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BMSC 220 > Chapters 1-5 > Flashcards

Chapters 1-5 Flashcards

1
Q

Characteristics of life:

A

Movement, metabolism, reproduction, response to stimuli

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2
Q

Cell theory:

A

All organisms are composed or one or more cells.
The cell is the structural and functional unit of life.
All cells arise from other cells. (Omnis cellula e cellula.)

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3
Q

Who came up with which parts of cell theory:

A

First two - Schleiden and Schwann. Last one - Virchow.

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4
Q

Requirements for the formation of the first cell:

A

Organic molecules (from inorganic molecules), molecules for catalysis of chemical reactions and self-replication, and a barrier between internal and external cell environments.

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5
Q

RNA as catalytic molecule:

A

The only molecule capable of both catalyzing chemical reactions (ribozyme) and self-replicating.

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6
Q

What was the first genetic material the precursor to the first cell?

A

RNA! Special because it can be a catalyst!

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7
Q

Present-day prokaryotes:

A

Archaebacteria, eubacteria, cyanobacteria

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8
Q

__bacteria are the most common form of bacteria.

A

Eu

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9
Q

__bacteria are often extremophiles.

A

Archae

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10
Q

The cytoskeleton is not solely structural…

A

It can also have functions in mobility. Ex: sperm.

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11
Q

Function of peroxisomes:

A

Perform various oxidative reactions

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12
Q

Function of ER:

A

Processing/transporting proteins; lipid synthesis.

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13
Q

Function of golgi apparatus:

A

Sorts and transports proteins destined for secretion; lipid synthesis.
In plant cells: cell wall polysaccharide synthesis

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14
Q

Yeast:

A

Saccharomyces cerevisiae. Unicellular with intercellular communication.

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15
Q

Volvox:

A

Colonial unicellular alga.

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16
Q

Main tissue systems of plants:

A

Ground, dermal, vascular.

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17
Q

Main tissue systems of animals:

A

Epithelial, connective, nervous, muscle, blood.

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18
Q

Epithelial cells:

A

Specialized for protection, secretion, absorption. Skin and lining of internal organs.

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19
Q

Connective tissues:

A

Bone, cartilage, adipose.

Fibroblasts: cells that fill the spaces between organs and body tissue.

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20
Q

Different kinds of erythrocytes:

A

Granulocytes (feathery purple thing with no envelope), monocytes (blobby middle bit), macrophages, lymphocytes (round middle bit).

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21
Q

What do different muscles look like?

A

Skeletal - super ordered.
Cardiac - striated, a little more random.
Smooth - like frog eggs.

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22
Q

Model organism - e coli:

A

Divides every 20 minutes under ideal conditions. Small genome - 4.6 million bp, 4300 genes.

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23
Q

Model organism - yeast:

A

12 million bp. Divides every 2 hours.

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24
Q

Model organism - nematode:

A

Caenorhabditis elegans. 959 somatic cells. Entire cell lineage is known.

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25
Q

Model organism - fruit fly:

A

Drosophila melanogaster. Effects of every gene mutation known.

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26
Q

Model organism - xenopus laevis:

A

Eggs are large single cells. All stages of development can be studied in a lab.

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27
Q

Model organism - zebrafish:

A

Transparent embryos, amenable to mutation.

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28
Q

List of model organisms:

A

E coli, yeast, nematode, drosophila, xenopus, zebrafish, mouse.

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29
Q

Microscopy - bright field:

A

Thin slice. Stain. Requires fixing. Light passes directly through specimen.

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30
Q

Microscopy - phase contrast and differential interference-contrast:

A

Stain. Live cells. Converts variations in density or thickness into contrast.

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31
Q

Microscopy - fluorescence:

A

Fluorescent markers, dyes, and proteins. Ex: GFP. Living cells. Light does not pass through, just excites the dye.

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32
Q

Microscopy - TEM:

A

Slice. Electrons through specimen.

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33
Q

Microscopy - SEM:

A

Whole thing. Electrons bounce of metal coating.

