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Biol 300 > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Proterozoic Eon

A

2500 to 540 MYA
-great oxygenation event (2.4 to 2.0 GYA): significant accumulation of atmospheric O2 (a waste product of photosynthetic prokaryotes) and extinction of many anaerobic organisms
-oldest fossil evidence of multicellular eukaryotes (2.1 billion years old)
-oldest fossil of eukaryotic cells (1.45 billion years old)
-appearance of animals, but no evidence of hard body parts (i.e shells)

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2
Q

Phanerozoic Eon

A

540 MYA to present
-appearance of many classes of organisms, especially animals
-appearance of hard body parts among animal fossils
-colonization of land (440 MYA)

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3
Q

What is the internal structure of the earth?

A

inner core
outer core
mantle
asthenosphere
upper mantle
crust

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3
Q

Inner Core

A

Solid
5100-6378 km

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4
Q

Outer Core

A

Liquid
2890-5100 km

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5
Q

Mantle

A

Liquid
700-2890 km

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6
Q

Asthenosphere

A

Soft solid
100-700 km

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7
Q

Upper mantle

A

Solid
35-100 km

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8
Q

Crust

A

Solid
0-35 km

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9
Q

Is there a correlation between the elemental composition of living systems and that of the Earth’s crust?

A

Yes, there are a lot of elements that make up the Earth’s crust that are essential for most forms of life

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10
Q

What were the likely sources of other biologically important elements?

A

-Atmospheric Synthesis
-Extraterrestrial Delivery
-Aqueous Phase Chemistry
-Hydrothermal/Geochemical Synthesis
-Interfacial Chemistry

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11
Q

Atmospheric Synthesis

A

CO2, CO, N2, H2S, H20, CH4
-Gas phase reactions: hv, ED, starting gases

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12
Q

Extraterrestrial Delivery

A

-Liquid/Ice phase reactions: conditions on parent bodies/space

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13
Q

Aqueous Phase Chemistry

A

-temperature (0-100C?), pH, reagents, concentration, etc

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14
Q

Hydrothermal/Geochemical Synthesis

A

CO2, NH3, H2S, H20
-Temperature (70-350C?), pH, reagents, concentration, time, etc

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15
Q

Interfacial Chemistry

A

-Drying, wetting, mineral interactions, UV

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16
Q

How did cells first arise?

A

-cannot say for certain
-many researchers are still working on finding the answer

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17
Q

What minimal physical attributes would the first living structures have had?

A

-compartmentalization
-self-replication
-metabolism

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18
Q

Compartmentalization

A

Purpose:
-sequestration, control, and transport of molecules
Modern example:
-membranes

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19
Q

Self-Replication

A

Purpose:
-reproduction of system and genetic material
Modern example:
-cell division
-DNA replication

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20
Q

Metabolism

A

Purpose:
-extraction of energy
-construction of new systems and genetic material
Modern Example:
-enzymes

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21
Q

What are 4 classes of small biological molecule?

A

-Amino acids
-Nucleotides
-Monosaccharides
-Acetyl group

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22
Q

What is the structure of an amino acid?

A

An alpha C atom is covalently bound to:
-hydrogen
-amino group
-carboxyl group
-R group

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23
Q

How many kinds of amino acid are found in living systems?

A

20
4 groups:
-Non polar
-Positive charge
-Polar
-Negative charge

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24
Q

What is the structure of a nucleotide?

A

-5 kinds of nitrogenous base
-2 kinds of sugar
-every nucleotide has the same phosphate group

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25
Q

Which 2 sugars are part of nucleotides?

A

-Ribose (RNA nucleotides only)
-Deoxyribose (DNA nucleotides only)

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26
Q

Which 5 nitrogenous bases are part of nucleotides?

A

U-uracil (RNA)
G-guanine
A-adenine
C-cytosine
T-thymine (DNA)

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27
Q

What are monosaccharides?

A

a carbohydrate that cannot be hydrolyzed into smaller molecules that are also carbohydrates
-monosaccharides = carbohydrates
-1C : 2H :1O

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28
Q

What is the structure of a monosaccharide?

A

monosaccharides can alter between linear and circular structures
-galactose
-fructose
-glucose

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29
Q

What is the structure of an acetyl group?

