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)
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)
3
Q
What is the internal structure of the earth?
A
inner core
outer core
mantle
asthenosphere
upper mantle
crust
3
Q
Inner Core
A
Solid
5100-6378 km
4
Q
Outer Core
A
Liquid
2890-5100 km
5
Q
Mantle
A
Liquid
700-2890 km
6
Q
Asthenosphere
A
Soft solid
100-700 km
7
Q
Upper mantle
A
Solid
35-100 km
8
Q
Crust
A
Solid
0-35 km
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
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
11
Q
Atmospheric Synthesis
A
CO2, CO, N2, H2S, H20, CH4
-Gas phase reactions: hv, ED, starting gases
12
Q
Extraterrestrial Delivery
A
-Liquid/Ice phase reactions: conditions on parent bodies/space
13
Q
Aqueous Phase Chemistry
A
-temperature (0-100C?), pH, reagents, concentration, etc
14
Q
Hydrothermal/Geochemical Synthesis
A
CO2, NH3, H2S, H20
-Temperature (70-350C?), pH, reagents, concentration, time, etc
15
Q
Interfacial Chemistry
A
-Drying, wetting, mineral interactions, UV
16
Q
How did cells first arise?
A
-cannot say for certain
-many researchers are still working on finding the answer
17
Q
What minimal physical attributes would the first living structures have had?
A
-compartmentalization
-self-replication
-metabolism
18
Q
Compartmentalization
A
Purpose:
-sequestration, control, and transport of molecules
Modern example:
-membranes
19
Q
Self-Replication
A
Purpose:
-reproduction of system and genetic material
Modern example:
-cell division
-DNA replication
20
Q
Metabolism
A
Purpose:
-extraction of energy
-construction of new systems and genetic material
Modern Example:
-enzymes
21
Q
What are 4 classes of small biological molecule?
A
-Amino acids
-Nucleotides
-Monosaccharides
-Acetyl group
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
23
Q
How many kinds of amino acid are found in living systems?
A
20
4 groups:
-Non polar
-Positive charge
-Polar
-Negative charge
24
What is the structure of a nucleotide?
-5 kinds of nitrogenous base
-2 kinds of sugar
-every nucleotide has the same phosphate group
25
Which 2 sugars are part of nucleotides?
-Ribose (RNA nucleotides only)
-Deoxyribose (DNA nucleotides only)
26
Which 5 nitrogenous bases are part of nucleotides?
U-uracil (RNA)
G-guanine
A-adenine
C-cytosine
T-thymine (DNA)
27
What are monosaccharides?
a carbohydrate that cannot be hydrolyzed into smaller molecules that are also carbohydrates
-monosaccharides = carbohydrates
-1C : 2H :1O
28
What is the structure of a monosaccharide?
monosaccharides can alter between linear and circular structures
-galactose
-fructose
-glucose
29
What is the structure of an acetyl group?
CH3 - C (bound to R and =O)
30
What are 4 classes of biological macromolecule?
-Proteins
-Nucleic acids
-Polysaccharides
-Lipids
31
What are proteins made of?
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
32
How could protein structures vary?
(G-Actin)
374 aa
-actin is a structural protein that is present in all eukaryotic cells
33
How could protein structures vary?
(Insulin)
alpha: 21 aa
beta: 30 aa
-insulin is a water-soluble hormone
34
How could protein structures vary?
(Hemoglobin)
alpha: 141 aa
beta: 146 aa
-hemoglobin is a four-protein complex that carries O2 in blood
35
What kinds of functions can proteins have?
-enzymes
-antibodies
-antimicrobial peptides
-hormones
-receptors
-transporters
-storage proteins
-structural proteins
-genetic-regulatory proteins
36
What are nucleic acids made of?
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
37
mRNA
messengerRNA
-carries information from gene to ribosome
38
rRNA
ribosomalRNA
-contributes to ribosome function
39
tRNA
transferRNA
-carries amino acids to ribosome
40
What is our understanding of the function of DNA?
DNA stores information
41
What are disaccharides composed of?
two monosaccharides that are covalently attached to each other
-maltose = 2 glucose
-sucrose = glucose + fructose
-lactose = glucose + galactose
42
What are polysaccharides composed of?
linear or branched series of covalently linked monosaccharides
-chitin
-NAG (N-acyetyl-glucosamine)
43
What are some functions of polysaccharides?
energy storage and structure
44
What structure are polysaccharides?
can be branched or linear
45
Glycogen is what type of polysaccharide?
energy reserve
46
What types of lipid molecules are there?
