Biology Midterm - Cycle 1-6 Flashcards
1
Q
What is the difference between eukaryotes and prokaryotes?
A
Eukaryotes: linear DNA and membrane bound nucleus
Prokaryotes: circular DNA and no nucleus
2
Q
How do prokaryotes and eukaryotes reproduce?
A
binary fission vs mitosis/meiosis
3
Q
Examples of eukaryotes?
A
Multicellular: animals (metazoans), plants, some fungi
Unicellular: protists, some fungi
4
Q
examples of prokaryotes?
A
Bacteria and Archaea
5
Q
Why are viruses not cellular life?
A
- not made of cells so they cannot create proteins on their own
6
Q
What are obligate parasites?
A
VIRUSES - must infect a host cell to create proteins and replicate
7
Q
What is the structure of a virus?
A
protein shell (some with lipid envelope) with NUCLEIC ACID genome - DNA or RNA; single or double stranded
8
Q
What is HIV?
A
- type of simian IV - retrovirus
- causes AIDS
- disrupts immune system
9
Q
What is an SIV?
A
- zoonotic disease that spills over from closely related nonhuman primates
10
Q
Why are spillover events dangerous?
A
more harmful for new host than the original host species
11
Q
How does a retrovirus impact protein creation?
A
REVERSE TRANSCRIPTION from RNA of virus –> DNA of host
1. DNA replication of HIV genome
2. DNA transcripts to RNA of HIV genes
3. RNA translates HIV genes to proteins
12
Q
What is the normal protein creation process?
A
- DNA replication
- DNA transcripts to RNA
- RNA translates to protein
13
Q
What is AZT?
A
First HIV treatment - almost looks like thymine which blocks the addition of more nucleotides when RNA reverse transcriptase uses AZT instead
14
Q
How does evolution relate to drug resistance?
A
- enzymes (like reverse transcriptase) develop proofreading ability
- many mutations from base sequence error that might make drug resistance or not
- creates genetic variation where susceptible viruses don’t reproduce and drug-resistant virus reproduce - NATURAL SELECTION
15
Q
How does mutations affect vaccine development?
A
- difficult to create a vaccine that is resistant to all possible variants
- multiple drugs can stop viral infection at different points (when it enters the immune cell, when it replicates, when it leaves)
16
Q
What is evolution?
A
change in allele frequencies from one generation to the next
17
Q
What are the principles of NATURAL SELECTION?
A
- mechanism to explain evolution
- variation of traits is heritable
- favoured traits = better survival = higher fitness
- genotypes with favourable traits become more common
variation (randomly generated) + heritability + non-random survival
18
Q
What is artificial selection?
A
selective breeding to ensure certain desirable traits appear more in future generations
19
Q
Why are belief systems contradictory to evolution?
A
Intelligent design: people do no descend from animals
Evolution: species change over time
20
Q
What is a belief system?
A
relies on beliefs not evidence to form religion
21
Q
What is scientific theory?
A
testable hypotheses that try to explain facts and are falsifiable
22
Q
What is a fact?
A
an indisputable observation
23
Q
What is biogeography of evolution?
A
- similar species found in distant places
- common ancestor produced genetic variation over time
24
Q
What is comparative morphology in macroevolution?
A
- similar skeletal structure of dissimilar species
25
What is a vestigial structure?
structures that served a purpose for an ancestor but not for the modern ancestor
26
How does geology prove evolution?
earth is billions of years old = plenty of time for slow geological changes
27
How do fossils prove macroevolution?
evidence of extinct forms of life/life on earth was different
28
What was Darwin's natural selection theory?
descent with modification
29
Jean-Baptiste Lamarck theory
evolution is VARIATIONAL not TRANSFORMATIONAL
30
What are characteristics evolution?
- GRADUAL
- cannot be "wanted" or "intentional"
- every organism doesn't perfectly suit their environment
- all species originated from one entity
31
What is a TRADE OFF?
compromise between traits of competing demands (ex. mating vs camoflauge)
32
How does a zygotes cell cycle compare to a normal cell cycle?
switches between interphase and mitosis quickly for higher turnover rate --> single cell to a human
33
How does a zygotes cell cycle compare to a normal cell cycle?
switches between interphase and mitosis quickly for higher turnover rate --> single cell to a human
34
What is the cell cycle?
