Genetics Flashcards
What are nucleotides composed of?
a nitrogenous base, a pentose sugar and one or more phosphate groups
What are the pentose sugars found in DNA and RNA?
deoxyribose
ribose
what is the difference between deoxyribose and ribose?
ribose has a hydroxyl group on the second carbon
How are carbons in pentose sugars labelled?
1 to 5
What does carbon 1 (1’) bond to in the formation of nucleotide?
the nitrogenous base
What is carbon 5 (5’) bonded to in the formation of a nucleotide?
a tail on the ring structure that is bonded to the phosphate group
What are the two categories of nitrogenous bases?
purine or pyrimidines
How many pyrimidines does DNA have?
2
What are the two pyrimidine nitrogenous bases of DNA?
cytosine
thymine
What are the pyrimidines found on RNA?
cytosine
uracil
What are the purines present in both DNA and RNA?
adenine
guanine
what is DNA a storage of?
genetic information
What does RNA act as a messenger between?
DNA and ribosomes to make proteins
How many strands do DNA and RNA have?
DNA: double strand
RNA: single strand
What are nucleotides linked by in DNA and RNA?
phosphodiester bonds
What do the phosphodiester bonds between nucleotides help to create?
a sugar phosphate backbone
Is the sugar phosphate backbone hydrophilic or hydrophobic?
hydrophilic
Is the sugar phosphate backbone positively or negatively charged?
negative
What are the 2 free groups found on each nucleotide?
5’ phosphate and 3’ hydroxyl (OH) group
In what direction is a nucleotide sequence always written?
5’ to 3’
In what direction do DNA strands run?
in opposite directions
What is the fact that DNA strands run in the opposite direction to each other also known as?
antiparallel
Do the 2 strands of DNA have the same sequence?
yes, complementary strands
What do the nitrogenous bases of the two anti-parallel strands pair together to form?
double stranded nucleic acids
What are adenine - thymine bases stabilised by?
two hydrogen bonds
What are guanine and cytosine bases stabilised by?
three hydrogen bonds
Why are the bonds between guanine and cytosine stronger than those between adenine and thymine?
because of the 3 hydrogen bonds rather than 2
What does the genetic code code for?
amino acids
How many bases code for an amino acid?
3
What is the name of the group of 3 bases that code for an amino acid?
codon
What is meant by the genetic code being degenerate?
some amino acids are coded for by more than one codon
What 3 bases signify the start codon (Met)?
AUG
What are the stop codons?
UAA, UAG, UGA
What do stop codons do?
direct the synthesis of the peptide to cease
What are genes?
sequences of DNA containing intron and exon regions
What do genes code for?
RNA
What is the DNA before the gene start site?
regulatory region
what is the regulatory region of DNA before the gene start site known as?
the promoter
What are genomes?
strands of DNA that contain genes
What do genomes contain as well as genes?
large amounts of non-coding DNA
What essential role does some of the non-coding DNA play in gene expression?
binds to transcription factors which regulate the transcription of genes
What is ‘junk DNA’?
DNA on a genome that has no apparent function
How many copies of each somatic gene do individuals contain?
2
What are copies of genes also called?
alleles
How many alleles of a gene are on each chromosome?
one on each
What sort of DNA is always maternally inherited?
mitochondrial DNA (mtDNA)
What does mitochondrial DNA (mtDNA) encode for?
a small number of mitochondrial proteins
Why is DNA condensed into chromosomes?
DNA is much longer than the cells that contain it
How are nucleosomes formed?
strands of DNA wrap around histones to form nucleosomes
What do multiple nucleosomes together create?
chromatin
how does chromatin form a chromosome?
loops and condenses
What are homologous chromosomes?
a pair of chromosomes
Do chromosome numbers vary between species?
yes
How many homologous do humans have?