A

CH3 - C (bound to R and =O)

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30
Q

What are 4 classes of biological macromolecule?

A

-Proteins
-Nucleic acids
-Polysaccharides
-Lipids

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31
Q

What are proteins made of?

A

linear series of covalently linked amino acids
-“N” terminal (start)
-“C” terminal (end)
-Kind of like a rattle snake, you always know which one is the head/tail even when its coiled up

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32
Q

How could protein structures vary?
(G-Actin)

A

374 aa
-actin is a structural protein that is present in all eukaryotic cells

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33
Q

How could protein structures vary?
(Insulin)

A

alpha: 21 aa
beta: 30 aa
-insulin is a water-soluble hormone

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34
Q

How could protein structures vary?
(Hemoglobin)

A

alpha: 141 aa
beta: 146 aa
-hemoglobin is a four-protein complex that carries O2 in blood

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35
Q

What kinds of functions can proteins have?

A

-enzymes
-antibodies
-antimicrobial peptides
-hormones
-receptors
-transporters
-storage proteins
-structural proteins
-genetic-regulatory proteins

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36
Q

What are nucleic acids made of?

A

linear series of covalently linked nucleotides (U,A,G,C,T)
-RNA: one linear strand of RNA 3’-5’ carbon
-DNA: two linear strands of DNA, run anti-parallel

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37
Q

mRNA

A

messengerRNA
-carries information from gene to ribosome

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38
Q

rRNA

A

ribosomalRNA
-contributes to ribosome function

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39
Q

tRNA

A

transferRNA
-carries amino acids to ribosome

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40
Q

What is our understanding of the function of DNA?

A

DNA stores information

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41
Q

What are disaccharides composed of?

A

two monosaccharides that are covalently attached to each other
-maltose = 2 glucose
-sucrose = glucose + fructose
-lactose = glucose + galactose

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42
Q

What are polysaccharides composed of?

A

linear or branched series of covalently linked monosaccharides
-chitin
-NAG (N-acyetyl-glucosamine)

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43
Q

What are some functions of polysaccharides?

A

energy storage and structure

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44
Q

What structure are polysaccharides?

A

can be branched or linear

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45
Q

Glycogen is what type of polysaccharide?

A

energy reserve

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46
Q

What types of lipid molecules are there?

A

-fatty acids
-triglycerides
-phospholipids
-steroids

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47
Q

What is the building block of lipids?

A

acetyl groups

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48
Q

What does saturated mean?

A

holding as many H atoms as possible
-free rotation

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49
Q

What does unsaturated mean?

A

at least one double bond
-no free rotation -> causing kink in chain

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50
Q

What makes up a Triglyceride?

A

-1 molecule glycerol
-3 fatty acids (don’t need to be the same)

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51
Q

What are the differences between the triglycerides oil and fat?

A

oil is liquid at room vs. fat is solid at room temperature

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52
Q

How are phospholipids built?

A

-2 fatty acids (hydrophobic)
-glycerol (hydrophilic)
-phosphate group (hydrophilic)
-charged group (hydrophilic) (can vary)

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53
Q

Are phospholipids hydrophobic or hydrophilic?

A

they are amphipathic

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54
Q

What is the basic subunit of all biological membranes?

A

phospholipids

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55
Q

If you throw a phospholipid in water, what will happen?

A

it will arrange itself in the most energy filled way

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56
Q

What is the order of abiogenesis?

A

prebiotic (hadean) -> proto-biological (archaean) -> biological (archaean)

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57
Q

Prebiotic phase

A

4.5 GYA
-self organizing systems
-reductive atmosphere
-dicarboxylic acids delivered to Earth
-carbon fixation occured
-fatty acids formed in ultramafic rocks by serpentrinization
-organic molecules produced in deep sea vents may have been transported to volcanic lan masses

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58
Q

Proto-biological phase

A

4.0 GYA
-RNA world

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59
Q

What was the RNA world?

