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Bioinformatics > Genetics and DNA - Khan Academy > Flashcards

Genetics and DNA - Khan Academy Flashcards

1
Q

What is an allele?

A

A specific version of a gene.

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2
Q

What is a heterozygous genotype?

A

A genotype where there are different alleles on the homologous chromosome pair.

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3
Q

What is a homozygous genotype?

A

When there are the same alleles in both homologous chromosomes.

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4
Q

Difference between genotype and phenotype.

A

Genotype are the actual genes (two sets). Phenotype is what is expressed, i.e. a trait.

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5
Q

What is incomplete dominance?

A

When heterozygous phenotype is intermediate between homozygous parent phenotypes.
e.g. a cross between a homozygous red plant and homozygous white plant will result in pink offspring

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6
Q

What is independent assortment?

A

When two traits are coded on different chromosomes or far apart on the same chromosome (e.g. eye color and teeth size), the alleles are inherited independently.
The allele that a gamete receives for one gene doesn’t influence the allele received for another gene.

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7
Q

What are linked traits?

A

Traits coded on the same chromosome. They are inherited together.

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8
Q

What is the law of segregation?

A

Only one of the two gene copies present in a parent are distributed to each gamete and the allocation is random.

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9
Q

What is a test cross?

A

Breeding an organism with a dominant phenotype to determine whether it’s homozygous or heterozygous. It is bred with a homozygous recessive organism.
If all offspring has dominant traits, the tested organism is homozygous. If not, it’s heterozygous.

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10
Q

What is pleiotropy?

A

When one gene affects many different characteristics, not just one.
e.g. in Mendel’s peas, one gene affects color of flowers, seed coats, and leaf axils.

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11
Q

What are lethal alleles?

A

Alleles that make an organism unable to survive.

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12
Q

What are sex linked traits?

A

Traits or mutations coded on sex chromosomes, e.g. color blindness, haemophilia. They are recessive on X chromosome.

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13
Q

What is codominance?

A

When both alleles are expressed simultaneously in the heterozygote.
e.g. AB blood types.

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14
Q

What is polygenic inheritance?

A

When a trait is controlled by more than one gene.
e.g. height which is linked to around 400 genes.

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15
Q

What is variable expressivity?

A

When a phenotype might be stronger or weaker in people with the same genotype.

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16
Q

What is incomplete penetrance?

A

When individuals with a certain genotype may or may not develop a phenotype associated with the genotype.

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17
Q

What are the reasons for variable expressivity and incomplete penetrance?

A
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18
Q

What are the reasons for variable expressivity and incomplete penetrance?

A

other genes and environmental effects, for example, disease-causing alleles of one gene may be suppressed by alleles of another gene elsewhere in the genome, or a person’s overall health may influence the strength of a disease phenotype

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19
Q

What is genetic linkage?

A

Genes that are sufficiently close together on a chromosome will tend to “stick together,” and the versions (alleles) of those genes that are together on a chromosome will tend to be inherited as a pair more often than not.

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20
Q

What are parental configurations of alleles?

A

When two genes are close to each other on a chromosome, they rarely cross over to separate chromosomes. They’re then often inherited together on the chromosome that was present in the organism before meiosis.

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21
Q

What are recombinant configurations of alleles?

A

When two genes are close to each other on a chromosome, they rarely cross over to separate chromosomes. When they (rarely) do, they’re called recombinant.

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22
Q

What is recombination frequency?

A

It’s the percentage of offspring with recombinant traits.

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23
Q

What are linkage maps?

A

Chromosomal maps based on recombination frequency.

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24
Q

What are X-linked genes?

A

Genes on the X sex chromosome.

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25
Q

What is the SRY gene?

A

sex-determining region of Y - a gene which encodes a protein that turns on other genes required for male development

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26
Q

What does it mean that an individual is hemizygous?

A

This is said of males for X-linked genes.

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27
Q

What is X-inactivation?