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34
Q

Ultracentrifuge stats:

A

100 000 rpm. Forces 500 000 times greater than gravity.

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35
Q

Order that components of broken cell suspension sediment:

A 
Nucleus.
Mitochondria, lysosomes, peroxisomes. 
Plasma membrane and ER.
Ribosomes. 
Cytosol remains.
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36
Q

Term - the stuff left over after something has been sedimented out:

A

Supernatant!

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37
Q

Nutrients in media for growing animal cells:

A

Serum, salts, glucose, amino acids, vitamins

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38
Q

Define - primary culture:

A

First culture established from a tissue. Limited number of divisions before death.

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39
Q

Define - permanent/immortal culture:

A

Embryonic stem cells or cancer cells. May proliferate indefinitely.

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40
Q

What percent of the wet weight of cells is water?

A

70%

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41
Q

Membrane solubility is dependent on ___.

A

Solubility in water.

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42
Q

80-90% of the dry weight of cells is composed of ___.

A

Macromolecular forms of proteins, lipids, nucleic acids, and carbs.

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43
Q

Cellular monosaccharides contain ___ carbons, with ___ being the most common.

A

3-7; 3, 5, 6

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44
Q

Major forms of polysacchs:

A

Glycogen, starch, cellulose

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45
Q

Shapes of glycogen, starch, cellulose:

A

Glycogen - branched alpha glucose polymer
Starch - un/branched alpha glucose polymer
Cellulose - unbranched beta glucose polymer

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46
Q

Saturated vs unsaturated fatty acids:

A

Saturated has only single bonds. Unsaturated has one or more double bonds.

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47
Q

Structures of different lipids:

A

Triacylglycerol - three fatty acids linked to a glycerol

Phospholipid - two fatty acids and a phosphate group bound to a glycerol (other things can be added to the phosphate)

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48
Q

New info about RNA:

A

Gene regulation, catalytic functions

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49
Q

Which nucleic acids are purines/pyrimidines?

A

Purines (big) - A, G

Pyrimidines (small) - C, T, U

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50
Q

Define nucleoside vs nucleotide:

A

Nucleoside - nitrogenous base linked to deoxy/ribose sugar

Nucleotide - includes the phosphate group

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51
Q

Which nucleic acid pairs form two/three hydrogen bonds?

A

AT form 2; CG form 3

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52
Q

Can RNA be double-stranded?

A

Not really, but it can form double-stranded secondary structures

53
Q

Tendency of R groups in secondary structures:

A

In alpha helix and beta sheets, R groups tend to stick out.

54
Q

Lipids constitute what percent of membrane mass?

A

50%

55
Q

Water travelling across a membrane:

A

Simple diffusion but it needs a little help because it’s so polar.

56
Q

Passive transport:

A

You know what it is. It uses a transport protein but doesn’t expend energy.

57
Q

Define: -omics

A

Large-scale analysis of cell molecules

58
Q

Define: proteome

A

All proteins expressed in a given cell

59
Q

Define: interactomics

A

How proteins interact with each other

60
Q

The reason we’re as complex as we are is that ___ are separate.

A

The processes of transcription and translation

61
Q

Composition of nuclear envelope:

A

Two bilayer membranes, underlying nuclear lamina, nuclear pore complexes

62
Q

Nuclear lamina:

A

Fibrous protein mesh that provides structural support. Composed of lamins (fibrous proteins) and other proteins.
Analogy: window screen holding up a blanket

63
Q

Nuclear pore complexes are complicated because they have to get which huge molecule through?

A

Ribosomes

64
Q

Which nuclear membrane is continuous with the ER?

A

Outer.

65
Q

Function of the perinuclear space:

A

Functions like an ER, since it’s continuous with it

66
Q

Define: phenotype

A

Basically any expressed trait.

67
Q

TH Morgan’s work on drosophila:

A

Phenotypic traits are inherited together in linkage groups.
# of linkage groups = # of chromosomes.
Evidence that chromosomes are the heritable material.

