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BS209: Molecular Biology > Chapter 1: Genomes and the Flow of Biological Information > Flashcards

Chapter 1: Genomes and the Flow of Biological Information Flashcards

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1
Q

the diversity of life is unified by 4 common themes; organisms must be:

A
  1. separate in some way from their environment
  2. able to store information in a stable way
  3. able to reliably replicate and pass information to the next generation
  4. able to extract energy from their surroundings
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2
Q

for an organism to be separate from its surroundings, it must be defined by a (1); this allows the organism to distinguish between (2)

A
  1. physical barrier
  2. self and non-self
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3
Q

all living organisms derive from a common original lie form referred to as (1) or (2)

A
  1. last universal common ancestor (LUCA)
  2. progenote
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4
Q

living organisms are constructed from 4 basic classes of ()

A

macromolecules

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5
Q

what is the basis of the theory that all life is derived from LUCA

A

when modern organisms are compared, the core building blocks of all organisms are the same (conserved)

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6
Q

nucleic acids are linear polymers of ()

A

nucleotides

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7
Q

a nucleotide is composed of:

A
  1. sugar molecule
  2. nitrogenous base
  3. phosphate group
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8
Q

main purpose of nucleic acids is to ()

A

store (DNA) and carry (RNA) information

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9
Q

proteins are linear polymers of ()

A

amino acids

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10
Q

an amino acid is composed of:

A
  1. amino group
  2. carboxyl group
  3. H atom
  4. side chain
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11
Q

workhorses of the cell

A

proteins

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12
Q

lipids are composed of ()

A

fatty acids

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13
Q

due to the (1) property of lipids, they can act as barriers for cells; separating them from their (2) environment

A
  1. hydrophobic
  2. aqueous
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14
Q

the 2 main parts of a fatty acid are:

A
  1. hydrophillic (polar) head
  2. hydrophobic tail
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15
Q

carbohydrates are polymers of ()

A

small sugars

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16
Q

main role of carbohydrates is to ()

A

store energy

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17
Q

because carbohydrates are hydrophilic, they can () of some proteins

A

increase the solubility

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18
Q

why is the storage and passage (flow) of biological information important for living organisms?

A
  1. faithful production of offspring
  2. proper tissue development/growth in multicellular organisms
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19
Q

the 4 nucleobases

A

guanine, cytosine, thymine, adenine

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20
Q

the 4 nucleosides

A

guanosine, cytidine, thymidine, adenosine

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21
Q

maintenance of life is based on the process of (1), both in the context of (2) and (3)

A
  1. reproduction
  2. growth of a specific tissue
  3. development of new offspring
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22
Q

properties of DNA

A
  1. double helix structure
  2. complementary base pairing
  3. antiparallel directionality
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23
Q

describe the double helix structure of DNA

A

phosphate backbone on the outside, complementary base pairs on the inside

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24
Q

describe the directionality of DNA

A
  • nucleic acids have distinct ends (5’ and 3’)
  • when 2 strands form DNA, 3’ aligns with 5’ (and vice versa)
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25
Q

properties of DNA that make it good for information storage

A
  1. stable (compared to RNA)
  2. 2 stranded structure allows for separation and copying of information
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26
Q

sequence of nucleotides in DNA of an organism; total DNA content of the cell

A

genome

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27
Q

why is the genome considered the blueprint for life?

A

it stores all the information needed to specify cellular function

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28
Q

give an overview of the transmission of the genome

A
  1. replication - accurate copying of information
  2. segregation - correct separation of copies
  3. transfer of copies into new cells
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29
Q

molecular machine responsible for synthesizing new DNA copies

A

DNA polymerase

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30
Q

the genome is composed of (1) and (2) regions in chromosomes

A
  1. genes (coding)
  2. intergenic (noncoding)
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31
Q

genes not only have instructions for a product but also instructions for ()

A

when and where a product should be made

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32
Q

all bacterial and some eukaryotic cells have (), which are small, circular DNA separate from chromosomes

A

plasmids

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33
Q

it is important to remember that organism complexity does not simply correlate with (1) or (2)

A
  1. genome size
  2. genome number
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34
Q

the process of making RNA by copying the sequence of a region in a gene; the first step in gene expression

A

transcription

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35
Q

in terms of usage, RNA is either (1) or (2)

A
  1. used directly by the cell
  2. used as information to direct manufacture of a particular protein
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36
Q

DNA : DNA polymerase :: RNA : ()

A

RNA polymerase

37
Q

in RNA, A pairs with ()

A

uracil (U)

38
Q

the initial product of a transcription event (RNA) is referred to as (); it is further reined into the final product

A

primary transcript

39
Q

process of turning the information in mRNA into a protein is called ()

A

translation

40
Q

coding RNAs that contain the information to produce a protein

A

messenger RNAs (mRNAs)

41
Q

start codon in translation

A

Met (methionine)

42
Q

each amino acid is represented (encoded) by 3 nucleotides in the mRNA molecule called a ()

A

codon

43
Q

translation is performed by the (), which has protein and RNA components

A

ribosome

44
Q

() interprets the information in mRNA into the protein sequence

A

transfer RNAs (tRNAs)