A

description of a hypothetical prebiotic environment that began 4.0 GYA

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60
Q

What are the 3 assumptions of RNA world?
(in Profs words)

A

1) RNA could be replicated before cells existed
2) base-pairing existed to replicate
3) RNA did it all themselves, meaning they didn’t rely on proteins -> much simpler molecules than ones today
(2018)

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61
Q

What are the 3 assumptions of RNA world?
(definition)

A

1) at some time in the evolution of life, genetic continuity was assured by the replication of RNA
2) Watson-Crick base-pairing was the key to replication
3) genetically encoded proteins were not involved as catalysts
(2018)

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62
Q

Biological phase

A

3.5 GYA
-protocell

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63
Q

What is a proto-cell?

A

cell-like structures that are spatially delimited by a growing membrane boundary, and that contain replicating genetic information
-proves first cells had RNA not DNA

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64
Q

What is the distinction between a proto-cell and a true cell?

A

they differ in that the evolution of genomically encoded advantageous functions has not occurred
-genetic molecules can make copies, but not store information

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65
Q

How do we think first proto-cells arisen?

A

-amino acids bound to self assembled fatty acid membranes, resulting in membrane stabilization and leading to more binding in turn
-high local concentrations of molecular building blocks at the surface of fatty acid membranes may have aided the eventual formation of proteins

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66
Q

Can abiotic process generate amino acids and lipid components?

A

yes, you can get all theses things abiotically

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67
Q

Can abiotic process generate acetyl/acetate moieties?

A

yes, rock in hadean times can make acetic acids -> acetyl groups

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68
Q

Can abiotic process generate RNA?

A

yes, NH3, CO2, H20 (all present in Hadean era) found ribose and U, A, C, and G

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69
Q

What are some characteristics of LUCA?

A

3.8 GYA
-anaerobic
-thermophilic
-fixed CO2
-dependent on H2
-Fe/S clusters
-had ribosomes
-used DNA as genetic material

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70
Q

How are modern cells related to LUCA?

A

-LUCA -> population of cells
-all descendants inherit variations so WE are evidence to reconstruct common ancestor

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71
Q

What was the first life on Earth?

A

the oldest fossil evidence of prokaryotic-like cells on Earth is about 3.4 billion years old

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72
Q

What 5 structures are common to ALL cells?

A

-plasma membrane
-cytoplasm
-chromosomes
-ribosomes
-cytoskeleton

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73
Q

What is the cell cycle?

A

a circular series of events in which one parent cell gives rise to two daughter cells that ideally carry the same genetic information as the parental cell and as each other

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74
Q

What 3 phases in the cell cycle are under interphase?

A

-G1
-S
-G2

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75
Q

What 2 phases in the cell cycle are under cell division?

A

-mitosis
-cytokenesis

76
Q

In what states can chromosomes be found?

A

-condensed: only during cell division (mitotic state)
-various changing levels of decondensation: all other times

77
Q

What is the width of a single chromatid?

A

700 nm fibers

78
Q

LUCA:

A

3.8 GYA
-gave rise to eukaryotic and prokaryotic cells

79
Q

Do prokaryotic cells have chromosomes?

A

-yes!
-nucleoid instead of nucleus
-have ONE circular chromosome

80
Q

What is the structure of a eukaryotic chromosome?

A

-MULTIPLE linear chromosomes
-46 in humans
-20 in corn
none of these are circular

81
Q

What is ploidy?

A

number of sets of chromosomes in a cell
-a cell is haploid if it has only one copy of each kind of chromosome
-a cell is diploid if it has two copies of each kind of chromosome
-sneaker analogy: you grab the left one out of each pair and throw into a bag

82
Q

Unfertilized egg or sperm is what type of ploidy?

A

haploid

83
Q

What ploidy is a zygote?

A

diploid

84
Q

What is the ploidy of prokaryotes?

A

haploid

85
Q

What are the structural components of a chromosome?

A

millions of proteins and ONE molecule of DNA

86
Q

So how many molecules of DNA are in the nucleus of a human hepatocyte?

A

46 molecules!

87
Q

What is chromatin?

A

non-specific collective term for DNA that is complexed with proteins
-non specific term like the word “cake”

88
Q

1/4 functions of chromosomal proteins

A

facilitate efficient packing of DNA into small volumes
-need an efficient way to pack BIG molecule into compact space

89
Q

2/4 functions of chromosomal proteins:

A

facilitate movement of DNA
-need to move DNA in a safe way that protects from damage

90
Q

3/4 functions of chromosomal proteins:

A

protect DNA from physical trauma
-physical trauma includes salt concentration, pH, radiation

91
Q

4/4 functions of chromosomal proteins:

A

control access to genetic information
-physically block access to genes or genome when necessary

92
Q

How big is 1 circular bacterial chromosomal DNA molecule?

