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Medneuro- neurophysiology (M1-2) > Neurogenetics > Flashcards

Neurogenetics Flashcards

1
Q

What is a nucleotide?

A

-Nucleotides are the basic monomer of DNA
-Consist of nucleoside, sugar and phosphate group.
-Purine base nucleotides are Guanine and Adenine
-Pyramidine base nucleotides are Thymine, Cytosine and Uracil (only in RNA)
-Purine base nucleotides bind to pyramidine base nucleotides.
A-T/U and G-C
A-T pair by two hydrogen bonds
G-C pair by three hydrogen bonds

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2
Q

What is a chromosome?

A
  • A Chromosome is the highest order organisational structure of DNA.
  • Humans have 23 pairs of these. 22 autosomal (not sexual) and 1 sex pair.
  • DNA, with the assistance of its helical structure and associated proteins, coils into higher order structures which culminates with the chromosome and its homologous partner
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3
Q

What is Chromatin?

A
  • Chromatin is the complex formed by DNA’s association with histone proteins.
  • DNA wraps around the histone proteins which forms “nucleosomes”.
  • This provides stability to the DNA and regulates expression and replication.
  • There are two types of chromatin. Heterochromatin and Euchromatin. Heterochromatin has much less distance between nucleosomes and therefore is far more compact.
  • Heterochromatin resistant to expression due to its compact structure.
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4
Q

What is a nucleosome?

A
  • A nucleosome is the structure formed by the association of DNA and a histone protein.
  • This facilitates the folding of DNA into higher order structures.
  • This is important to provide compact and stable storage of DNA and regulate gene expression and replication.
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5
Q

What are histone proteins?

A

Histone proteins are proteins which assemble into an Octameric (consisting of 8 protein subunits) protein complex which then wraps DNA around itself forming a nucleosome.

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6
Q

What is DNA replication?

A
  • This is the process of producing an identical copy of a piece of DNA, usually in humans of a Chromosome.
  • This involves the “unzipping” of DNA and the extentioin of primers or existing strands by DNA polymerase.
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7
Q

What is DNA polymerase?

A
  • DNA polymerase is the enyzme responsible for the addition of deoxyribonucleotides (DNA nucleotides) to the primers associated with the template strand of DNA that is being replicated.
  • They extend the primers in a 5’ to 3’ direction.
  • They also have proof reading cabibilities
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8
Q

What is RNA polymerase?

A
  • RNA polymerase is the enzyme responsible for production of RNA from a DNA template (mainly)
  • It locally unzips the DNA strand with the assistance of a transcription factor which has bound at the upstream promoter sequence.
  • It then makes an RNA stand complementary to the DNA template strand.
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9
Q

What is transcription?

A
  • Transcription is the process of converting stored DNA code into RNA.
  • This could be for the process of mobilising the protein code stored in the DNA to be translated at a ribosome.
  • It could also be for the production of functional RNA such as transferRNA, RibosomalRNA or RNA aptamers.
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10
Q

What is translation?

A
  • Translation is the process of a messengerRNA (mRNA) being used at a ribosome to produce a polypeptide chain.
  • This works by each codon being “read” by the RNA component of the ribosome which then indicates which transferRNA (tRNA) should bind. Different tRNAs transfer different amino acids.
  • The ribosome then forms a peptide bond between ajacent aminoacids forming the peptide chain.
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11
Q

What is a transcription factor?

A

-A transcription factor is a protein which binds to upstream elements of a gene in order to up or downregulate the transcription of that gene.

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12
Q

What is methylation?

A
  • Methylation is that addition of a methyl group (CH3)to something.
  • In the human genome this could be the methylation of histone proteins or the DNA nucleotides themselves.
  • Methylation plays an important role in the regulation of gene expression.
  • Methylation of DNA promoter regions silences expression and demethylation promotes expression
  • Methylation of histone proteins can either cause promotion or repression of gene expression depending upon which of the amino acids of the protein are methylated.
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13
Q

What is acetylation?

A
  • Acetylation is the addition of an acetyl group (H3CCO) to a molecule.
  • This only happens to the histone proteins.
  • Acetylation of lysine residues promotes gene expression by relaxing the chromatin structure.
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14
Q

What are mRNA and tRNA?

A
  • mRNA is messengerRNA. This is an RNA version of the exons of the protein coding region of a DNA gene.
    • mRNA is translated at a ribosome into an amino acid sequence, which is done by reading the codon sequence of the molecule.
  • tRNA is transferRNA. This functions by binding with different amino acids and then being bound at the ribosome in order to facilitate the formation of a peptide bond between the chain and the tRNA amino acid.
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15
Q

What is an amino acid?