A

In XX females, one X chromosome is compacted into a small, dense structure, called a Barr body. Most of the genes in the Barr body are inactive (not transcribed).

It happens randomly in individual cells during embryonic development.
In kangaroos and other marsupials it’s always the paternal X chromosome which undergoes X-inactivation.

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28
Q

What is a Barr body?

A

It’s the crumpled, compacted, inactive X chromosome in XX females.

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29
Q

What is an aneuploid organism?

A

An organism which has an extra or missing copy of a chromosome.

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30
Q

What is an euploid organism?

A

An organism which has correct number of chromosomes.

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31
Q

What are the most common types of aneuploidy?

A

monosomy - when an organism has only one copy of a chromosomes which should be paired
trisomy - when an organism has three copies of a chromosome

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32
Q

What is nondisjunction?

A

When a pair of chromosomes fails to separate during meiosis or mitosis.

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33
Q

What are chromosomal rearrangements? What are the types?

A

Large scale mutations of chromosomes.
e.g.
- duplication - part of a chromosome is copied
- deletion - part of a chromosome is deleted
- inversion - chromosomal region is flipped around
- translocation - a part of a chromosome is attached to another chromosome

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34
Q

What does mitochondrial DNA look like?

A

Small and circular, similarly to bacterial DNA. There are multiple copies of DNA in a single mitochondrium.

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35
Q

Difference between mitochondrial and nuclear DNA.

A
  • high copy number - a cell has multiple copies, even thousands - there are multiple copies of DNA in mitochondrium, and there are multiple mitochondria in a cell
  • random segregation - mitochondria are randomly distributed to daughter cells
  • single-parent inheritance - non-nuclear DNA is usually inherited from only one parent, in humans - from mothers
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36
Q

What are the bases that form DNA?

A

Adenine
Thymine
Guanine
Cytosine

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37
Q

How many genes are there on all 46 human chromosomes?

A

Around 6 billion.

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38
Q

What is a codon?

A

A three-base sequence in RNA which codes for one amino acid.

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39
Q

What is ribose?

A

It’s a 5-carbon sugar that in its cyclical form forms RNA.

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40
Q

What is deoxyribose and how is it different from ribose?

A

It’s a 5-carbon sugar that is a part of DNA structure. It has 2 oxygens fewer than ribose.

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41
Q

What are purines?

A

Nitrogenous bases which have 2 carbon-nitrogen rings.

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42
Q

What are pyrimidines?

A

Nitrogenous bases with 1 carbon-nitrogen ring.

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43
Q

What is adenine?

A

It’s a nitrogenous base with 2 rings (purine) which is a part of DNA and RNA structure.
Bonds with thymine.

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44
Q

What is guanine?

A

A nitrogenous base with 2 rings (purine) which is a part of DNA and RNA structure.
Bonds with cytosine.

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45
Q

What is thymine?

A

A nitrogenous base with 1 ring (pyrimidine) which is a part of DNA tructure.
Bonds with adenine.

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46
Q

What is cytosine?

A

A nitrogenous base with 1 ring (pyrimidine) which is a part of DNA and RNA structure.
Bonds with guanine.

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47
Q

What kind of bonds are there between base pairs?

A

Hydrogen bonds - between partially positive nitrogen in one base and partially negative oxygen in another base or between partially positive hydrogen and partially negative oxygen.

Cytosine and guanine form 3 hydrogen bonds, and adenine and thymine form 2.

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48
Q

What are the 3 basic molecule types in DNA?

A
  • phosphate group
  • deoxyribose (sugar)
  • nitrogenous bases (adenine, thymine, guanine, cytosine)
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49
Q

What does it mean that DNA structure is antiparallel?

A

The sugars in each strand are oriented in opposite directions.
Carbons in the sugar molecule that are bonded to phosphate groups are 3’ and 5’ carbons.
One chain is directed from 5’ carbon to 3’ carbon, while the other - from 3’ to 5’.

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50
Q

What is nucleotide made of?

A

A phosphate group, a 5-carbon sugar, and a nitrogenous base.