-fatty acids
-triglycerides
-phospholipids
-steroids
47
What is the building block of lipids?
acetyl groups
48
What does saturated mean?
holding as many H atoms as possible
-free rotation
49
What does unsaturated mean?
at least one double bond
-no free rotation -> causing kink in chain
50
What makes up a Triglyceride?
-1 molecule glycerol
-3 fatty acids (don't need to be the same)
51
What are the differences between the triglycerides oil and fat?
oil is liquid at room vs. fat is solid at room temperature
52
How are phospholipids built?
-2 fatty acids (hydrophobic)
-glycerol (hydrophilic)
-phosphate group (hydrophilic)
-charged group (hydrophilic) (can vary)
53
Are phospholipids hydrophobic or hydrophilic?
they are amphipathic
54
What is the basic subunit of all biological membranes?
phospholipids
55
If you throw a phospholipid in water, what will happen?
it will arrange itself in the most energy filled way
56
What is the order of abiogenesis?
prebiotic (hadean) -> proto-biological (archaean) -> biological (archaean)
57
Prebiotic phase
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
58
Proto-biological phase
4.0 GYA
-RNA world
59
What was the RNA world?
description of a hypothetical prebiotic environment that began 4.0 GYA
60
What are the 3 assumptions of RNA world?
(in Profs words)
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)
61
What are the 3 assumptions of RNA world?
(definition)
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)
62
Biological phase
3.5 GYA
-protocell
63
What is a proto-cell?
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
64
What is the distinction between a proto-cell and a true cell?
they differ in that the evolution of genomically encoded advantageous functions has not occurred
-genetic molecules can make copies, but not store information
65
How do we think first proto-cells arisen?
-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
66
Can abiotic process generate amino acids and lipid components?
yes, you can get all theses things abiotically
67
Can abiotic process generate acetyl/acetate moieties?
yes, rock in hadean times can make acetic acids -> acetyl groups
68
Can abiotic process generate RNA?
yes, NH3, CO2, H20 (all present in Hadean era) found ribose and U, A, C, and G
69
What are some characteristics of LUCA?
3.8 GYA
-anaerobic
-thermophilic
-fixed CO2
-dependent on H2
-Fe/S clusters
-had ribosomes
-used DNA as genetic material
70
How are modern cells related to LUCA?
-LUCA -> population of cells
-all descendants inherit variations so WE are evidence to reconstruct common ancestor
71
What was the first life on Earth?
the oldest fossil evidence of prokaryotic-like cells on Earth is about 3.4 billion years old
72
What 5 structures are common to ALL cells?
-plasma membrane
-cytoplasm
-chromosomes
-ribosomes
-cytoskeleton
73
What is the cell cycle?
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
74
What 3 phases in the cell cycle are under interphase?
-G1
-S
-G2
75
What 2 phases in the cell cycle are under cell division?
-mitosis
-cytokenesis
76
In what states can chromosomes be found?
-condensed: only during cell division (mitotic state)
-various changing levels of decondensation: all other times
77
What is the width of a single chromatid?
700 nm fibers
78
LUCA:
3.8 GYA
-gave rise to eukaryotic and prokaryotic cells
79
Do prokaryotic cells have chromosomes?
-yes!
-nucleoid instead of nucleus
-have ONE circular chromosome
80
What is the structure of a eukaryotic chromosome?
-MULTIPLE linear chromosomes
-46 in humans
-20 in corn
none of these are circular
81
What is ploidy?
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
Unfertilized egg or sperm is what type of ploidy?
haploid
83
What ploidy is a zygote?
diploid
84
What is the ploidy of prokaryotes?
haploid
85
What are the structural components of a chromosome?
millions of proteins and ONE molecule of DNA
86
So how many molecules of DNA are in the nucleus of a human hepatocyte?
46 molecules!
87
What is chromatin?
non-specific collective term for DNA that is complexed with proteins
-non specific term like the word "cake"
88
1/4 functions of chromosomal proteins
facilitate efficient packing of DNA into small volumes
-need an efficient way to pack BIG molecule into compact space
89
2/4 functions of chromosomal proteins:
facilitate movement of DNA
-need to move DNA in a safe way that protects from damage
90
3/4 functions of chromosomal proteins:
protect DNA from physical trauma
-physical trauma includes salt concentration, pH, radiation
91
4/4 functions of chromosomal proteins:
control access to genetic information
-physically block access to genes or genome when necessary
92
How big is 1 circular bacterial chromosomal DNA molecule?
-length of cell = 500nm
-circular molecule = 4,639,221 bp
-circumference = 502 um (micrometers)
-diameter = 159.8 um (micrometers)
93
How long is 1 eukaryotic chromosomal DNA molecule?