45
Q

() allows for different proteins to emerge from a single gene

A

alternative splicing

46
Q

ways to regulate gene expression

A
  1. concentrations of RNAs and proteins
  2. activity states (conformations) of RNAs and proteins
47
Q

how can gene expression be regulated through the concentrations of RNAs and proteins

A
  • certain RNAs and proteins can either promote or
    inhibit the expression of genes
  • increased concentrations of these RNAs or proteins can affect expression of genes
48
Q

gene expression is regulated in both (1) and (2), allowing the genome to express the correct genes when and where needed

A
  1. time
  2. space
49
Q

temporal and spatial gene regulation can determine:

A
  1. tissue cell types during development
  2. cellular responses to environmental changes
50
Q

main difference between prokaryotes and eukaryotes

A

eukaryotes have a nucleus while prokaryotes do not

51
Q

components of cells are spatially organized into regions to ()

A

help facilitate functions

52
Q

despite not having a nucleus, DNA in prokaryotes is concentrated in a region called ()

A

nucleoid

53
Q

the non-specialized regions of a cell make up the ()

A

cytoplasm

54
Q

examples of membrane-bound organelles in eukaryotes

A
  1. nucleus
  2. endoplasmic reticulum and Golgi apparatus
  3. mitochondria and chloroplasts
  4. lysosomes and peroxisomes
55
Q

why is the nuclear membrane porous

A

to allow for molecular machines to interact with DNA for cellular processes

56
Q

benefits of cellular compartmentalization

A
  1. compartmentalization facilitates biochemical reactions via the co-localization of materials
  2. physical separation provides an opportunity for regualtion
57
Q

how does co-localization of materials aid in efficiency of cellular processes

A
  1. reactants are localized together -> more efficient biochemical rxns
  2. related processes with shared materials are localized together -> more efficient use and transport of materials
58
Q

how does physical separation of processes help in regulation of cellular processes

A

processes cannot proceed unless certain regulatory conditions are met, preventing faulty products from being utilized

59
Q

genes operate in (), where the activity of one gene affects the activity of another

A

networks

60
Q

refers to the visual features and properties of an organism

A

phenotype

61
Q

organisms have () - number of copies of its genome

A

ploidy

62
Q

what is the advantage of diploid or polyploidy

A

presence of a ‘back-up’ version of a gene, in case one version is defective

63
Q

() refer to the normal, typical organisms that occur most frequently in a natural population

A

wild-type

64
Q

copies of a gene that are similar (have same function) but different (may express different phenotype); version of a gene

A

allele

65
Q

explain the basis of forward genetics

A

mutant phenotype is observed and the gene that causes the phenotype is then discovered

66
Q

explain the basis of reverse genetics

A

a gene of interest is disrupted, and the phenotype is observed to determine disrupted gene’s function

67
Q

any change in the gene sequence

A

mutation

68
Q

in diploids, mutations can be (1) or (2)

A
  1. dominant
  2. recessive
69
Q

one mutant copy in heterozygotes is enough to produce a mutant phenotye

A

dominant mutation

70
Q

phenotype of mutant version is masked by presence of wild-type allele; thus mutant phenotype is only expressed in homozygotes with this mutation

A

recessive mutation

71
Q

kinds of gene mutations

A
  1. point mutations
  2. insertions
  3. deletions
  4. rearrangements
72
Q

gene mutations can either alter the (1) of a protein or the (2) and change gene expression

A
  1. sequence and structure
  2. regulatory regions of a gene
73
Q

mutations that result in a loss of the wild-type function are referred to as

A

null or loss-of-function mutations

74
Q

mutations that result in a gain of a new abnormal function are referred to as

A

gain-of-function mutation

75
Q

single nucleotide changes (point mutations) can have a variety of effects

A
  1. missense mutation
  2. nonsense mutation
  3. silent mutation
76
Q

single nucleotide changes alter the encoded amino acid

A

missense mutations

77
Q

single nucleotide changes introduce a premature stop codon

A

nonsense mutations

78
Q

single nucleotide changes do not alter encoded amino acid

A

silent mutations

79
Q

why are frameshift mutations (due to insertions or deletions) catastrophic

A

entire amino acid sequence can be disrupted/affected

80
Q

() can lead to phenotypic changes without altering the underlying DNA

A

epigenetic changes

81
Q

examples of epigenetic changes

A

regulation of the compactness of chromatin -> genes tightly wound around chromatin are inaccessible and thus not expressed

82
Q

a mutation in a single gene causes a disease

A

monogenic diseases

83
Q

diseases that result from changes in several genes

A

polygenic (multifactorial) diseases

84
Q

percentage of people with the gene mutation that will develop the disease

A

penetrance of mutation

85
Q

relatedness among organisms is indicated using a ()

A

phylogenetic tree

86
Q

phylogenetic trees are typically based on comparisons of ()

A

multiple genes

87
Q

in phylogenetic trees, the () indicates how related organisms are

A

length of the branch

88
Q

characteristics of model organisms

A
  1. have fast generation times
  2. relatively small and cultivatable in a lab
  3. biochemically or genetically tractable
89
Q

how do viruses provide insights into replication and gene expression mechanisms

A

viruses must infect and use a host cell’s cellular machinery to reproduce; studying how viruses reproduce allows for a closer look at how cellular machinery of the host cell works

BS209: Molecular Biology (8 decks)

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