68
Q

Historically, scientists weren’t sure if __ or __ was the genetic material.

A

Proteins or DNA

69
Q

Not all genes code for proteins. What do those genes code for?

A

Structural/regulatory RNAs that are never translated into a protein.

70
Q

Basic unit of genetic code?

A

Codon.

71
Q

General trend between complexity and genome size:

A

Increase in one increases the other. NOT LINEARLY THOUGH.

72
Q

Define: gene

A

A segment of DNA within a chromosome that is expressed to yield a functional product.

73
Q

Some numbers concerning the makeup of genes:

A

35% of human genome is introns
10% of the average gene sequence is exons
1% of human genome is exons that encode proteins

74
Q

What’s the point of introns?

A

Info for regulatory RNA

75
Q

Which organisms do we have complete genomes for?

A

E. coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Arabidopsis, and the mouse

76
Q

Genome of mycoplasma genitalium:

A

Simplest present-day prokaryote. Second-smallest genome with 580k BPs / 470 genes. Likely represent the minimal gene set required to maintain a self-replicating organism.

77
Q

The human genome: how many genes?

A

20-25000

78
Q

The human genome: how come we’re so complicated with so few genes?

A

Spread over greater distances with more introns between, may be subject to more alternative splicing

79
Q

The human genome: what’s the significance of sharing 40% of genome with lower eukaryotes?

A

It’s probably the minimum required proteins involved in basic cellular processes.

80
Q

The human genome: what do the other 60% of unshared genes do?

A

Dedicated to making us more complex. Lots are only actives in embryonic development.

81
Q

Define: chromatin

A

Eukaryotic chromosomal DNA complexed with proteins.

82
Q

Ratio of proteins and DNA in chromatin:

A

Twice as much protein as DNA

83
Q

Chromatin is super compressed. Here are some numbers.

A

Human DNA is 2 m long; chromatin is packed into 5-10 um nucleus.

84
Q

Chromosome number and organism complexity:

A

UNRELATED!!!!!!

85
Q

Nucleosomes:

A

The basic structural unit of chromatin. Composed of DNA and histones.

86
Q

Histones:

A

Small proteins containing a high proportion of the basic amino acids (arg and lys). This facilitates binding to the negatively charged DNA sugar-phosphate backbone.
H1, H2a, H2b, H3, H4

87
Q

Nucleosome core particles:

A

147 base pairs of DNA wrapped twice around an octamer consisting of two molecules of each histone except H1.

88
Q

Chromatosome:

A

166 bp and histone H1.

89
Q

Forms of chromatin in interphase cell:

A

Eu, hetero (constitutive or facultative)

90
Q

Euchromatin:

A

Least condensed form. Transcriptionally active, usually as 10 and 30 nm fibres.

91
Q

“Naked” DNA:

A

You never seen DNA without proteins.

92
Q

Heterochromatin:

A

Highly condensed, transcriptionally inactive chromatin. Contains highly repetitive DNA sequences. Two types.

93
Q

Constitutive heterochromatin:

A

Contains DNA that is not transcribed in any cell type. Ex: some DNA sequences at centromeres.

94
Q

Facultative heterochromatin:

A

Contains DNA sequences that are not transcribed in the cell being examined but may be transcribed in other cell types. Ex: the chromosomal region containing some genes expressed only in developing red blood cells is packaged into facultative heterochromatin in all other cell types.

95
Q

When are chromosomes most condensed?

A

During mitosis

96
Q

What does DNA look like during metaphase?

A

Large loops attached to a protein scaffold. In 30 nm fibres.

97
Q

Centromere:

A

A specialized region of the chromosome that plays a critical role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis

98
Q

Kinetochore:

A

A protein structure associated with the centromere, to which microtubules bind. They act as a molecular motor during mitosis and meiosis. Not associated with centromere during interphase. Not present in normal growth.