-84.645 mm
-longer than USB drive
94
Do all human cells have nuclear DNA?
nope!
-think of erythrocytes (RBC) they don't have nuclei
-leukocytes have nuclei
95
Do mammalian erythrocytes have nuclei?
nope
96
Do other vertebrates that aren't mammalian erythrocytes have nuclei?
yep
97
How many erythrocytes in men?
25.2 x 10^12 total human cell count
98
How many erythrocytes in women?
17.6 x 10^12 total human cell count
99
How many cells have nuclei in men?
4.8 x 10^12 have nuclei
100
How many cells have nuclei in women?
3.36 x 10^12 have nuclei
101
What is the percentage of erythrocytes in human body? Basically how much of the body's cells don't carry chromosomal DNA?
84%
102
How much nuclear DNA do we carry?
1.93 m (a little under 2m)
~ 9.2 billion km
103
How much nuclear DNA does an adult man carry?
62 AU
astronomical unit = distance from center of sun to center of Earth
104
How much nuclear DNA does an adult woman carry?
44 AU
astronomical unit = distance from center of sun to center of Earth
105
Can molecules change shape?
yes!
-a single covalent bond acts as an axle
-can spin or rotate
-think newman projections!
106
So would you expect nucleic acids to be flexible?
yes!
-DNA is really flexible
107
What is the structural relationship between DNA and chromosomes?
-DNA can twist into tight coils to fit into the tight space of chromosomes
-think back to functions of chromosomal proteins
108
By mass, how much of chromosome is DNA and proteins?
50% DNA
50% proteins
109
How many base pairs in chromosomal DNA molecules?
~ 249,956,422 bp
110
What is a nucleosome?
DNA wrapped around cluster of 8 proteins (histone octamer - 11nm)
-146 bp ~ wrapped around 1 2/3 times
-orderly decreases volume!
111
What does condensin do?
multi-protein complex that takes 11-nm fiber and organize into bigger loops that can be controlled
-pinches or "hair pins" strand
112
What is linker DNA?
in between clusters of nucleosomes
~ 54 bp space
113
How are condensin structures arranged?
radially like petals on a flower
114
Where are condensin structures concentrated?
in the core
-condensin 1 complex is outer ring
-condensin 2 complext is inner ring
115
How are chromosomes arranged during interphase?
-more dispersed
-chromosome territory: volume of nuclear space that is occupied by a specific chromosome
-46 territories for 46 chromosomes
116
Ratio and number of condensin 1 vs condensin 2?
4:1 ratio of condensin 1 vs 2
~140,000 condensin 1 vs ~35,000 condensin 2
117
Why is it an advantage to have order in structure?
-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
What is biology?
scientific study of living systems
-"bios legein" greek for to gather life
119
What is a living system?
any system that uses energy for the purposes of growth, maintenance, and reproduction
120
What are living systems made of?
cells
121
How have we obtained evidence for the existence of cells?
microscope: device that uses lenses to magnify objects for an investigator to see
122
Who codified the mathematical foundation for microscopy?
Alhazen
-1021: wrote book of optics "kitab al-mahizir"
123
When was the first microscope built?
1609 by Galileo Galilei
124
Who first observed cells?
Robert hooke in 1665
125
Were researchers always certain that all living things were made of cells?
1839 researchers accepted that all living things were made of cells
126
What is cell theory?
all living things are composed of at lease one cell
-all cells arise from pre-existing cells
3 scientists: Schleiden, Schwann, Virchow
127
How many basic types of cell have evolved?
-prokaryotic cells: no nucleus
-eukaryotic cells: have nucleus
-LUCA: last universal common ancestor
128
Where can prokaryotes be found?
-in the air
-in the water
-on the land
-in the soil
-in the crust
-in and on the bodies of organisms
129
Where are majority of prokaryotic cells live?
they live in environments in which eukaryotic cells/organisms could not survive
130
What is the number of total bacterial and archael cells on Earth?
1x10^30
131
Are multicellular eukaryotic organisms made just of eukaryotic cells?
no, they are made of trillions of human cells, bacterial cells, and archaeal cells
132
How many human cells, bacterial cells, and archaeal cells are in adult female?
human cells: 21x10^12
bacterial cells: 44x10^12
archaeal cells: 4.4x10^12
133
How many human cells, bacterial cells, and archaeal cells are in adult male?
human cells: 30x10^12
bacterial cells: 38x10^12
archaeal cells: 3.8x10^12
134
What are two unifying concepts of biology?
evolution and genetics
135
What are the mechanisms that contribute to evolution of a population?