A
  • An amino acid is the monomer of proteins. When it polymerises forms polypeptides or peptides.
  • It consists of an amino group, an “R” group and an acid group.
  • The R group is the part which makes the amino acid unique among the 20 amino acids in humans. For example glycine’s R group= H.
  • The general formula of an amino acid is: H2NCRHCOOH
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16
Q

What is a peptide?

A

A peptide is just an amino acid chain, but typically one which is shorter than 10 amino acids in length.

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17
Q

What does Degenerate Genetic Code mean?

A

We have a Degenerate Genetic Code. This means that we have more codon combinations than we have amino acids. So multiple codons coding for one amino acid/stop codon is what is “degenerate” about our genetic code.

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18
Q

What is a promoter?

A
  • A promoter is a region of non-coding DNA upstream of the protein coding region of a gene.
  • It is to the promoter that transcription factors bind and well as providing a secure binding site for RNA polymerase.
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19
Q

What is an enhancer?

A

An enhancer is a region of DNA to which transcription factors can bind in order to increase the probilbility that transcription of a gene will occur.

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20
Q

What is a silencer?

A

A silencer is a region of DNA which is capable of binding Transcriptional repressors which then silence a gene.

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21
Q

What is a template?

A

A template is a DNA sequence which is being used to produce a replicated strand of DNA in DNA replication or it is a DNA sequence being used to transcripe a RNA Sequence.

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22
Q

What is complementary base pairing?

A
  • Complementary base pairing is the binding of complementary nucleotides using hydrogen bonds.
  • The nucleotides that are complementary for each other are those that can produce the same amount of hydrogen bonds. A and T both produce 2 and are therefore complementary. C and G both produce 3 and are therefore complementary.
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23
Q

What does 5’ and 3’ mean?

A
  • 5’ means phosphate end and 3’ means sugar end of a nucleotide.
  • Nucleotides are joined together along a Phosphate sugar backbone the phosphate end is 5’ and the sugar end is 3’. Nucleic acids are constructed in a 5’ to 3’ direction.
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24
Q

What does Sense and Antisense mean?

A
  • A sense nucleic acid is a nucleic acid which codes for a protein, or more precisely in in the format needed to perform its function. example- an mRNA which is going to produce the desired protein.
  • An Antisense nucleic acid is the complementary base pairing “opposite” of a sense nucleic acid.
25
Q

What are Exons and Introns?

A
  • EXons are the parts of the gene which will be EXpressed. These are the parts of the transcribed region of the gene which will remain in the finished mRNA product.
  • Introns are the parts of the transcribed region of a gene which are spliced out of the intermediate mRNA transcript and do not make it to the finished mRNA and therefore are not protein encoding.
26
Q

What is RNA splicing?

A
  • RNA splicing is the process by which the immediately transcribed parts of the gene are refinied to only contain sequences which actually code for the protein.
  • This is the removal of introns from the intermediate RNA to leave only the exons.
27
Q

What are Splice Junctions?

A

Splice Junctions are the locations in the intermediate RNA where the splicing takes place. That is the locations where the sequence is cleaved in order to excise the introns.

28
Q

What is a Consensus Splice Site?

A
  • These are sequences within the immature (unspliced) mRNA which indicates the start and end of the introns and therefore where on the RNA transcript splicing needs to take place.
  • The consensus sequence for the 5’ end of the intron (Donor) is G-G-[cut]-G-U-R-A-G-U
  • For the branch (middle part) of the intron its Y-U-R-A-C where y means a pyramidine.
  • For the 3’ end of the intron the sequence (Acceptor) its Y-rich-N-C-A-G-[cut]-G
29
Q

What is the “GT-AG” or GU-AG rule?

A

That the first two and last two nucleotides of an intro are GT and AG respectively, in DNA. In RNA it would be GU/AG.

30
Q

What are the 3 stop codons?

A

UAA UAG UGA

31
Q

What is the start codon? and what amino acid does it code for?

A

AUG

Methionine

32
Q

What are the 3 letter and one letter codes for the amino acids; Aspartic acid, Glutamine, Glutamic Acid and Phenylalanine?

A

Aspartic Acid Asp D
Glutamic Acid Glu E
Glutamine Gln Q
Phenylalanine Phe F

33
Q

What is Sarah Stoichet’s definition of mutation?

A

 Mutation: an error somewhere in the process
of transcription/translation/replication/division that
leads to a functional loss (or negative alteration
of function)
This is not the actual definition

34
Q

What is a polymorphism?

A

-A polymorphism is any gene, small sequence or single nucleotide in the genome which has multiple versions extant in the population.
Poly(multiple)morph(form)ism

35
Q

What type of mutations are inherited by the progeny?

A

Mutations during meiosis which produces the gametes which are successful in forming a zygote. Or in the Mitosis of the cells which produce the gametes. (In the Germline)
Vs Somatic mutations.

36
Q

What are the potential consequences of single nucleotide alterations?