A

-length of cell = 500nm
-circular molecule = 4,639,221 bp
-circumference = 502 um (micrometers)
-diameter = 159.8 um (micrometers)

93
Q

How long is 1 eukaryotic chromosomal DNA molecule?

A

-84.645 mm
-longer than USB drive

94
Q

Do all human cells have nuclear DNA?

A

nope!
-think of erythrocytes (RBC) they don’t have nuclei
-leukocytes have nuclei

95
Q

Do mammalian erythrocytes have nuclei?

A

nope

96
Q

Do other vertebrates that aren’t mammalian erythrocytes have nuclei?

A

yep

97
Q

How many erythrocytes in men?

A

25.2 x 10^12 total human cell count

98
Q

How many erythrocytes in women?

A

17.6 x 10^12 total human cell count

99
Q

How many cells have nuclei in men?

A

4.8 x 10^12 have nuclei

100
Q

How many cells have nuclei in women?

A

3.36 x 10^12 have nuclei

101
Q

What is the percentage of erythrocytes in human body? Basically how much of the body’s cells don’t carry chromosomal DNA?

A

84%

102
Q

How much nuclear DNA do we carry?

A

1.93 m (a little under 2m)
~ 9.2 billion km

103
Q

How much nuclear DNA does an adult man carry?

A

62 AU
astronomical unit = distance from center of sun to center of Earth

104
Q

How much nuclear DNA does an adult woman carry?

A

44 AU
astronomical unit = distance from center of sun to center of Earth

105
Q

Can molecules change shape?

A

yes!
-a single covalent bond acts as an axle
-can spin or rotate
-think newman projections!

106
Q

So would you expect nucleic acids to be flexible?

A

yes!
-DNA is really flexible

107
Q

What is the structural relationship between DNA and chromosomes?

A

-DNA can twist into tight coils to fit into the tight space of chromosomes
-think back to functions of chromosomal proteins

108
Q

By mass, how much of chromosome is DNA and proteins?

A

50% DNA
50% proteins

109
Q

How many base pairs in chromosomal DNA molecules?

A

~ 249,956,422 bp

110
Q

What is a nucleosome?

A

DNA wrapped around cluster of 8 proteins (histone octamer - 11nm)
-146 bp ~ wrapped around 1 2/3 times
-orderly decreases volume!

111
Q

What does condensin do?

A

multi-protein complex that takes 11-nm fiber and organize into bigger loops that can be controlled
-pinches or “hair pins” strand

112
Q

What is linker DNA?

A

in between clusters of nucleosomes
~ 54 bp space

113
Q

How are condensin structures arranged?

A

radially like petals on a flower

114
Q

Where are condensin structures concentrated?

A

in the core
-condensin 1 complex is outer ring
-condensin 2 complext is inner ring

115
Q

How are chromosomes arranged during interphase?

A

-more dispersed
-chromosome territory: volume of nuclear space that is occupied by a specific chromosome
-46 territories for 46 chromosomes

116
Q

Ratio and number of condensin 1 vs condensin 2?

A

4:1 ratio of condensin 1 vs 2
~140,000 condensin 1 vs ~35,000 condensin 2

117
Q

Why is it an advantage to have order in structure?

A

-you can move things quickly
-you could move from parent cell to daughter cell quickly without break or damage
-still loose enough that if maybe other proteins still need to get in or get transcribed, they can do so

118
Q

What is biology?

A

scientific study of living systems
-“bios legein” greek for to gather life

119
Q

What is a living system?

A

any system that uses energy for the purposes of growth, maintenance, and reproduction

120
Q

What are living systems made of?

A

cells

121
Q

How have we obtained evidence for the existence of cells?

A

microscope: device that uses lenses to magnify objects for an investigator to see

122
Q

Who codified the mathematical foundation for microscopy?