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51
Q

What is uracil?

A

A nitrogenous base with 1 ring (pyrimidine) which is a part of RNA tructure.
Bonds with adenine.

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52
Q

What does it mean that polynucleotide chain is directional?

A

It “begins” with a phosphate group bonded to sugar’s 5’ carbon, and “ends” with 3’ carbon.
When new nucleotides are added to DNA or RNA, they attach at the 3’ carbon.
DNA sequences are usually written in 5’ to 3’ direction.

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53
Q

What does ribosome do?

A

It assembles proteins from amino acids.

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54
Q

What is the role of mRNA?

A

Messenger RNA, it serves as an intermediate between DNA and protein production.
A RNA copy (transcript) is made of a gene, then RNA associates with a ribosome which in turn builds proteins.

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55
Q

What is the role of rRNA?

A

Ribosomal RNA. It helps mRNA to bind in the right spot. Some mRNA act as enzymes which help catalyze the formation of bonds that link amino acids to form a protein.

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56
Q

What is the role of tRNA?

A

Transfer RNA. It act as carrier, bringing amino acids into the ribosome.

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57
Q

What are regulatory RNA?

A

miRNA (microRNA) and siRNA (small interfering RNA)
they regulate expression of genes

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58
Q

What was Thomas Hunt Morgan’s experiment?

A

Morgan established that heritable factors were most probably carried on chromosomes. He studied how mutations are inherited in fruit flies, specifically white eyes in males.

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59
Q

What was Frederick Griffith’s experiment?

A

Griffith studied pneumonia bacteria in mice. He was able to establish “transforming principle” - where dead virulent bacteria were able to transform non-virulent bacteria.

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60
Q

What did Oswald Avery, Maclyn McCarty, and Colin MacLeod discover?

A

They wanted to identify Griffith’s transforming principle. They were able to separate and purify the “transforming principle” and their data suggested that it’s DNA.

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61
Q

What were the Hershey-Case experiments?

A

They studied bacteriophage viruses which “tricked” bacteria into producing more of the viruses. They created two groups of the bacteriophages - with DNA marked (by radioactive phosphorus) and with protein marked (by radioactive sulphur).
It turned out that viruses inject DNA into the bacteria and it’s DNA that is the “transforming principle”.

62
Q

Who discovered structure of the DNA?

A

James Watson, Francis Crick, based on the work on the chemists - Rosalind Franklin and Maurice Wilkins.

63
Q

What is topoisomerase?

A

An enzyme which helps “unwinds” DNA for replication. It creates temporary “nicks” in the backbone of DNA and the seals them.

64
Q

What is the role of helicase?

A

It “unzips” DNA by breaking hydrogen bonds between base pairs.

65
Q

When DNA is separated - what are the names of the two strands and how are they different.

A

leading strand - which “ends” with 3’ carbon, so new nucleotides can be easily attached continuously

lagging strand - which “ends” with 5’ carbon, so new nucleotides are added in Okazaki fragments

66
Q

What is DNA polymerase?

A

It is an enzyme which, during DNA replication, attaches new nucleotides at the 3’ end.
It needs a template (one DNA strand), and a starting point - a primer. It also proofreads the copies.

67
Q

What is an Okazaki fragment?

A

During DNA replication, the lagging strand is duplicated in batches (fragments), called Okazaki fragments.

68
Q

What is RNA primer?

A

Aa short nucleic acid sequence that provides a starting point for DNA synthesis during DNA replication.

69
Q

What is DNA ligase?

A

It connects Okazaki fragments on the lagging DNA strand during DNA replication.

70
Q

What does it mean that DNA replication is semiconservative?

A

Each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.

71
Q

Where does the energy to form new bonds during replication come from?

A

Nucleotides have 3 phosphate groups attached to them. When the bond is broken, the energy released is used to form a bond between the uncoming nucleotide and the growing chain.

72
Q

What is origin of replication?

A

It’s a specific location in the DNA where replication can start and are recognized by their sequence.

