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General genetics Flashcards

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1
Q

define gene

A

is a DNA coding sequence for a protein or ribosomal RNA

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2
Q

give me a bulk idea of how the gene is comosep

A
  1. Initiation codon 2. ORF (open reading frame) 3. exons and intronsfollowiin the last exon is the 3’UTR - untranslated regio
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3
Q

what percentage of DNA is junk?

A

97%

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4
Q

what does junk DNA do?

A

nothing. does not code for proteins and does not code for RNAr it has SINE (short interspersed elements) LINE (long interspersed elements) mini and micro satellites

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5
Q

what is the most repetitive sequence of junk DNA?

A

Alu sequencew occures 500K in the human genome

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6
Q

Genes controls cell activity through 2 processes

A
  1. transcription (DNA gives rise to RNA) 2. translation (RNA directs protein synthesis)
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7
Q

what are the 4 transcription factors?

A
  1. HTH helix-turn-helix 2. zinc finger 3. leucine zipper 4. heliz-loop-helix (HLH
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8
Q

many eye diseases result from transcription factor mutations….give examples

A

PAX2 (colobomas, ON hypoplasia, renal hypoplasia) PAX3 Waardenburg syndrome) PAX6 aniridia, peters,dominant foveal hypoplasia)

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9
Q

tell me about intron excision

A

The purpose is to leave the chain only with EXONS the process of removing introns is called Splicing sliciing takes places in splisosomes Aprox 15% of point mutations are cause by splicing errors Splicing errors can cause RP

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10
Q

what is the name for the process of removing introns?

A

splicing

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11
Q

besides splicing is there anothewr way to remove introns?

A

yes, by Alternative splicing The produict of this are called ISOFORMS (instead of proteins)

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12
Q

what is imprinting?

A

is a process by which a gene is modified example of errors in imprinting are Prader-Willi and Angelman syndromes

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13
Q

what is DNA damage and repair?

A

-each cell looses 10K bases per day. -this DNA is damages by many factors such as temperature, UV light, chemicals, etc -the repair mechanism svaes the cells. - if the DNA can not be repaired a tumor occurs. - 80-90% of cancers are a results of damaged DNA - DNA rapair occurs excision and mismatch repair

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14
Q

what if DNA is damages and can not be repaired?

A

the cell becomes a tumor and gives cancer

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15
Q

what is a gene?

A

the unit of coding sequence for a protein

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16
Q

what is the gene structure?

A
  • it has introns (not coding for proteins
  • exons (code for proteins)
  • starts with 5’
  • has a Promoter
  • then a transcription factor
  • stop codon 5’ UTR
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17
Q

what % of DNA is JUNK?

A

97%

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18
Q

what is the most repetitive junuk sequence?

A

ALU sequence

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19
Q

what is the process to produce a protein?

A
  1. transcription *gives rise to RNA)
  2. splicing (remove introns)
  3. translation (luego viene el traductor tarde) RNA directs synthesis of proteins
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20
Q

what are the 4 transciption factors?

A
  1. HTH helox-turn helix
  2. HLH heliz loop heloz
  3. zinc finger
  4. leucine zipper
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21
Q

what are the ophthalmic diseases that result from transcription facvtos mutations?

A

the PAX family

  • pax 2 = optic nerve coloboma and hypoplasia
  • pax 3 = waardenburg syndrome
  • pax 6 = aniridia, dominant foveal hypoplasia, Peters and AD keratitis
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22
Q

what is the name of the process to remove introns? and how is it done?

A
  • its called splicing (RNA goes from full to only exons)
  • takes place in spliceosomes
  • errors in splicing can cause disease
    • point mutations
    • retinitis pigmentosa
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23
Q

what is alternative splicing?