-natural selection
-mutation
-gene flow
-non-random mating
-genetic drift
-incorporation of new genomic material
136
Allele frequency =
. # of copies of an allele in pop./
total # of copies of gene in a pop.
137
What does allele frequency readout to:
0.0 to 1.0
138
Mouse example:
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
What is evolution?
evolution is a change over generations in the allele frequency of a population
-evolutus: "an unrolling" latin
140
Can evolution be measured?
yes
141
Differences between evolution and speciation
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
Speciation is what?
a PRODUCT of evolution that usually requires hundreds of thousands, or millions of years
143
Are evolution and speciation synonymous?
NO
144
What is he discipline of genetics?
the scientific study of the structure, function and inheritance of units of heredity information
145
How did the era of modern genetics begin?
"pisum sativum" garden pea
146
Why can you assume that planting peas will grow more peas?
living systems make more of their own kind
147
What is genetic information?
information about characteristics and potentialities of an organism
148
What is heredity?
the transmission of genetic information from ancestor to descendant
149
What is genetic material?
the physical material that holds genetic information
150
What is parthogenesis?
no recognition of biological paternity
i.e: Athena with her son Erikhthonios
151
What is androgenesis?
no recognition of biological maternity
i.e: Dionysios is born from Zeus' thigh
152
What is blending?
information from both parents is mixed in offspring
153
What is preformation?
ova or sperm possess complete miniature human beings
154
What is the theory of inheritance of acquired characteristics?
mechanism by which environment and choices of behavior somehow altered genetic information that was passed to offspring
155
What is pangenesis?
mechanism of inheritance by which hypothetical gemmules (which are constructed by cells) carry information from all cells to ova and sperm
156
Who built the foundation for our understanding of inheritance?
Gregor Johan Mendel
157
When did Mendelian Age begin?
1866
158
What did Mendel not know?
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
When was DNA first isolated?
in 1871 by Johannes Miescher
160
When was meiosis first described?
in 1875 by Wilhem Hertwig
161
When were chromosomes first identified and mitosis first described?
1878 by Walter Flemming
162
When did we know that gametes are haploid?
in 1883 by Edouard Beneden
163
When did we know that the majority of genetic material is in the nucleus of an eukaryotic cell?
in 1889 by Theodor Boveri
164
When did it become clear that the rules of Mendelian inheritance could be applied to other organisms?
in 1900 with by Carl Correns with his study of corn
165
When did we know for certain that chromosomes hold genetic information?
in 1915 by TH Morgan, HJ Muller, AH Sturtevant, and CB Bridges
166
When did we know for certain that DNA is the genetic material?
in 1952 by Martha Chase and Alfred Hershey with the Chase-Hershey experiment
167
When did we have a model for DNA?
in 1953 by Rosalind Franklin, Francis Crick, James Watson, and Maurice Wilkins
168
When was the first artificial recombinant DNA molecule constructed?
in 1972 by Paul Berg
169
When was the first natural genomic molecule sequenced?
in 1976 by Walter Fiers with bacteriophage MS2 retrovirus
170
When did large-scale DNA sequencing become available?
in 1977 by Frederick Sanger
171
When was first eukaryotic genome sequenced?
in 1996 by Andre Goffeau with baker's yease
172
When was the first draft of the human genome (euchromatin only) published?
in 2001 by John Venter
173
When was second-gen (next gen) DNA sequencing made available?
in 2008 by Shanker Balasubramanian and David Klenerman
174
When was CRISPR/cas9 system constructed?
in 2013 by Feng Zhang
175
Why invest money, time, and care sequencing DNA?
precision medicine because "one-size-fits-all" medicine doesn't work for everyone
176
What is the universe made of?
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
How old is the universe?
13.77 billion years old
-the only thing that increased was the volume that held all energy that exists
178
How long does it take for gravity to cause a cloud of gas to contract into a star like the sun?
40 mil years
-radius reduces by a factor of 700,00
179
When did solar system form?
4.567 GYA
180
Are elements evenly distributed throughout the solar system?
denser elements were pulled by gravity towards the proto-sun
181
How old is the Earth?
4.543 bil years old
182
Why is it important to understand the structure and the history of the Earth?
"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
When do we think the moon formed and how?
4.51 GYA
-proto Earth: initial larger planet
-theia: initial smaller planet
184
When did Earth's oceans first appear?
4.4 GYA
185
Has the Earth always been the same?
no
186
What are the geological/biological eons of the Earth?
-Hadean eon
-Archaean eon
-Proterozoic eon
-Phanerozoic eon
187
What was Earth like in the Hadean Eon?
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
What was Earth like in Archaean Eon?
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