73
Q

What is a replication fork?

A

A structure where two DNA strands are split open for replication.

74
Q

What is the role of single-strand binding protein?

A

It coats separated DNA strands near replication forks keeping them from coming back together as double helix.

75
Q

What is primase?

A

An enzyme which makes a RNA primer.

76
Q

What is sliding clamp?

A

An enzyme which holds polymerase molecules in place as they synthesize new Okazaki fragments.

77
Q

What is the role of DNA polymerase I?

A

On the lagging strand, it replaces RNA primers with DNA between Okazaki fragments.

78
Q

What was the Meselson-Stahl experiment?

A

They discovered that DNA replication was semi-conservative, using E.Coli and two different nitrogen isotopes.

79
Q

How does DNA proofreading work?

A

DNA polymerase immediately checks each base that it adds and replaces it right away if it’s incorrect.

80
Q

What is mismatch repair?

A

It’s an error correction mechanism after DNA synthesis. It corrects mismatched pairs, small insertions and deletions.

81
Q

How does mismatch repair work?

A

First, a protein complex (group of proteins) recognizes and binds to the mispaired base. A second complex cuts the DNA near the mismatch, and more enzymes chop out the incorrect nucleotide and a surrounding patch of DNA. A DNA polymerase then replaces the missing section with correct nucleotides, and an enzyme called a DNA ligase seals the gap.

82
Q

How is the new DNA strand recognized from the old one (template)?

A

In eucariotes, new DNA strand has “nicks”, i.e. single-stranded breaks.
In bacteria, old DNA strand has methyl groups attached to some of its bases.

83
Q

What are the DNA repair mechanisms outside of replication?

A
  1. direct reversal
  2. excision repair
  3. double-stranded break repair
84
Q

What is direct reversal?

A

A DNA repair mechanism.
Some DNA-damaging chemical reactions can be directly “undone” by enzymes in the cell.

85
Q

What is excision repair?

A

A DNA repair mechanism
Damage to one or a few bases of DNA is often fixed by removal (excision) and replacement of the damaged region.
In base excision repair, just the damaged base is removed.
In nucleotide excision repair, a patch of nucleotides is removed.

86
Q

What is double-stranded break repair?

A

DNA repair mechanism for entire chromosomes breaking into two pieces.

87
Q

How does non-homologous end joining work?

A

When a chromosome breaks in two, e.g. due to high-energy radiation, it’s glued together, although it typically includes a small mutation at the break site.

88
Q

How does homologous recombination work?

A

Information from the homologous chromosome or a sister chromatid is used to repair a break in a chromosome.

89
Q

What is the telomere sequence in mammals?

A

5’-TTAGGG-3’

90
Q

What are telomeres?

A

Repetitive regions at the ends of chromosomes in eucariotic species which protect DNA from information loss when it shortens during replication.

91
Q

Why do chromosomes shorten during replication?

A

On the lagging strand, the final stretch of DNA cannot be covered by an Okazaki fragment, because it’s too short for a primer.
Also, the primer of last Okazaki fragment cannot be replaced by DNA like other fragments, because there is no hydroxyl group to act as a “hook” for polymerase.

92
Q

Why are there loops at telomere ends?

A

After replication, leading strand is slightly longer, creating a single-stranded overhang. This overhang binds to complementary repeats in the nearby double-stranded DNA, causing the telomere ends to form protective loops.
There are also proteins in telomeres which prevents triggering DNA repair pathways.

93
Q

What is telomerase?

A

It is an enzyme, a RNA-dependent DNA polymerase which extends the telomeres of chromosomes.

94
Q

What is a polypeptide?

A

Chain of amino acids.

95
Q

What can be coded by a gene?

A

Protein of functional RNA

96
Q

What does the protein coding process work?

A
  1. Transcription - DNA sequence is copied to create an mRNA molecule
  2. Translation - sequence of the mRNA is decoded to specify the amino acid sequence of a polypeptide.
97
Q

What is the central dogma of molecular biology?

