Exam 2: Ch 6 Flashcards Preview

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Flashcards in Exam 2: Ch 6 Deck (87):
1

noncoding DNA constitutes ___% of human chromosomal DNA

98.5%

2

DNA fingerprint

variations between repetitious stretches of DNA can be used to identify a person

3

transposable (mobile) DNA elements

within cellular genomes these mobile elements can copy themselves and move throughout the genome

45% of human genome

4

gene

the entire nucleic acid sequence that codes for synthesis of a protein or functional RNA

5

intron and exons

intron: noncoding regions of DNA found between genes and within genes

exon: relatively similar sequences in coding region selected for by evolution

6

2 types of short noncoding RNAs and basic functions

siRNA and miRNA

miRNA: regulate translation and mRNA stability

siRNA: breaks down mRNA after transcription so no translation

7

introns can process some RNA...

siRNA

miRNA

long noncoding RNA (regulate transcription by influencing chromatin structure)

8

where did mitochondria and chloroplasts evolve from?

intracellular eubacteria that developed symbiotic relationships with ancient eukaryotic cells

their DNA is an evolutionary remnant

9

chromatin

complex of DNA and the proteins that organize it

can be visualized as chromosomes during mitosis

10

genomics

computer based methods for analyzing and interpreting vast amounts of sequence DNA

11

nucleosomes

fundamental building blocks of chromatin

complex of DNA and histones

12

coding region

the nts that code an amino acid sequence or functional RNA

13

what does a gene contain

the coding region

all the DNA sequences required to synthesize a particular RNA transcript (these sequences can be located anywhere... not just in coding region)

14

enhancer

transcription control region

can be >50kb away from the coding region

15

cistron

a genetic unit encoding a single pp

16

most eukaryotic mRNAs are ____cistronic

mono

each mRNA encodes a single pp

17

in a bacterial polycistronic mRNA where is the ribosome located?

near the start site for each of the cistrons

translation initiation can begin at any of these sites

produces multiple proteins

18

in eukaryotic monocistronic mRNA where is the ribosome located?

5'-cap structure where ribosome binds

translation begins at closest AUG start codon

19

are introns usually longer than exons?

yes

longest in tintin gene...17,106bp

20

mutations in ____, _____, and _________ ______ ______ may all influence expression of the protein encoded by a simple transcription unit

exons, introns, transcription control regions

21

approximately ___% of human transcription units are ____

90%, complex

22

alternative splicing in fibronectin

multiple copies of 5 types of exons separated by introns

determines whether or not the secreted protein contains domains that adhere to cell surfaces

in fibroblasts and hepatocytes...ECM component

23

a mutation in the control region or in an exon shared by alternatively spliced mRNAs will affect...

all the alternative proteins

24

a mutation in an exon present in only one alternative mRNA will affect...

only the protein encoded by that mRNA

25

isoform

various proteins encoded by alternatively spliced mRNAs expressed from a single gene

26

solitary gene

25-50% of protein-coding genes are represented only once in the haploid genome

27

lysozyme

an enzyme that cleaves polysaccharides in bacterial cell walls

found in egg white protein and human tears

28

duplicated gene

genes with close but nonidentical sequences often located within 5-50kb of one another

29

gene family

a set of duplicated genes that encodes proteins with similar but nonidentical aa sequences

ex. genes encoding beta-like globins

30

protein family

the encoded, closely related, homologous proteins produced by a gene family

ex. kinases, vertebrate immunoglobulins, olfactory receptors

31

all hemoglobins formed from the different beta-like globin gene family carry oxygen in the blood, but....

exhibit different properties that are suited to their specific functions in human physiology

ex. A(y) and G(y) pp are expressed only during fetal life and have a higher affinity for oxygen

32

pseudogene

nonfunctional sequences even though they have exon-intron structure

mark location of gene duplication that occurred in our ancestors

not deleterious

33

segmental duplication

duplication of segments of a chromosome

occurred fairly often during evolution of multicellular plants and animals

34

members of gene families that arose relatively recently in evolution are often found...

near each other on the same chromosome

could also be found on different chromosomes

35

major cytoskeletal proteins

actins

tubulins

intermediate filaments (keratin)

36

heavily used gene products are encoded by...

multiple copies of genes

37

tandemly repeated arrays

genes encode identical or nearly identical proteins or functional RNAs

for genes encoding rRNA and nonprotein-coding RNAs like those involved in RNA splicing

38

why are tandemly repeated RNA genes needed?

to meet the great cellular demand for their transcripts

ex. during early embryonic development cells have a doubling time of 24 hrs and need enough rRNA to manage this

39

smRNA

small nuclear

function in RNA splicing

40

snoRNA

small nucleolar RNA

function in rRNA processing and base modification in the nucleus

41

miRNA

micro RNA

regulates the translation and stability of specific mRNAs

42

non-protein coding genes can encode...

functional RNAs

43

globin proteins comprise > __% of the total protein in developing red blood cells

50%

globin genes expressed at maximum rate

44

2 types of repetitious DNA

interspersed repeats (more common)

simple-sequence/satellite (less common)

45

satellite DNA (simple sequence DNA)

perfect or nearly perfect repeats of short sequences

6% of genome

1-500 bp

46

interspersed repeats

more common type of repetitious DNA

longer sequences of repeated DNA consisting of several types of transposable elements