A
  • occurs during splicing
  • process that creates multiple copies of RNA
  • but some skip exons
  • the product is called isoforms
  • these isoforms are tissue specific
    • an example of useful isoforms are in the cornea
    • VEGF-1 receptor has a role in angiogenesis
    • in the cornea the VEGF-1 isoforms anct as VEGF trap and keep the cornea avascular
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24
Q

what is the name of the process of X chromosome inactivation? and what is the purpose or significance?

A
  • its called Lyonization (in honor to Mary Lyon)
  • has importance in x-linked disease because affects the severity or phenotype of these diseases
  • for example in x-linked RP
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25
Q

when looking at the pedigree, if MOST of the males are affected, what should you think?

A

its an x-linked disease

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26
Q

when looking at the pedigree, is the ration of male and female affected is 50/50, what should you think?

A

in an autosomal disease

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27
Q

is autosomal disease how can you tell it is dominant or recessive?

A
  • if the parents do not have the disease it is RECESSIVE
  • if one of the parents have the disease then its DOMINANT (but if only the mother passes the disease then it must be mitochondrial)

remember that on the pedigree you have to see males and females almost equally affected.

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28
Q

tell me key features of autosomal recessive inheritance

A
  • parents unaffected
  • skips generations
  • offsping of two heterozygous has 25% chances of inheriting the disease
  • more frequent in consanguinity
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29
Q

key features of autosomal dominant

A
  • appears in both sexes
  • one of the parents must have the disease
  • offspring of affected has a 50% chance of inhering
  • does not skip generations
    • if the parent does not have the disease it could be a DE NOVO mutation
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30
Q

rules of x-linked Recessive

A
  • father does not transmit to son
  • classic, more males than females are affected
  • a carrier mother has 50% chance to pass to her son
  • trait skips generations
  • all daughters of affected fathers are carriers

Basicamente el padre hipocrita. Porque nunca la pasa al hijo pero si le encarga a la hija a que le pase al nieto.

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31
Q

rules of x-linked dominant

A
  • Father never passes to son
  • both sexes affected but more females
  • does not skip generations
  • affected fathers PASS the DISEASE to all daughters
  • affected mothers will pass the disease to 50% sons and 50% daughetrs

El papa machista.NUNCA se lo pasa al hijo pero si a la hija. La mama mas equitativa se los pasa a los dos.

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32
Q

rules of mitochondrial inheritance?

A

inherited from mother only

33
Q

rules of -ylinked?

A

only males affected

passed from father to son

does not skip generations

ex: color blindness?

34
Q

what is th emost likely inheritance pattern on this pedigree?

A
  • X-linked recessive
  • Hemophilia
  • Only males are affected
  • skips generations: RECESSIVE
35
Q

inheritance pattern on this pedigree?

A

mitochondrial

36
Q

if on a pedigree both sexes are affected what could it be?

A

AR

AD

x-linked DOMINANT

but no XLR because that is in males

37
Q

what is the inheritance on this pedigree?

A

x-linked dominant

  • both sexes
  • does not skip generation (so no AR)
  • father al queso pasa a las hijas
  • madre justa pasa a los dos
38
Q

what is the inheritance pattern on this pedigree?

A

autosomal recessive

  • parents unaffected
  • skips generations
  • offsping of two heterozygous has 25% chances of inheriting the disease
  • more frequent in consanguinity
39
Q

what is the inheritance pattern?

A

autosomal dominant

  • appears in both sexes
  • one of the parents must have the disease
  • offspring of affected has a 50% chance of inhering
  • does not skip generations
  • if the parent does not have the disease it could be a DE NOVO mutation
40
Q

what is the inheritance pattern?

A

x-linked dominant

  • father does not transmit to son
  • classic, more males than females are affected
  • a carrier mother has 50% chance to pass to her son
  • trait skips generations
  • all daughters of affected fathers are carriers
  • Basicamente el padre hipocrita. Porque nunca la pasa al hijo pero si le encarga a la hija a que le pase al nieto.
41
Q

what is the inheritance pattern?

A

mitochondrial

  • passed by mother only
42
Q

what is imprinting?