A

Information flows DNA -> RNA -> protein.

98
Q

What is gene expression?

A

The process of going from DNA to functional product.

99
Q

What are two strands called in transcription?

A

Non-coding (template) strand
Coding strand

100
Q

What are the roles of coding and non-coding strand in transcription?

A

Non-coding strand serves as template for the synthesis of RNA which carries the same information as the coding strand.

101
Q

What is primary transcript?

A

RNA which is synthesized in transcription.

102
Q

How mRNA gets its name?

A

Because it serves as a messenger between DNA and ribosomes where proteins are produced.

103
Q

How many different codons are there?

A

64

104
Q

What are codons?

A

A sequence of 3 nucleotides in mRNA which codes one amino acid.

105
Q

What is genetic code?

A

Relationship between codons and amino acids.

106
Q

What indicates start and stop of translation?

A

There are special start and stop codons. Most polypeptides start with methionine which is coded by the start codon.

107
Q

Where does translation take place?

A

In ribosomes.

108
Q

In what cells is telomerase active?

A

In germ cells and some adult stem cells, as well as in some cancer cells.

109
Q

What is the role of RNA polymerase?

A

It is an enzyme which reads the non-coding DNA strand and synthesizes mRNA in DNA to RNA transcription.

110
Q

What are ribosomes made of?

A

Protein and rRNA (ribosomal RNA).

111
Q

What is the bond between two amino acids?

A

A covalent peptide bond.

112
Q

What is chaperone complex?

A

It is a protein that polypeptides fold.

113
Q

What molecule is at the 5’ end of a DNA or RNA chain?

A

The phosphate group of the first nucleotide. It is attached to the 5’ carbon of the sugar ring.

114
Q

What molecule is at the 3’ end of the DNA or RNA chain?

A

The hydroxyl (OH) group of the last nucleotide. It is attached to the 3’ carbon of the sugar ring.

115
Q

What are the ends of a polypeptide?

A

N-terminus and C-terminus.

116
Q

What is an N-terminus in a polypeptide?

A

The amino group is exposed. The amino acid in the N-terminus is the first amino acid in the order.

117
Q

What is a C-terminus in a polypeptide?

A

It’s the last amino acid, where carboxyl group is exposed.

118
Q

How many amino acids are there in protein?

A

20

119
Q

What was the Beadle-Tatum experiment?

A

They established the one gene one enzyme hypothesis. Through a series of experiments with mutated bread mold, they established that a mutation causes inability of an organism to produce certain amino acid.

120
Q

What are the updates to one gene one enzyme hypothesis?

A
  1. some genes encode protein that are not enzymes
  2. some genes encode a subunit of a protein, not a whole protein, a gene encodes one polypeptide, and some proteins are composed of more than one polypeptide
  3. some genes don’t encode polypeptides, but functional RNA molecules
121
Q

Where does DNA transcription take place in eukaryotic cells?

A

In the nucleus.

122
Q

How does RNA polymerase know where to start and stop transcribing a gene?

A

For each gene, there is a promoter and a terminator.
Promoter is a spot that indicates where RNA polymerase is supposed to attach itself to start transcription of that gene.
Terminator signals end of transcription.

123
Q

How does DNA to RNA translation differ in prokaryotes and eukaryotes?

A

In prokaryotes, DNA is transcribed directly to mRNA. In eukaryotes, the process has an additional step. DNA is transcribed to pre-mRNA, and then it’s processed to create the actual mRNA.

124
Q

What are introns?

A

“Junk” RNA sequences that are spliced out during pre-mRNA processing.

125
Q

How is pre-mRNA processed to create mRNA?

A
  1. 5’cap is added at the beginning (modified guanine)
  2. poly-A tail is added at the end (100-200 adenine nucleotides)
  3. introns are spliced out
126
Q

What are the stages of transcription?

A

Initiation
Elongation
Termination

127
Q

In DNA transcription, what is the initiation site (or +1 site)?