99
Q

Common thread in centromeres:

A

Contain a histone variant within the nucleosomes known as centromeric histone H3 (CenH3). Centromeric DNA sequence is not conserved across organisms.

100
Q

Telomere:

A

Sequences at the ends of eukaryotic chromosomes. Critical role in maintaining stability of linear chromosomes. Repeated clusters of G residues. Exonuclease can’t attach here because it’s a loop.

101
Q

Reasons DNA has to have high fidelity, reasons why not:

A

Cell reproduction has to be very accurate. However, genetic variation needs to be maintained.

102
Q

DNA polymerases:

A

Enzymes that catalyze DNA synthesis.

103
Q

DNA replication in prokaryotes vs eukaryotes:

A

Pretty much the same process, just with different players.

104
Q

Two fundamental properties of all DNA polymerases:

A

Synthesize only in 5’-3’ - read template only in 3’-5’. Can only add to a free 3’ OH.

105
Q

Replication fork:

A

The region of DNA synthesis where parental strands separate and daughter strands elongate. Contains the replication complex.

106
Q

How long is an Okazaki fragment?

A

1000-3000 BPs

107
Q

Primase:

A

Enzyme that synthesizes short fragments of RNA (3-10 nucleotides) complementary to the lagging strand at the replication fork.

108
Q

Exonuclease:

A

Enzyme activity that hydrolyses DNA or RNA molecules from their ends.

109
Q

RNase H:

A

Exonuclease that degrades the RNA stuck in RNA-DNA hybrids.

110
Q

E coli’s special DNA polymerase I:

A

DNA polymerase I has RNase H-like exonuclease activity that can degrade RNA primers in 5􏰀’ to 3’􏰀 direction.

111
Q

DNA ligase:

A

Seals breaks in DNA after RNase H does its job.

112
Q

Is DNA polymerase the same across cells?

A

Different kinds of cells have different polymerases.

113
Q

Accessory proteins: list

A

Clamp-loading proteins, sliding clamp proteins, helicases, single-stranded DNA-binding proteins

114
Q

Clamp-loading proteins:

A

Loads clamp proteins onto the replication fork at the primer

115
Q

Sliding clamp proteins:

A

Load and hold polymerase onto template

116
Q

Helicase:

A

Catalyzes DNA unwinding (with ATP use)

117
Q

Single-stranded DNA-binding proteins:

A

Stabilize the unwound single-stranded DNA

118
Q

Topoisomerases:

A

Enzymes that catalyze the breakage and rejoining of the double helix ahead of the replication fork

119
Q

How many oris does a human cell have?

A

Approximately 30,000 origins (every 50-300 kilobase pairs)

120
Q

Theoretically, how many oris should there be?

A

Minimum one per chromosome or else it would take 5ever.

121
Q

of oris vs how fast a cell replicates:

A

Fast-replicating cells have more oris, slow ones will have fewer.

122
Q

First oris in eukaryotes were studied in:

A

Yeast!

123
Q

Exons:

A

DNA segments that code proteins and 5’ and 3’ UTRs.

124
Q

Autonomously replicating sequence (ARS):

A

Origin of replication in yeast. 100 bp with common 11 bp core. Origin recognition complex binds to it to initiate replication bubble.

125
Q

Analog of ARS in bacteria:

A

Initiator

126
Q

Telomerase:

A

Enzyme that maintains the ends of eukaryotic chromosomes. Possesses reverse transcriptase activity. Elongates 3’ end of lagging strand to allow one more Okazaki fragment to synthesize.

127
Q

Reverse transcriptase:

A

A DNA polymerase that uses an RNA template.

128
Q

How DNA replication fidelity arises:

A

Need less than 1/10^9 errors.
Simple free energy differences in correct vs incorrect hydrogen bonding; polymerase actively selecting the right base; proofreading by polymerase; DNA repair mechanisms.

129
Q

The process of proofreading:

A

Polymerase chops off the incorrect base using 3-5 exonuclease, then regular synthesis proceeds.

BMSC 220 (2 decks)

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