INTERPHASE: G1, S, G2
MITOSIS: Prophase, Metaphase, Anaphase, Telophase (cytokinesis)
35
Why do cells divide?
multicellular growth, tissue repair, regeneration
36
What is TURNOVER RATE?
frequency of cell moving through cell cycle
37
Which cells don't divide? What stage of the cell cycle are they in?
neurons --> G0
38
Why do we have so many cells? Why is cell division important?
+ SA:-Volume ratio
- able to satisfy demands faster
- more cell membrane for in/out of cell interactions
- not much loss if one cell dies
39
What are the stages of Interphase?
G1 - cell growth
Synthesis - DNA replication by chromosomal protein duplication
G2 - cell prepares for division
40
What are cell cycle checkpoints?
internal control that prevents a cell from continuing to the next phase before it is ready
41
What is the G1/S checkpoint?
- determines if cell is ready to divide
- stops damaged DNA
- checks if the size is big enough
- checks for mutations that need to be fixed
42
What is the G2/M checkpoint?
- commits a cell to mitosis
- stops DNA if replication error from S
- checks for mutation/DNA damage
43
What is the MITOTIC SPINDLE CHECKPOINT?
- before metaphase
- are chromosomes properly attached to mitotic spindle for proper alignment at metaphase plate
- influences correct separation at anaphase
44
What are POSITIVE REGULATORS?
promotes movement to the next cell cycle step (CDKs)
45
How do CDKs and CYCLINS work?
1. Cyclin binds with CDK and gets activated
2. Phosphate donating protein phosphorylates complex
3. Complex is activated
4. Complex phosphorylates target protein
5. target protein activated
6. Signals cell to move to the next stage
46
What is a CYCLIN?
protein that regulates CDK activity - 4 types for different stages of cell cycle
47
What is a CDK?
cyclin-dependent kinase; protein that is a positive regulator
48
What is phosphorylation?
Donating a phosphate group
49
When are cyclins PRESENT? ACTIVATED? DEACTIVATED?
- when in CDK complex
- always present
- deactivate when cyclins are degraded
50
When are CDKs PRESENT? ACTIVATED? DEACTIVATED?
- present only when needed for complex
- activated in complex
- degraded when unnecessary
51
What are NEGATIVE REGULATORS?
proteins that stop the cell cycle
52
What is APOPTOSIS?
cell self-destruction when the cell cannot fix itself
53
What is p53?
important negative regulator
54
How does p53 work?
1. detects DNA damage
2. Binds to p21 promotor to increase p21 production
3. p21 is a cyclin-CDK inhibitor
4. CDK-cyclin complex cannot phosphorylate target protein (cell cycle arrest)
5. Sends repair enzyme to DNA damage
6. If repaired positive regulation stimulated -- if not repaired apoptosis
55
What happens when p53 is mutated?
- cell doesn't get repaired or have apoptosis (no cell cell arrest)
- leads to cancer
56
What is PLOIDY?
the number of chromosome SETS a species has
57
What is a DIPLOID?
TWO copies of EACH type of chromosome; TWO SETS
58
What is a HAPLOID?
ONE copy of EACH type of chromosome; ONE SET
59
What is a CHROMOSOME?
the nuclear unit of genetic information consisting of a DNA molecule and associated protein
60
What are SISTER CHROMATIDS?
TWO IDENTICAL COPIES of a chromosome held together by a centromere; created during S Phase
61
What are COHESINS?
Proteins that HOLD sister chromatids together; removed during mitosis
62
What is ANEUPLOIDY?
ABNORMAL number of chromosomes AFTER ANAPHASE
63
What is NONDISJUNCTION?
- Both chromosomes connect to the same spindle in anaphase I or anaphase II
- one pole gets BOTH chromosomes the other get NONE
64
MEIOSIS I vs. MEIOSIS II
MEOSIS I:
- reductional
(diploid - 2n --> haploid - n)
(4 chromosomes --> 2 chromosomes)
- interphase
MEIOSIS II:
- equational
(haploid --> haploid)
(2 chromosomes --> 1 sister chromatid from each)
- no interphase
65
Why is there no Interphase before Meiosis II?
- policy must change from meiosis I to meiosis II, so no need for S phase
66
What is RECOMBINATION?