23 (46 single chromosomes)
What are the sister chromatids joined at a central point by?
centromere
What is a kinetochore?
an associated protein that is involved in cell division
What are the ends of the chromosomes called?
telomeres
What are the telomeres?
sections of non-coding DNA that act as buffers to prevent shortening of the chromosomes during cell division
What can telomeres only be extended by?
telomerase
what is the shorter arm of the chromosome called?
the p arm
What is the longer arm of the chromosome called?
the q arm
What can be used to identify and map loci (locations) on the chromosomes?
when stained banding occurs
What is a chromosome karyotype?
a picture of an individuals chromosomes
What is a karyotype used to identify?
chromosomes, sex, characterization of cancer and any abnormalities associated with inherited defects
When is the DNA double helix replicated?
when the cell divides
Why is replication of genetic material in mitosis a semi-conservative process?
both new helixes have one parent strand of DNA in
What do the sequence of bases on the parent stand act as?
template for synthesis of the daughter strand
what are the 3 phases of genome replication?
initiation, elongation, termination
What happens during the initiation phase of genome replication?
Recognition of the position (s) on a DNA molecule where the replication will begin.
What enzyme unwinds the DNA helix?
topoisomerase
what enzyme unzips the double helix?
helicase
What is the leading strand of DNA copied by?
DNA polymerase
in what prime direction are bases added?
5’ to 3’
What are Okazaki fragments?
short 5’ to 3’ sections of the lagging strand of DNA
What does DNA polymerase need in order to bind to DNA?
short RNA primers
What enzyme are the short RNA primers required by DNA polymerase formed by?
DNA primase
What enzyme joins adjacent Okazaki fragments?
DNA ligase
When does DNA replication end?
when the replication bubbles meet
What reamins on the lagging strand when DNA replication ends?
a small gap
Why might the extreme 3’ end of the lagging strand not be copied?
the final Okazaki fragment cannot be primed – the priming site is beyond the end of the template
What is removed from the very end of a DNA molecule?
a primer
What do the telomeres at the end of a chromosome prevent?
any genes being lost
What is produced from DNA in order to facilitate protein production?
RNA
What is the process of producing RNA from DNA known as?
transcription
What sequences direct the RNA polymerase to bind to DNA?
promoter
How many strands of DNA serve as a template for RNA synthesis?
one (the template strand)
What is the non-template strand of DNA called?
the coding strand
in what direction is RNA synthesised?
5’ to 3’
When does RNA synthesis end?
when the termination sequence is reached
What happens to the resulting RNA transcript prior to translation?
modified and processes
What are the RNA transcripts produced from the template strand known as?
pre RNA
Why are RNA transcripts known as pre RNA?
they still have non coding introns in them
What is added to protect the RNA from degradation by nucleases and aid binding to the ribosome?
a modified guanosine 5’ cap
What is added at the 3’ end of the pre RNA to protect from degradation?
a poly A tail
What happens during splicing of pre RNA?
introns are removed and exons joined together before RNA is exported to the cytoplasm
What are the 3 main classes of RNA involved in protein production?
mRNA: messenger RNA
tRNA: transfer RNA
rRNA: ribosomal RNA
What does mRNA do?
encodes the amino acid sequences of proteins
What does tRNA do?
reads the information encoded on mRNA and transfers the appropriate amino acid to the polypeptide chain during protein synthesis
What does rRNA do?
is a constituent of ribosomes
Where does translation occur?
in the ribosomes in the cytoplasm/on the endoplasmic reticulum.
what do ribosomes catalyse?
the joining of amino acid monomers
What is the joining of amino acid monomers directed by?
mRNA sequence
in what prime direction do ribosomes read the mRNA?
5’ to 3’
In what segments is the mRNA read by ribosomes?