A

Alhazen
-1021: wrote book of optics “kitab al-mahizir”

123
Q

When was the first microscope built?

A

1609 by Galileo Galilei

124
Q

Who first observed cells?

A

Robert hooke in 1665

125
Q

Were researchers always certain that all living things were made of cells?

A

1839 researchers accepted that all living things were made of cells

126
Q

What is cell theory?

A

all living things are composed of at lease one cell
-all cells arise from pre-existing cells
3 scientists: Schleiden, Schwann, Virchow

127
Q

How many basic types of cell have evolved?

A

-prokaryotic cells: no nucleus
-eukaryotic cells: have nucleus
-LUCA: last universal common ancestor

128
Q

Where can prokaryotes be found?

A

-in the air
-in the water
-on the land
-in the soil
-in the crust
-in and on the bodies of organisms

129
Q

Where are majority of prokaryotic cells live?

A

they live in environments in which eukaryotic cells/organisms could not survive

130
Q

What is the number of total bacterial and archael cells on Earth?

A

1x10^30

131
Q

Are multicellular eukaryotic organisms made just of eukaryotic cells?

A

no, they are made of trillions of human cells, bacterial cells, and archaeal cells

132
Q

How many human cells, bacterial cells, and archaeal cells are in adult female?

A

human cells: 21x10^12
bacterial cells: 44x10^12
archaeal cells: 4.4x10^12

133
Q

How many human cells, bacterial cells, and archaeal cells are in adult male?

A

human cells: 30x10^12
bacterial cells: 38x10^12
archaeal cells: 3.8x10^12

134
Q

What are two unifying concepts of biology?

A

evolution and genetics

135
Q

What are the mechanisms that contribute to evolution of a population?

A

-natural selection
-mutation
-gene flow
-non-random mating
-genetic drift
-incorporation of new genomic material

136
Q

Allele frequency =

A

. # of copies of an allele in pop./
total # of copies of gene in a pop.

137
Q

What does allele frequency readout to:

A

0.0 to 1.0

138
Q

Mouse example:

A

some mouse have white hair and some have black hair, the cat is the natural selection that causes the white hair mouses to be less than black hair mouse

139
Q

What is evolution?

A

evolution is a change over generations in the allele frequency of a population
-evolutus: “an unrolling” latin

140
Q

Can evolution be measured?

A

yes

141
Q

Differences between evolution and speciation

A

evolution is a PROCESS and speciation is a PRODUCT of that process
-the overwhelming process of evolution does not result in the appearance of new species

142
Q

Speciation is what?

A

a PRODUCT of evolution that usually requires hundreds of thousands, or millions of years

143
Q

Are evolution and speciation synonymous?

A

NO

144
Q

What is he discipline of genetics?

A

the scientific study of the structure, function and inheritance of units of heredity information

145
Q

How did the era of modern genetics begin?

A

“pisum sativum” garden pea

146
Q

Why can you assume that planting peas will grow more peas?

A

living systems make more of their own kind

147
Q

What is genetic information?

A

information about characteristics and potentialities of an organism

148
Q

What is heredity?

A

the transmission of genetic information from ancestor to descendant

149
Q

What is genetic material?

A

the physical material that holds genetic information

150
Q

What is parthogenesis?

A

no recognition of biological paternity
i.e: Athena with her son Erikhthonios

151
Q

What is androgenesis?

A

no recognition of biological maternity
i.e: Dionysios is born from Zeus’ thigh

152
Q

What is blending?

A

information from both parents is mixed in offspring

153
Q

What is preformation?

A

ova or sperm possess complete miniature human beings

154
Q

What is the theory of inheritance of acquired characteristics?

A

mechanism by which environment and choices of behavior somehow altered genetic information that was passed to offspring

155
Q

What is pangenesis?

A

mechanism of inheritance by which hypothetical gemmules (which are constructed by cells) carry information from all cells to ova and sperm

156
Q

Who built the foundation for our understanding of inheritance?

A

Gregor Johan Mendel

157
Q

When did Mendelian Age begin?

A

1866

158
Q

What did Mendel not know?

A

he did not know what genetic material is, nor how it separated into gametes
-his work enabled the prediction of statistical outcomes, but could not explain how outcomes were generated

159
Q

When was DNA first isolated?

