Quiz #11 Flashcards

1
Q

What are mutations?

A

heritable changes in DNA sequence, as compared to a “normal” reference sequence, the reference is usually referred to as wild type

a change in DNA might nor change any characteristics or functions of a cell (or organism), it depends on the location (in the protein) and nature of the mutation

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2
Q

What are the structures a mutation can effect?

A

proteins: by altering the coded information in different ways

rRNAs, tRNAs, or other non-coding RNA (e.g. snRNP RNA)

regions of DNA that have other functions that depend on the sequence (e.g. promoters, origins, centrosomes)

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3
Q

What is an allele?

A

each variant form of a gene

a diploid organism has two alleles of each gene (may be the same or different, AA or Aa or aa)

the most common allele in a population is often referred to as “wild type”

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4
Q

What is a substitution mutations?

A

base-pair substitutions are the replacement of one nucleotide and it’s partner with another pair

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5
Q

What are the different types of substitution mutations?

A

silent mutations

missense mutations

nonsense mutations

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6
Q

What are silent mutations?

A

because of redundancy in the genetic code, some mutations do not change the primary sequence of a polypeptide encoded by a gene

always has no effect on the amino acid sequence, but the efficiency of translation might change due to the different codon used

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7
Q

What are missense mutations?

A

result in a change in the primary sequence of a polypeptide

may have little or no effect on a protein’s function

if it changes an amino acid within the active site of an enzyme it could cause it not to work, but if it changes an amino acid on the outside of an enzyme it might not affect function

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8
Q

What are nonsense mutations?

A

changes a codon for an amino acid into a STOP codon

causes premature termination of translation

most nonsense mutations lead to non-functional proteins

a large portion of protein could be missing if it occurs early

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9
Q

What are insertion or deletion mutations?

A

all nucleotides downstream of a frameshift mutation will be improperly grouped into codons that convey extensive missense information

an insertion or deletion of 3 nucleotides would result in one less or one more amino acid but no reading frame shift

eventually, a STOP codon will be encountered, or the ribosome will reach the end of the mRNA

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10
Q

What is an example of a mutation that causes a disease?

A

the common type form of sickle cell anemia is caused by a single base pair substitution in the gene that encodes the beta hemoglobin polypeptide

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11
Q

What are spontaneous mutations?

A

most due to errors in DNA replication that are not corrected

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12
Q

What are induced mutations?

A

caused by mutagens, x-rays, gamma rays, nucleotide analogs, oxidizing agents, benzene

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13
Q

What are carcinogens?

A

mutagens that are known to cause cancer

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14
Q

How does the regulation or control of genes happen?

A

by turning gene transcription on or off, a cell controls which proteins it makes under different conditions

in prokaryotes (bacteria) or simple eukaryotes (yeasts), gene expression is often directly influenced by the environment (which nutrients are present or absent)

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15
Q

What are the two general ways genes may be transcribed in prokaryotes?

A

single units (one gene transcribed from one promoter)

multiple gene units that share the same promoter (derived from genes that occur in clusters called operons)

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16
Q

What is tryptophan (Trp)?

A

is an amino acid required for growth, and is present in virtually all proteins in a cell

if Trp accumulates, it can bind to Enzyme 1 (allosteric inhibition) and shut it off

the cell can quickly respond to fluctuating levels of Trp

17
Q

What are the steps of regulation of tryptophan synthesis in bacteria?

A
  1. Trp synthesis is regulated at the protein level by allosteric inhibition
  2. Trp synthesis is controlled via transcriptional regulation of the Trp operon
  3. Trp synthesis is also regulated by attenuation, which interferes with the completion of transcription
18
Q

How is Trp synthesis controlled via transcriptional regulation of the Trp operon?

A

mechanism was discovered in E. coli bacteria

involves a cluster of genes that encode enzymes required for the synthesis of Trp

operon is expressed (on) when Trp levels are low and repressed (off) when Trp levels are high

operon is regulated by the Trp repressor, encoded by the TrpR gene, when bound to Trp, the Trp repressor binds to the Trp operator sequence and blocks transcription of Trp genes

19
Q

How is Trp synthesis regulated by attenuation which interferes with the completion of transcription?

A

woks because of coupled transcription and translation in prokaryotes

monitors the availability of Trp amino acids for incorporation into polypeptides

20
Q

What does gene repression look like in prokaryotes?

A

initiation of transcription is relatively simple (sigma and a promoter is sufficient to transcribe most typical genes)

thus repression is often used to prevent transcription of some genes when the proteins they encode are not needed (Trp operon)

21
Q

What are inducible operons?

A

those that are OFF most of the time, but can be induced or turned ON

22
Q

What are some examples of inducible operons in prokaryotes?

A

Repressor is always bound to the operator except under certain conditions

When the promoter is imperfect and requires another protein (that is regulatable) to help recruit the RNA polymerase

23
Q

What does gene repression look like in eukaryotes?

A

in many cases, another region of DNA “loops around” and is used to help recruit the RNA pol II (these are referred to as enhancer elements)

differential gene expression determines a cell’s characteristics and this is how complex organisms create specialized cells and/or tissues with the same DNA

the decision of whether to transcribe a gene or not, starts with the compaction state of the chromatin where the gene is located

24
Q

What is the difference between heterochromatin and euchromatin in eukaryotes?

A

DNA in eukaryotes can exhibit multiple levels of compaction, due to nucleosomes and higher-order structures

heterochromatin: highly condensed
euchromatin: not condensed

because of it’s compaction, heterochromatin is largely inaccessible to transcription factors, loosely packed euchromatin is more accessible to the transcription factors

25
Q

What is chromatin remodeling?

A

can alter the state of chromatin in a specific (sometimes small) region of the chromosome

26
Q

What are histone modifications?

A

histone acetylation cause the chromatin to become less compact

enzymes called histone acetyltransferases (HATs) add acetyl groups to positively-charged lysine amino acids in histones

histones can be modified in many ways to change the chromatin compaction state, and/or “mark” a region of the chromosome for recognition by other proteins

27
Q

What is ATP-dependent chromatin remodeling?

A

complexes of specific enzymes use ATP energy to transiently change the compaction state of chromatin at different regions of the chromosome

chromatin remodeling complexes reposition (i.e. slide) the nucleosomes across the DNA, or even cause histones to be ejected from the DNA

in this way, the remodelers create “open” regions of DNA that are accessible to general transcription factors that can activate gene transcription