crossing over - 40How is crossing over regulated?-Has to be the same sequence on homologous chromosomes that are regulated
-Covalent bond is formed - 41Difference between meiosis and mitosis?-2 daughter cells in mitosis, 4 in meiosis
-Mitosis produces diploid cells while meiosis produces haploid cells
-Meiosis has 2 anaphase stages while mitosis has 1
-Meiosis produces genetically diverse cells while mitosis produces genetically identical cells - 42How many divisions are needed to produce human gametes?-Each spermatogonium in the testes at age 15 is the result of 30 previous divisions
-Each egg in the ovaries is the result of 22 cell divisions by 5 months gestation (meiosis I completed at ovulation. Meiosis II completed at fertilisation) - 43What are the different types of variation in the genome?1) Alterations in the sequence of bases
2) Repetitive elements
3) Larger deletions/duplications
4) Changes in the number/structure of chromosomes - 44What effects can variation cause?-No effect
-Normal human variation
-Differences in response to medication
-Likelihood of disease
-Genetic condition - 45How can genome variants be classified?-size
-frequency ie. rarity
-clinical effects - 46Clinical definition of a mutation? How do they arise generally?Harmful sequence variant that alters gene function/phenotype.
It arises from exposure to mutagenic agents or spontaneously through errors in DNA replications/repair - 47What are polymorphisms?-Sequence changes that have no negative impact.
Can be in:
-non-functional DNA eg. introns
-within gene but does not change aa
-changes aa but not protein function - 48What is a SNP?Single Nucleotide Polymorphism
-Most common type of genome variation
-A change in a single base at a particular position
-Base change frequency has to be >1%
-Can have an impact but often doesn't - 49How is the genome examined at these levels? -bases -large blocks of DNA -Chromosomal-Sequencing/Microarray analysis
-Microarray analysis/FLuorescence in situ hybridisation
-Light microscopy - 50How is DNA sequenced? Uses?-By the dideoxy method
-Used to determine the exact position of the mutation in a gene
-Determines type of mutation - 51When do mutations occur? What causes mutations in meiosis?-Cell division (when DNA is replicated)
-From intrinsic/extrinsic attacks on DNA
-Meiosis I (initial replication generates errors)
-Meiosis II (non-disjunction/anomalies of chromosome structure)
- 2 populations of cells leads to mosaicism eg. females are mosaics - 52What are germline and somatic mutations?Germline:
-mutation present in egg/sperm (heritable)
-all cells are affected in offspring
Somatic:
-occur in non-germline areas
-non-heritable - 53Types of endogenous mechanisms causing DNA damage?-Depurination (spontaneous fission of purine/ribose)
-Deamination (C deaminates to U)
-Reactive oxygen (attacks bases)
-Methylation of cytosines at CpG dinucleoties - 54Extracellular agents causing DNA damage?-UV light (causes adjacent T to cross-link to create a stable dimer)
-Environmental chemicals (intercalate into DNA/cause DNA creaks/chromosome aneuploidy)
-Ionisation radiation (causes breaks in DNA) - 55How are... fixed? -replication errors -thymine dimers -chemical adducts-Mismatch is identified
Usually repaired by excision repair mechanism:
-newly synthesised DNA strand is removed
-gap is repaired by DNA polymerase/ligase - 56How are DNA double strand breaks repaired?-Homologous recombination (sequence from another homologous chromosome is used to synthesise the missing DNA)
OR
-End-joining broken ends (error prone). This is only used if a homologous copy is not available as material is lost at the repair site - 57Describe a ... mutation -silent -missense -nonsense-Base change pair that does not change the aa sequence eg. 3rd base position (can create a cryptic splice site)
-Changes a codon for another aa (may/may not affect structure and function of protein)
-Changes from an aa codon to a stop codon (causes transcript to be too short/stable) - 58Describe: -splice-site mutation-A change that results in altered RNA sequence
-Protein is inactive as there are mutations in the splice site that prevent the correct splicing of pre-mRNA
-Changes size and content of a protein - 59Describe: -frameshiftInsertion/deletion of base pairs (not in multiple of 3) producing a new stop codon downstream
- 60What are copy number variants?-Small arrays of triplet repeats in coding sequences of genes
-Disrupts function of the gene
-Can mispair and cause pathogenic deletions/insertions/duplications - 61How are larger deletions and insertions caused?-By unequal crossing-over between repeat sequences
-Leads to mis-alignment and chromosomes are too short/long
-Clinical effects depend on genes involved and gene dosage - 62What is epigenetics?-Understanding of how genes can be switched on/off
-It is a reversible decision affected by the environment
-This means gene expression can be modified by genes, without changing the DNA sequence - 63What is the phenotype determined by?Genotype and environment
- 64What are housekeeping genes? Define differentiationGenes that are present and on in all cells
Patterns of gene expression change - 65How does gene expression change as cell differentiate from stem cells to terminally differentiated cells?-Genes needed for terminally differentiated cells are turned on
-Genes for totipotency are turned off - 66What is a gene?Transcriptional units composed of:
-structural info coding for a protein
-regulatory sequences giving instructions for expression - 67What are general transcription factors?-They recognise and bind to the gene promotor
-They recruit RNA polymerase II
-They allow a basal level of transcription - 68What controls the rate of transcription?-Enhancers
-Gene-specific transcription factors (activate and repress) that create to different stimuli
Together they signal RNA polymerase to produce mRNA - 69Define alleleDifferent versions of the same gene
- 70Describe a nucleosome-Occurs every 200bp
-DNA wraps around the ball of protein twice
-Protein has 2 copies of each histone
-Forms a histone octomer (since there are 4 different proteins) - 71Describe histone tails-Common and variable
-Every aa in a histone is essential (for life)
-Have chemical tags which act as regulatory information.
-Chemical tags determine if genes are switched on/off and for how long - 72How are histone tails modified?Histone acetyl transferases switch genes on
Histone de-acetylases turn genes off - 73What in the environment affects if genes are switched on/off?On- cell metabolism
Off- environmental factors like diet and (epigenetic) therapeutic drugs which act on enzyme inhibitors - 74Describe x inactivation-Females born with XX chromosomes which males are born with an X and a gene poor Y
-In early development, 1 of the Xs is inactivated in each cell by condensing tightly (transcriptionally inactive) in the inner blastocyst
-This balances the difference between males/females
-Either the maternal/paternal X chromosome is inactivated. This is expressed differently in different parts of the body leading to mosaics
-Example of a heritable epigenetic state
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- Storage and retrieval of genetic information The genome and its transmission
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- Dolu Falowo
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