A

in 1871 by Johannes Miescher

160
Q

When was meiosis first described?

A

in 1875 by Wilhem Hertwig

161
Q

When were chromosomes first identified and mitosis first described?

A

1878 by Walter Flemming

162
Q

When did we know that gametes are haploid?

A

in 1883 by Edouard Beneden

163
Q

When did we know that the majority of genetic material is in the nucleus of an eukaryotic cell?

A

in 1889 by Theodor Boveri

164
Q

When did it become clear that the rules of Mendelian inheritance could be applied to other organisms?

A

in 1900 with by Carl Correns with his study of corn

165
Q

When did we know for certain that chromosomes hold genetic information?

A

in 1915 by TH Morgan, HJ Muller, AH Sturtevant, and CB Bridges

166
Q

When did we know for certain that DNA is the genetic material?

A

in 1952 by Martha Chase and Alfred Hershey with the Chase-Hershey experiment

167
Q

When did we have a model for DNA?

A

in 1953 by Rosalind Franklin, Francis Crick, James Watson, and Maurice Wilkins

168
Q

When was the first artificial recombinant DNA molecule constructed?

A

in 1972 by Paul Berg

169
Q

When was the first natural genomic molecule sequenced?

A

in 1976 by Walter Fiers with bacteriophage MS2 retrovirus

170
Q

When did large-scale DNA sequencing become available?

A

in 1977 by Frederick Sanger

171
Q

When was first eukaryotic genome sequenced?

A

in 1996 by Andre Goffeau with baker’s yease

172
Q

When was the first draft of the human genome (euchromatin only) published?

A

in 2001 by John Venter

173
Q

When was second-gen (next gen) DNA sequencing made available?

A

in 2008 by Shanker Balasubramanian and David Klenerman

174
Q

When was CRISPR/cas9 system constructed?

A

in 2013 by Feng Zhang

175
Q

Why invest money, time, and care sequencing DNA?

A

precision medicine because “one-size-fits-all” medicine doesn’t work for everyone

176
Q

What is the universe made of?

A

energy and matter
-living systems are made of the same matter that makes up the universe
-matter that makes up living systems must follow same rules as living systems

177
Q

How old is the universe?

A

13.77 billion years old
-the only thing that increased was the volume that held all energy that exists

178
Q

How long does it take for gravity to cause a cloud of gas to contract into a star like the sun?

A

40 mil years
-radius reduces by a factor of 700,00

179
Q

When did solar system form?

A

4.567 GYA

180
Q

Are elements evenly distributed throughout the solar system?

A

denser elements were pulled by gravity towards the proto-sun

181
Q

How old is the Earth?

A

4.543 bil years old

182
Q

Why is it important to understand the structure and the history of the Earth?

A

“abiogenesis, the chemical process by which simplest life merged from inanimate beginnings - and biological evolution may actually be one single continuous physio-chemical process..”
-you need to understand the environment

183
Q

When do we think the moon formed and how?

A

4.51 GYA
-proto Earth: initial larger planet
-theia: initial smaller planet

184
Q

When did Earth’s oceans first appear?

A

4.4 GYA

185
Q

Has the Earth always been the same?

A

no

186
Q

What are the geological/biological eons of the Earth?

A

-Hadean eon
-Archaean eon
-Proterozoic eon
-Phanerozoic eon

187
Q

What was Earth like in the Hadean Eon?

A

4.6-4.0 GYA
-sun emitted hundreds of times as much UV radiation as it does today
-frequent meteorite impacts
-atmosphere: CO2, H20, SO2, N2
-occurrence of the impact that produced the moon 4.5 GYA
-some geological evidence for oceans 4.4 to 4.0 GYA
-oldest rock record: 4.363 GYA
-biochemical evidence for life possibly 4.28 GYA

188
Q

What was Earth like in Archaean Eon?

A

4.0-2.5 GYA
-solar output was 75% of todays
-atmosphere: CH4, NH3, H2, CO
-likely appearance of LUCA 3.8 GYA
-oldest indirect evidence of photosynthesis is 3.7 bil yrs old
-oldest fossil evidence: 3.4 bil yrs old of single cell similar to modern prokaryotes

Biol 300 (6 decks)

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