A
  • is an epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner.
    • if the allele is inherited from the father is imprinted, it is thereby silenced, and only the allele from the mother is expressed
    • If the allele from the mother is imprinted, then only the allele from the father is expressed.
    • Forms of genomic imprinting have been demonstrated in fungi, plants and animals.[1][2] As of 2014, there are about 150 imprinted genes known in the mouse and about half that in humans
  • example: Wims tumor
43
Q

examples of diseases with abnormal DNA repair?

A

xeroderma pigmentosum

tricodermatophytosis

44
Q
A
45
Q
  1. what happens if there is no DNA repair?
  2. what are the 2 mechanisms of DNA repair?
A
  1. cancer tumors occur. 80-90% of tumors are cuased by deffects in DNA repair
  2. DNA repair done by
    1. excision repair
    2. mismatch repair
    • basicaly done by antioncogene p53, also know as… THE GUARDIAN of the GENOME
    • it senses if there is repair that can be done it starts repair but if its too much damage then causes cell apoptosis
46
Q

what is the antioncogene p53 gene?

A

its the GENOME GUARDIAN

DNA repair done by

  • excision repair
  • mismatch repair
  • basicaly done by antioncogene p53, also know as… THE GUARDIAN of the GENOME
  • it senses if there is repair that can be done it starts repair but if its too much damage then causes cell apoptosis
47
Q

what are the requisites to identify a mutation?

A
  1. the mutation does not occur in the normal population
  2. it produces a DNA mutation that alters the protein function and this correlaqtes with the phenotype
  3. the mutation cosegregates in the family according to inheritance pattern
48
Q

what are all the types of mutations?

A
  1. Missense mutation substitution of one amino acid for another in the protein made by a gene. Creates a different protein
  2. Nonsense mutation Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein.
  3. Insertion An insertion changes the number of DNA bases in a gene by adding a piece of DNA.
  4. Deletion larger deletions can remove an entire gene or several neighboring genes.
  5. Duplication A duplication consists of a piece of DNA that is abnormally copied one or more times.
  6. Frameshift mutation occurs when the addition or loss of DNA bases changes a gene’s reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. A frameshift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations.
  7. Repeat expansion Nucleotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated.
49
Q

how do you calla mutation that results in a gene WITHOUT and active product?

A

NULL mutation

Null mutaitons include

Missense mutation

is a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.

Nonsense mutation

Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all.

50
Q
A
51
Q

what ia a polymorphism?

A

a DNA variation that occurs in >1% of the population

52
Q

name some tumor suppressor genes

A
  1. retinoblastoma
  2. NF1
  3. NF2
  4. tuberous sclerosis
  5. VHLD
53
Q

what is a feature in mitochondrial diseases?

A
  • disease worsens with age
  • number of involved organs inicreases with time
    *
54
Q

name some mitochondrial diseases

A
  • Kearn-sayre syndrome
  • CPEO
  • LHON
  • maternal inherited sensorineural deafness
  • adult-onset diabetes and deafness
  • NARP (neuropathy, ataxia, RP)
  • streptomycin suceptibility to ototoxicity
55
Q

features of CPEO

A
  • ptosis
  • paralysis of EOM
  • pigmentary retinopathy
56
Q

features of Kearns-sayre syndrome

A
  • ptosis
  • EOM paralysis
  • severe RP
  • heart blocks

All this patients have LARGE DELETIONS!!!!

57
Q

features of Leber hereditary optic neuropathy

A
  • mitochondrial disease
  • causes
    • optic atrophy
    • peripapillary microangiopathy
  • more in males than females
  • the trait not transmited to offspring of males PADRES BUENOS
  • MADRES al queso. All daughters and sons of affected mothers will have the disease
  • Its cause by one single change G to A
    • at the nucleotide position 11778 in ND-4 gene
      • ND-4 gene involved in NADH dehydrogenase synthesis
    • nucleotide 3460 ND-1
    • nucleotide 14484 ND-6 and 14459
    • 12 other mutaitons but they may be variants
  • THIS DISEASE causes severe vision loss
  • SOME CAN IMPROVE (recover vision)
    • 14484 greates recovery
    • 11778 worse recovery
58
Q

what is the importance of finding the gene in LHON?