A
  • frame-shift
  • truncation
  • critical amino acid exchange
  • splice-site mutations in intronic sequence
  • alteration of critical promoter or regulatory sequences
37
Q

What are three potential consequences of triplet repeat alterations?

A
  • in promoter sequence (e.g. Fragile X)
  • in coding sequence (e.g. Huntington’s)
  • in intronic sequence (e.g. Friedreich’s ataxia)
38
Q

What is a frame shift mutation?

A
  • Firstly DNA is read in frames, there are six possible frames within which to read DNA and these consist of triplet repeats.
  • An addition or deletion of any number of nucleotides that is not a multiple of 3 can change all nucleotides being read downstream of the alteration within a frame to completely change as a consequence.
39
Q

What is a truncation?

A

This is where a mutation leads to a codon being changed to a stop codon leading to the premature cessation of translation and the consequent truncation of the protein.

  • Truncation meaning being chopped, like a tree trunck becoming a stump
  • This could be caused by a single nucleotide replacement or by a frame shift
40
Q

What is a critical amino acid exchange?

A

This is where an amino acid in the protein which is important for the determination of the structure of the protein is exchanged for another amino acid, thereby altering the structure of the protein.

41
Q

What are Splice site mutations in intronic sequence?

A
  • These are mutations which occur in the nucleotides which indicate the location where splicing must occur.
  • The potential consequences of this manner of mutation are that the splicing of an intronic sequence may occur at a different location, or not at all.
42
Q

What are the potential consequences of the alteration of critical promoter or regulatory sequences?

A

The potential consequences of this manner of mutation are an increase or decrease in expression of a gene or the complete knock out of a gene.

43
Q

What kinds of Chromosomal abberations are there?

A
  • duplications or deletions

* gross chromosome rearrangements

44
Q

What is a genetic loci?

A
  • A genetic loci is simple a location on a chromosome.

- Usually used when refering to the location of a gene/allele.

45
Q

What are heterozygosity and homozygosity?

A

Heterozygosity is when someone has two different alleles at a specific genetic loci.
homozygosity is when someone has the same allele on both chromosomes for a specific genetic loci.

46
Q

What does it mean for an allele to be recessive?

A
  • An allele is recessive if when with a dominant allele in a homozygous individual it is silent and the individual has the phenotype of the dominant allele
  • Recessive alleles must be homozygous for the phenotype to be present.
47
Q

What does it mean for an alleles to be dominant?

A
  • An allele is dominant if only one copy of the allele is required in order for the phenotype of the allele to be fully present.
  • In other words a dominant allele DOMINATES a recessive allele in a heterozygous individual such that it is as if the individual is homozygous for the dominant allele.
48
Q

What is Independent assortment?

A
  • Independent assortment is when two or more genes are inherited in the progeny according to random Chance.
  • When genes are not genetically linked
  • occurs when genes are not on the same chromosome or are far apart on the same chromosome.
49
Q

What is genetic linkage?

A
  • Genetic linkage is when two genes/gene variants have a greater likelihood of being inherited together than by random Chance.
  • This occurs when two genes are on the same chromosome
  • There is greater genetic linkage of genes/alleles the Closer they are to each other on a chromosome. This is because of the shuffling of the pair of chromosomes during meiosis.
50
Q

What does Wild Type (WT) mean?

A

Wild type means non-Mutant or “Normal”

51
Q

What is a consanguinous marriage?

A

This is a marrage between two individuals who share an ancestor.

52
Q

What is the difference between Y-linked dominant and recessive diseases?

A

There is no difference.

53
Q

What is an autosomal dominant disease allele?

What would the Pedigree be like?

A
  • This is a disease allele which occurs on a non-sex chromosome that is dominant.
  • The Pedigree would have a random assortment of affected males and females ~50/50 split. There would be no carriers of the disease. Roughly half of the progeny of an affected individual would be affected (assuming heterozygosity of the individual).
54
Q

What would an autosomal recessive disease allele Pedigree look like?

A
  • Both males and females affected in equal measure.
  • Even if both parents are carriers only 1/4 of the Offspring will be affected.
  • “Skipping Generations”
55
Q

What would an X-linked recessive disease allele Pedigree look like?

A
  • Almost Always only men who are affected.
  • Female carriers
  • All male Offspring of a female carrier will be affected.
56
Q

What would an X-linked dominant disease alleles Pedigree look like?

A
  • All female Offspring of an affected male will be affected and None of the males.
  • Roughly half of all Offspring of an affected female will be affected, regardless of sex.
57
Q

What would a Y-linked disease Pedigree look like?

A
  • Only men affected.

- All Offspring of an affected male will be affected.

58
Q

What is Penetrance?

A

Penetrance is the

Medneuro- neurophysiology (M1-2) (6 decks)

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