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Biotech final > Chapter 11 (book) > Flashcards

Chapter 11 (book) Flashcards

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1
Q

Annotation

A

Once a genome is sequenced, scientists have to identify the functions of different base pair sequences in it. This process is known as annotation

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2
Q

Any DNA sequence can be read in any of six different reading frames. If one of those frames contains a relatively long sequence of codons uninterrupted by a stop codon, it is called []

A

open reading frames (ORFs)

DNA sequences with long stretches of codons in the same reading frame uninterrupted by stop codons.

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3
Q

A DNA segment in one species is said to be a homolog of a DNA segment in another species if _____.

A

there is evidence that the two segments are derived from the same ancestral DNA sequence
Homolog: homologous chromosomes; also refers to genes or regulatory DNA sequences that are similar in different species because of descent from a common ancestral sequence.

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4
Q

A sequence is [] if homologs of that sequence are found in many different species.

A

Conserved

conserved (DNA sequence): describes a DNA sequence that has homologs in many different species.

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5
Q

[] exhibit the highest degree of similarity in two different species, such as, for example, humans and a bird

A

Coding sequences of exons

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6
Q

Equation for calculating probability that two random sequences of DNA are identical.

A

.25^# of Bp

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7
Q

tRNAs, rRNAs, and snRNAs are all examples of _____.

A 
noncoding RNAs (ncRNAs) 
a transcript that lacks an open reading frame and functions as an RNA molecule.
Are not translated into proteins
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8
Q

conserved DNA sequence

A

Homologs of this sequence are found in many different species.

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9
Q

easiest way to identify the gene that encodes an mRNA in the genome

A

Reverse transcriptase: Make cDNA corresponding to the mRNA, clone the cDNA, and sequence the clone.
Produces complementary DNA (cDNA) from mRNA transcripts; cDNA clones thus represent only the exons of genes

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10
Q

Degree of similarity of exons and introns

A

Exons have higher degree of similarity

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11
Q

reverse transcriptase

A

a retroviral RNA-dependent DNA polymerase that synthesizes DNA strands complementary to an RNA template.
Retroviruses can convert RNA into dsDNA by using this special RNA-dependent DNA polymerase

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12
Q

activity of reverse transcriptase

A

After infection of retrovirus it makes a cDNA copy of an RNA strand, then, it converts the ssDNA into a dsDNA.

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13
Q

complementary DNA (cDNA)

A

complementary DNA; a DNA molecule synthesized using mRNA as a template; a single or double-stranded DNA representation of an mRNA.

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14
Q

what serves as a primer to produce dsDNA?

A

Single-stranded cDNAs fold back on themselves at their 3’ ends which then serve as primers.

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15
Q

If an RNA molecule can be purified and sequenced, the gene for that RNA can be identified in the genome by its corresponding base-pair sequence. This can be easily done for _____.

A

a specific rRNA

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16
Q

cDNA library

A

a large collection of cDNA clones that represent the mRNAs expressed by a particular cell type, tissue, organ, or organism.
Only includes exons
It only contains parts of the genome used to make proteins in a specific tissue.

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17
Q

During the production of cDNA from RNA, what primers are used?

A

oligo-dTs

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18
Q

Scientists can sequence many clones from a cDNA library and use those sequences to identify ______.

A

the exons of genes

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19
Q

proteome

A

the complete set of proteins encoded by a genome.

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20
Q

A scientist isolates all of the mRNAs in a kidney cell and reverse transcribes them into dsDNA. The dsDNA copies are then inserted into vectors and cloned into E. coli. The scientist has produced a(n) []

A

cDNA library

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21
Q

What type of a library would you use if you were interested in studying the entire genome of an organism?

A

A genomic library

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22
Q

The number of different proteins produced is much [] than the number of different genes present in the genome.

A

Larger (almost 4 times)

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23
Q

Exome

A

The part of an organism’s genome that corresponds to all of the exons of protein-coding genes
made of all of the exons in its genome

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24
Q

Once a cDNA library is prepared, scientists sequence many cDNA clones and compare them to the genome of the organism they are studying. Areas where the cDNA sequences and the genome are identical represent the [] of genes.