A

the type of gene is associated with chances of recovering vision

14484 greates recovery

11778 worse recovery

59
Q
A
60
Q

what is a nucleoside?

what is a nucleotide?

A

they are chemical compounds

  • nucleoside: SUGAR + NB (purine or pyrimidine)
  • nucleoTIDE: nucleoside + phosphate
62
Q

which is the DNA backbone?

A

tje SUGA….

ribose or desoxiribose

63
Q

what is the difference between a triplet and a codon?

A

they are similar terms

  • 1 sugar + 1 NB = 1 nucleoside
  • 1 nucloside + 1 phosphate = 1 NUCLEOTIDE
  • 3 nuclotides = 1 triplet
  • if the triplet encodes an aminoacid its called a codon
    • so…. CODON is the functional name of a triplet
64
Q

why is the genetic code degenerate?

how many aminoacids are there ?

how many codon combinations are possible?

A
  • there are only 20 aminoacids!!!!
  • there are 4 Nitrogenate bases
  • there are 64 combinations available
    • the code is degenerate because more than one codon codes for an AA
65
Q

which is the START codon?

A

AUG

codes for Methionine

66
Q

what is the definition of the genetic code?

A

set of rules by which information encoded within genetic material is translated into proteins

67
Q

what are the metric units of DNA?

A

measured in base pairs (BP)

a base pair is the nucleotide

kilobases (1000 bases)

Mb megabases (million bases)

68
Q

where is the DNA located in the cel?

A

in the nucleous

69
Q

how many BP are there in the human genoma?

A

3.2 billion of bp x2

70
Q

how many chromosome we have?

how many are autosomes?

home many sex chromosomes?

A
  • 46 chromosomes
    • 23 pairs
      • 22 pair autosomes
      • 1 pair autosomes
71
Q

what percentage of a DNA is conserved?

what is the importance or meaning of DNA conservation?

A
  • 5% of DNA is conserved across species
    • this means that if we compare all the human genome to one of mice or nematodes there is 5% that is exactly equal
    • this means that this 5% is extremely important for cell survival
72
Q

what percentage is junk DNA?

A
  • 30% but its not junk, we just don’t know what is the function yet.
  • it may have to do with packaging, segregation, replication , etc
73
Q

what percentage of DNA is protein coding?

A

1.5%

at least that is what we know.

80% might be functional

74
Q

what is the ENCODE project?

A

The Encyclopedia of DNA Elements (ENCODE)

https://www.genome.gov/10005107/

  • is a public research project launched by the US National Human Genome Research Institute (NHGRI)
  • in September 2003.
  • Intended as a follow-up to the Human Genome Project (Genomic Research),
  • theENCODE project aims to identify all functional elements in the human genome.
    *
75
Q

what is a gene?

A
  • its the UNIT of HEREDITY
  • its a region of DNA that is transcribed
    • transferred from parents to offspring
    • determines the characteristics of the offspring
76
Q

what does a gene produce?

what is the gene structure of components?

A
  • produces: proteins, enzymes, signalling molecules
  • a gene has:
    • PROMOTER
    • EXONS
    • INTRONS
    • STOP region
77
Q

what is the average size of a gene

A
  • average size is 20 KB
  • an average of 8 exons ( 1 exon - hundreds of exons)
  • There are 22,000 of genes
78
Q

how many genes are there in the human genoma?

A

22,000 protein coding genes

79
Q

what is splicing?

what is the translation to spanish?

A
  • in Spanish is EMPALME
  • is the EDITING of pre-RNA transcript
    • with splicing, INTRONS ARE REMOVED and exons are ligated

Genetics Fellowship (22 decks)

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