3 nucleotide segements/codons
What do tRNA molecules match to codons on the mRNA?
amino acids
What does de novo synthesis of nucleotides begin with?
their metabolic precursors
What are the metabolic precursors of nucleotides?
amino acids, ribose 5-phosphate, CO2 and NH3
adenosine triphosphate (ATP) is the nucleotide that contains ___?
adenine
guanosine triphosphate is the nucleotide that contains ___?
guanine
Cytidine triphosphate (CTP) is the nucleotide that contains ____?
cytosine
Uridine triphosphate (UTP) is the nucleotide that contains ___?
uracil
Deoxythymidine triphosphate (dTTP) is the nucleotide that contains ____?
thymine
What is the precursor for purines?
inosinate (IMP)
How is adenylate (AMP) created?
Aspartate is added to inosinate (IMP) to form adenylosuccinate by adenylosuccinate synthetase, using GTP for energy. Adenylosuccinate is converted to adenylate/adenosine monophosphate (AMP)
How is guanylate created?
IMP is converted to xanthylate (XMP). An amine group from glutamine is added to xanthylate to form Guanylate/guanosine monophosphate (GMP) using ATP for energy.
What are pyrimidines synthesised from?
carbamoyl phosphate and aspartate
What is added to carbamoyl phosphate and aspartate to create pyrimidine ribonucleotides?
ribose
What inhibits the creation of
carbamoyl aspartate.
What molecule does the production of dTMP start with?
cytidine diphosphate (CDP) or uridine diphosphate (UDP)
Once dTMP is formed what is it converted from and to?
monophosphate to triphosphate in the same way as the other nucleotides
What are nucleoside monophosphates converted to?
nucleoside triphosphates
what enzyme is phosphorylation of AMP to ADP promoted by?
adenylate kinase
How are other nucleoside diphosphates formed?
by the action of nucleoside monophosphate kinases
Nucleoside diphosphates (NDPs) are converted to triphosphates (NTPs) by the action of which molecule?
nucleoside diphosphate kinase
What do salvage pathways recycle?
the free bases and nucleosides released from nucleic acid breakdown
how does the salvage pathway of purines work?
The enzyme adenosine phosphoribosyltransferase catalyses the formation of AMP from free adenine and 5-phosphoribosyl-1-pyrophosphate (PRPP). The enzyme hypoxanthine-guanine phosphoribosyltransferase catalyses the same reaction with guanine instead of adenine
how does the salvage pathway of pyrimidines work?
Pyrimidines are recycled by a similar pathway as purines
Give 5 examples of drugs that affect the way nucleotides are biosynthesised
Azaserine and acivicin – glutamine analogues which inhibit glutamine amidotranferases
Fluorouracil – converted to FdUMP via salvage pathways and binds to and inactivates thymidylate synthase Methotrexate – folate analogue which inhibits dihydrofolate reductase
Trimethoprim – antibiotic which binds to bacterial dihydrofolate reductase nearly 100,000 times better than to the mammalian enzyme
What are drugs that affect the way nucleotides are biosynthesised often used for?
to target cancer cells which have greater requirements for nucleotides due to their excessive growth, and are therefore more susceptible to nucleotide synthesis inhibition
What does cytogenetics do?
Cytogenetics uses an individual’s karyotype to determine its sex
What does polymerase chain reaction allow?
PCR allows detection of DNA with a very high sensitivity
What is meant by high sensitivity in PCR?
it can detect a very small amount of the DNA
How does PCR work?
having primers that bind to specific fragments of DNA, and then using DNA polymerase to repeatedly copy that DNA fragment.
how does the number of DNA copies change through each cycle of PCR?
doubles with each cycle
What does PCR exponentially ampilfy and for what reason?
the DNA target region so that the product can be visualised
How is DNA seperated by size in PCR?
by agarose gel electrophoresis
What dye is DNA stained with during PCR?
commonly ethidium bromide
What are used as markers in PCR?
Ladders (sequences of DNA with known sizes)
What can be done with DNA amplified by PCR?
sequenced in order to identify genetic mutations
What is RT-PCR or RT-qPCR?