A

Exons

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25
3 non-protein-coding sequences in the humans genome
Centromeres Introns Intergenic regions
26
In the human genome, most of the DNA outside of genes is repetitive. The two main types of repetitive sequences are [] and []
Multicopy tandem repeats; transposable elements
27
Number of human genes
28000
28
tandem repeat
a region of the genome that contains repeat units of a small number of base pairs that appear many times in a row at each location where they exist
29
transposable element
A DNA sequence that can move around the genome, and is found in many locations throughout it.
30
What explains the extensive variation seen in the size of genomes of different eukaryotic species?
Expansions and contractions of noncoding DNA regions
31
Direction of transcription of most genes in the human genome
No discernible pattern exists in the directions of transcription of different genes on a chromosome.
32
A scientist discovers the sequence CAG repeated multiple times (i.e., CAGCAGCAG...) in many different locations spread around the human genome. This is an example of _____.
a multicopy tandem repeat
33
Gene desert
a gene-poor region of the genome where no genes have been discovered in it They can be as long as several million base pairs.
34
3 features of transposable elements in the human genome.
At each location in the genome they exist as a single copy. They are usually thousands of base pairs long. They can move around the genome.
35
How are the exons of a protein-coding gene related to the protein domains in the encoded polypeptide?
Usually each domain in a protein is encoded by a separate exon.
36
distribution of genes in the human genome
In some regions genes can be densely packed, while in other regions there might be long stretches (millions of bases) without any genes.
37
domain architecture
the number and order of a protein’s functional domains determined by the different number and kinds of protein domains, and their order in the final polypeptide(s).
38
While studying a new protein encoded in the human genome, a scientist finds that the amino acid sequence implies that the protein contains a domain which is known to bind to DNA in other, well described proteins. Based on this information, the scientist can _____.
speculate about the function of the new protein
39
protein domains
discrete functional regions of a protein. | a linear sequence of amino acids that folds up in a way to produces a single functional unit.
40
Result of exons can be shuffled, added, or deleted
They often result in new genes which encode proteins with novel domain architectures.
41
Suppose that an exon from gene A was inserted, together with its flanking introns, into gene B. Which of the following accurately describes where this insertion can occur in order to produce a novel protein?
The exon can be inserted at any nucleotide position within any of the introns of gene B. Does not matter where the introns are
42
Homeodomains
A particular DNA binding motif and transcription factor important for the development of multicellular organisms.
43
gene family
a set of closely related genes with slightly different functions that most likely arose from a succession of gene duplication events. two processes are responsible for the evolution of gene families Duplication and divergence
44
In humans, the β-globin locus is located on chromosome [] and has [] functional genes.
11; 5
45
Humans and chimpanzees have the same genes in the same order in their β-globin locus, while other primates have one fewer β-like gene. What does that tell us about the evolution of the β-globin locus?
The last duplication event in the β-globin locus occurred in a common ancestor of chimpanzees and humans.
46
orthologous genes
genes with sequence similarities in two different species that arose from the same gene in the two species’ common ancestor.
47
paralogous genes
genes that arise by duplication within the same species, often within the same chromosome; paralogous genes often constitute a gene family.
48
pseudogene
a nonfunctioning gene; the result of duplication and divergence events in which one copy of an originally functioning gene has undergone mutations such that it no longer functions. a sequence in DNA that looks like a gene bit does not actually function as such (due to the accumulation of mutations and/or loss of regulatory regions).
49
de novo genes
genes lacking homologs except in closely related species, thought to have evolved anew from intergenic DNA sequences. Several hundred genes in the human genome are unique to humans
50
features of the α-globin gene family in humans.
2 introns in exactly the same positions. | 5 functional genes.
51
A de novo gene can arise when a small ORF in intergenic DNA acquires ______.
transcriptional activation sequences.
52
Humans have two clusters of globin genes in the hemoglobin family: the α-globin locus and the β-globin locus. All globin genes can be traced back to _____.
a single ancestral gene
53
syntenic blocks
blocks of linked loci within a genome. | Blocks of chromosomal sequences found in two species, which contain homologous genes in the same order
54
chromosomal rearrangement
a change in the order of base sequences along one or more chromosomes. chromosomal blocks of sequences can be cut and reassembled in a different way
55
describes the rearrangement of the β T-cell receptor chain gene during the maturation of T cells
A D element is randomly joined to a J element and the D-J element is joined to a random V element. In both cases, the intervening DNA is deleted.
56
describe how, theoretically, the three neurexin genes in the human genome can generate more than 2000 different proteins
Each neurexin gene contains 2 promoters and five sites at which alternative splicing can occur.
57
A typical human cell may contain only about 50,000 different mRNA transcripts, but millions of different proteins. How is this possible?
After the mRNAs are translated, proteins can be posttranslationally modified in different ways.
58
describe the relationship between orthologous, paralogous and homologous genes
Both orthologous and paralogous genes are also homologous.
59
Inversion
a region of DNA is flipped 180o with respect to the rest of the chromosome.
60
Bioinformatics
Using high powered computers and specialized software to study the information contained within the genome of an organism science of using computers with specialized software to study the information contained in biological systems (for example, the information contained in the genome of an organism).
61
In humans, almost 1000 different types of the β T-cell receptor chain can be generated though combinatorial amplification from 58 elements. This is possible because in each T cell, ______.
the DNA is rearranged during development to generate a particular version of the β T-cell receptor chain.
62
BLAST
When you identified the nucleotide sequence of a gene and wants to find out if this gene has any homologs in other organisms' genomes
63
A human cell can potentially generate up to a million proteins from 50,000 different mature mRNAs through [] modifications, such as phosphorylation, or cleavage.
Posttranslational modification
64
all of the polypeptide chains found in a normal adult hemoglobin molecule.
Two beta chains | Two alpha chains
65
Embryonic hemoglobin
Made of 2 zeta and 2 epsilon chains
66
• Fetal hemoglobin
2 alpha and 2 gamma chains
67
Adult hemoglobin
Made of 2 alpha and 2 beta chains
68
A typical human cell may contain only about 50,000 different mRNA transcripts, but millions of different proteins. How is this possible?
After the mRNAs are translated, proteins can be posttranslationally modified in different ways.
69
Within the β-globin locus, how are the different globin genes oriented relative to chromosome 11?
They are all oriented in the same direction.
70
Heme
In hemoglobin, each polypeptide chain surrounds a small iron-containing structure
71
locus control region (LCR)
a cis-acting regulatory element (a collection of enhancers) that regulates transcription from individual genes within a gene complex such as the α-globin complex.

Biotech final (11 decks)

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