47

microsatellite DNA

1-13 bp (most common is 1-4)

causes Huntington disease and myotonic dystrophy type 1

48

2 functions of satellite DNA

formation of centromeric heterochromatin that is necessary for proper segregation of chromosomes to daughter cells in mitosis

telomeres

49

minisatellites

larger than microsatellites

slight differences in lengths in individuals can be directed with Southern blotting

used for DNA fingerprinting

50

unclassified ____ DNA occupies a significant portion of the genome

spacer

25%, occurs between transcription units and is not repeated elsewhere in the genome

enhancers found here sometimes

51

what are transposable/mobile DNA elements

interspersed repeats, moderately repeated DNA, intermediate repeat DNA

sequences are copied and inserted into new sites in the genome by transposition

"selfish DNA" exist only to maintain themselves

52

during transposition of a mobile element, adjacent DNA...

is sometimes also mobilized

2nd mechanism for causing chromosomal DNA rearrangements

53

2 categories of mobile elements

those that transpose directly as DNA

those that transpose via an RNA intermediate that is transcribed from the mobile element by an RNA polymerase then converted back into dsDNA by reverse transcriptase

54

DNA transposons (transposons)

mobile elements that transpose directly as DNA

55

retrotransposons

mobile elements that transpose using an RNA intermediate

move but also remain at original location

analogous to infection by a retrovirus

56

insertion sequence

IS element

inserted stretches of DNA into the middle of a gene

57

inverted repeat

region that encodes transposase (enzyme required for transposition of IS element to new site)

58

3 functions of transposase in transposons

excise IS element in donor DNA

makes staggered cuts in a short sequence in target DNA

ligates 3' termini of IS element to 5' ends of cut donor DNA

59

2 types of retrotransposons

those containing long terminal repeats

those lacking long terminal repeats (most common)

60

long terminal repeats

250-600bp that are found on either end of the coding region in LTR retrotransposons

can function as a promoter and directs RNA processing

61

most common LTR retrotransposons in humans are

ERVs: endogenous retroviruses

62

nonviral retrotransposons

lack LTRs and are most common in mammals

moderately repeated DNA sequences

form 2 classes

63

2 classes of nonviral retrotransposons

long interspersed elements (LINEs)

short interspersed elements (SINEs)

64

key step in retroviral life cycle

forming retroviral genomic RNA from integrated retroviral DNA

65

LINEs are found in... and in humans...?

found in protozoans, insects, plants, and mammals

in humans... 3 families similar in mechanism of transposition but different in sequence (only L1) functional

66

LINE structure

flanked by short direct repeats

2 long ORFs

ORF1: encodes an RNA binding protein

ORF2: encodes a reverse transcriptase protein w/ DNA endonuclease activity

67

SINEs

2nd most abundant class of mobile elements in human genome

do not encode protein

transcribed by same nuclear polymerase used for tRNA

68

processed pseudogene

nonfunctional genomic copies of mRNA

flanked by short direct repeats

69

mobile element human diseases

hemophilia, Duchenne muscular dystrophy

70

exon shuffling

recombination between mobile DNA elements in introns of 2 separate genes

generates new genes made from new combinations of preexisting exons

71

3 ways mobile DNA elements are not parasitic selfish molecules, and have contributed to evolution

promote generation of gene families

creation of new genes via exon shuffling

forming complex regulatory regions that provide multifaceted control of gene expression

72

multiple genetic systems of eukaryotes

primary nuclear system

secondary systems with their own DNA: ribosomes, tRNAs in mitochondria and chloroplasts

73

mtDNA

mitochondrial DNA

some cells contain more than others

mitochondria contain multiple mtDNA molecules

inherited maternally and cytoplasmically

74

products of mitochondrial genes are not _____

exported

75

heteroplasmy

when mutations in mtDNA are found, cells contain a mix of mutant and wild-type mtDNAs

76

chloroplast transformation has led to the engineering of plants that are resistant to...

bacterial and fungal infections, drought, and herbicides

77

bioinformatics

use of computers to analyze sequence data (genomes)

78

by comparing aa sequences of a protein encoded by a newly cloned gene with he sequences of proteins of known function an investigator can look for...

sequence similarities that provide clues to the function of the encoded protein

related proteins exhibit more sequence similarity than the genes encoding them

BLAST computer program

79

BLAST

basic local alignment search tool

divides new protein sequence into shorter fragments and searches database for matches--assigns P values

80

low vs high p values

low p value: higher sequence similarity

high p value: less sequence similarity

81

structural motifs

short sequences recurring in many different proteins

similar functions

82

homologous (BLAST)

sufficiently similar in sequence to suggest a common ancestral sequence

ex. tubulin family of genes

83

paralogous (BLAST)

sequences that diverged as a result of gene duplication

84

orthologous (BLAST)

sequences that arose due to speciation (different species)

85

ORF

open reading frame where protein-coding sequences are found

stretch of DNA >100 codons beginning with start codon and ending with a stop codon

86

expressed sequence tag (EST)

aligned to a partial cDNA sequence

87

phenomena that generate more complexity in expressed proteins of higher eukaryotes

alternative splicing yielding multiple functioning mRNAs

variations in post-translational modification of proteins

increased numbers of cells built of the same kinds of proteins