A

It’s the site on the DNA from whcih the first RNA nucleotide is transcribed.

128
Q

What are upstream and downstream nucleotides?

A

Upstream nucleotides are the ones before initiation site.
Downstream nucleotides - the ones after.

129
Q

What is a TATA box?

A

It’s a DNA sequence in a promoter recognized by basal transctiption factors, allowing the factors and RNA polymerase to bind.

130
Q

What is a basal (general) transcription factor?

A

Helper proteins which help RNA polymerase to attach to DNA.

131
Q

Where does DNA translation happen in eukaryotes?

A

In cytosol.

132
Q

What is the role of 5’ cap.

A

It protects the transcript from being broken down and helps the ribosome attach to mRNA during translation.

133
Q

What is polyadenylation signal?

A

It’s the signal, during DNA transcription, for an enzyme to chop RNA at that site.

134
Q

What is the role of the poly-A tail?

A

It makes the transcript more stable and helps get it exported from the nucleus to the cytosol.

135
Q

What is RNA splicing?

A

It’s a part of processing pre-mRNA where specific parts (introns) are recognized and removed by spliceosome.

136
Q

What is spliceosome?

A

A protein-and-RNA complex which recognizes and removes introns.

137
Q

What are exons?

A

The parts of RNA that remain after splicing out introns.

138
Q

What is alternative splicing?

A

A gene can be spliced in two or more ways, leading to encoding more different protein from the same gene.

139
Q

What are ribosomes made of?

A

Protein and rRNA (ribosomal RNA).

140
Q

What are anticodons?

A

They are located in tRNA (transfer RNA) which uses them to match with mRNA codons to deliver appropriate amino acid.

141
Q

What are A-site, P-site, and E-site?

A

They refer to stages in DNA translation and the progress of a ribosome along mRNA strand.
A-site (aminoacyl) is where next tRNA attaches with its anticodon.
P-site is where the polypeptide bond forms by transfering the amino acid from the first mRNA site to the A-site
E-site is where the first tRNA detaches after releasing the polypeptide chain.

142
Q

What are the stages of translation?

A

Initiation, elongation, termination.

143
Q

What is wobble?

A

In mRNA translation, at the third position in a codon, atypical base pairs can form (other than A-U, G-C).

144
Q

What is the role of aminoacyl-tRNA synthetases?

A

These are enzymes which ensure that tRNA pairs with an appropriate amino acid.
Each amino acid has its synthetase which recognizes relevant tRNA. The enzyme pairs the two together using energy from an ATP.

145
Q

What is the initiation complex?

A

All the molecular pieces which allow for the mRNA translation to start, i.e.
- ribosome
- mRNA
- “initiator” tRNA carrying the start amino acid (almost always methionine)

146
Q

What happens during translation initiation phase?

A
  • tRNA attaches to the smaller ribosome unit
  • together they bind to the 5’ end of mRNA by recognizing the 5’ GTP cap
  • they “walk” along the mRNA in the 3’ direction
  • they stop when they reach the start codon (AUG)
  • large ribosomal subunit joins to form initiatin complex
147
Q

At which end new amino acids are attached?

A

At C-terminus.

148
Q

How does translation termination occur?

A

The stop codons are recognized by release factors which fit in the P site. They interfere with an enzyme which forms peptide bonds and make it attach a water molecule to the last amino acid of the polypeptide chain. This separates the chain from tRNA.

149
Q

What are signal peptides?

A

An amino sequence which signals that proteins should be directed to endoplasmic reticulum during translation.

150
Q

Wchich protein are directed to endoplasmic reticulum during translation?

A

Generally those bound for organelles in the endomembrane system, i.e. ER, Golgi apparatus, and lysosome or for the exterior of the cell.

151
Q

What is the role of 5’ cap and poly-A tail?

A

They protect the mRNA transcript from attack by enzymes in the cytoplasm called exonucleases that specifically target RNA molecules with exposed 5’ ends.

Bioinformatics (7 decks)

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