Quantitative Reverse Transcriptase Polymerase Chain Reaction
what is qPCR or qRT-PCR?
Quantitative Real Time Polymerase Chain Reaction
What is Quantitative Reverse Transcriptase PCR (RT-PCR or RT-qPCR) used for?
to determine the levels of mRNA in a sample by using reverse transcriptase (RT), an enzyme from retroviruses (e.g. FIV and HIV) that converts RNA to DNA
what can the resulting DNA from Quantitative Reverse Transcriptase PCR (RT-PCR or RT-qPCR) be amplified by?
PCR
What sort of organisms often only have RNA and protein?
viruses (including coronavirus)
What is quantitative real time PCR (qPCR or qRT-PCR) use to quantify DNA (or mRNA) concentration?
a florescent readout
What dye does the simplest method of quantitative real time PCR (qPCR or qRT-PCR) use?
SYBR green which fluoresces when it binds to double-stranded DNA
What can be useful in multiplex PCRs using quantitative real time PCR (qPCR or qRT-PCR)?
Specific probes can also be used which will only label specific DNA strands
What is the level of florescence of SYBR green related to in quantitative real time PCR (qPCR or qRT-PCR)?
the quantity of DNA, useful for comparing different samples
What are quantitive PCR results often quoted as?
Cycle Threshold (CT) values
With every quantitative real time PCR (qPCR or qRT-PCR) cycle what is measured in real time?
the fluorescence, related to the DNA quantity
When do samples with a lower (CT) value reach target florescence value?
after fewer cycles, meaning they had higher initial DNA concentrations.
What are the advantages of testing for DNA?
identify mutations in patient genes or detect pathogen DNA or RNA
Quantitative or qualitative
very high sensitivity (few false negatives)
what are the disadvantages of testing for DNA?
Currently require samples to be sent to a lab –less convenient but better quality control
Poorer sample stability, DNA more stable than RNA (heat, pH, nuclease enzymes degrade both)
Lower specificity (some false positives)
Typically more expensive than routine protein tests
What does gene therapy aim to do?
replace a defective gene with a functional copy
What 2 ways can functional copies of genes be delivered to the defective genes?
via vectors such as modified viruses that are able to directly enter the target cells in the individual
via cells from the individual that have had the genes grown in them in a lab
How does direct delivery gene therapy via vectors work?
therapeutic transgene is packaged into a delivery vehicle such as a virus and injected into the patient
How does cell based delivary gene therapy via an individuals cells work?
therapeutic transgene is packaged into a delivery vehicle such as a virus, the therapeutic transgene is then introduced into a delivery cell, such as a stem cell, that is usually derived from the patient. The genetically modified cells (e.g. stem cells) are multiplied in the laboratory and re-administered to the patient
What are GMOs?
organisms that have modified genomes that are able to be transmitted to subsequent generations
What are examples of GM bacteria?
Genetically modified bacteria that produce insulin Genetically modified plaque bacteria which reduce tooth decay
What are examples of GM mice?
Models of human and animal disease
“Knockout” mice to study gene function
What are examples of GM pigs?
Engineered so that their organs can be transplanted into humans
what are examples of GM foods?
Genetically modified to be resistant to diseases or pests Engineered to have a higher nutritional value
What is a clone?
a genetically identical copy of an animal
What are the 2 donors involved in cloning?
mammary cell donor and egg cell donor
What happens to the mammary and egg cells once they are removed from their donors?
mammary cells are cultured
egg cell from ovary has nucleus removed
What happens once the cultured mammary cells and egg cell without it’s nucleus are fused?
they are grown in a culture until an early embryo forms. they are then implanted into the uterus of a third sheep who beocomes the surrogate mother.
Who will the offspring produced by cloning be genetically identical to?
the mammary cell donor
what is the difference between de novo synthesis and salvage pathways?
de nonvo synthesis is the main pathway for synthesis of brand new nucleotides.In salvage pathways used nucleotides are recycled.