1. During prophase I, homologous pairs stack on top of each other and homologous CHROMATID exchange any number of segments at the chiasma
67
What are LINKED GENES?
genes that are more likely to get inherited together on a chromatid because their loci are located closer together
68
What is INDEPENDENT ASSORTMENT?
chromosomes at the metaphase plate are segregated to daughter cells independently of each other in metaphase I & II
69
What is RANDOM FERTILIZATION?
two parents bring different genomes and unite to make a unique zygote
70
How does the zygote form?
Haploid sperm fertilizes haploid oocyte = diploid zygote
71
What is chromosome segregation?
daughter chromosomes are equally distributed to daughter cells
72
Where does GENETIC VARIABILITY occur in meiosis?
1. recombination
2. independent assortment
3. random fertilization
**all by chance/random
73
MITOSIS vs. MEIOSIS
MITOSIS:
- one division
- two identical daughter cells
- ploidy remains diploid
MEIOSIS:
- two divisions
- four different daughter cells
- ploidy changes from diploid to haploid
74
What us a KARYOTYPE?
number of chromosomes condensed from nucleus and arranged from biggest to smallest
**at metaphase = 2x the number of chromosomes
75
What is Down syndrome?
Trisomy 21 (extra chromosome 21)
76
Examples of NONDISJUNCTION of X/Y chromosomes?
Turner: no X, only Y
Kleinfelder: XXY (difficult to detect
Triple X syndrome
Super male: XYY
**may be severe or normal
77
Why characterize the genome?
- quantify the genome
- comparison between species
- insight into evolution, function, and complexity of an organism
78
What is a GENOME?
all of the DNA sequence in one copy of an organism's chromosome
79
What is the n-value? What is the COEFFICIENT of N?
n-value: number of UNIQUE chromosomes (how many chromosomes in each set) - never changes
coefficient of n: number of SETS of chromosomes (ploidy) - changes after synthesis
80
What is the c-value? What is the COEFFICIENT of C?
c-value: AMOUNT of DNA in quantity of base pairs or mass (pm) in ONE SET
coefficient of c: how many times the entire genome is present in a cell - number of sister chromatids)
81
What is the relationship between n and c?
There is none!
82
What are the main parts of DNA structure?
Nitrogenous bases
Deoxyribose sugar-phosphate backbone
83
What does the backbone of DNA look like?
Anti parallel strands causes polarity. One is 5'-3' with a free hydroxyl group and the other is 3'-5' with a free phosphate.
5-carbon deoxyribose sugar and phosphodiester bond links 3' to 5' carbons
84
What are the hydrogenous bases?
Adenine-Thymine have two hydrogen bonds
Cytosine-Guanine have three hydrogen bonds
85
How does DNA unwind?
Semi conservative
86
What are PURINES? What are PYRIMIDINES?
Purine: double ringed - A&G
Pyrimidines: single ringed - T&C
87
DNA REPLICATION
1. Helicase unwinds hydrogen bonds and topoisomerase relieves tension and prevents supercoiling
2. RNA primer attaches to 3' end
3. DNA polymerase III adds deoxiribonucleoside triphosphate with matching base
4. Sliding clamp encircles DNA binding DNA polymerase to template strand
5. Ligase seals gaps in lagging strand fragments on 3' end
6. DNA polymerase I (exonuclease) replaces RNA primer with DNA
7. Telomerase extends the new 3' end
88
What are the LEADING and LAGGING strands?
Leading: runs 3' to 5'
--> new strand is 5' to 3'
Lagging: runs 5' to 3'
--> new strand is 3' to 5'
--> builds in OKAZAKI FRAGMENTS
89
What is the Hayflick limit?
the number of times a cell divides before p53 protein signals cell senescence
90
What is cell senescence?
cell reacts irreversible cell cycle arrest - G0 - because there are no more telomeres
91
What is a replication bubble?
Two replication forks; many bubbles can start simultaneously to increase efficiency for large eukaryotes
92
What is a TELOMERE?
non-coding sequence of DNA that buffers the end of chromosome so that DNA is not lost
93
What causes cell senescence?
When telomeres become too short after many divisions
94
Where is Telomerase active?
- embryo
- stem cells
- white blood cell
- male germ cell
95
What happens when telomerase is reactivated?
cancerous cells -- unlimited cell division
96
TELOMERASE PROCESS
1. Single stranded region left on template strand after primer removal
2. Telomerase binds to 3' end of single strand and adds more RNA primer
3. Telomerase shifts and synthesizes more new telomerase DNA
4. Telomerase leaves the extended template strand
5. RNA primer added by primase
6. DNA polymerase III matches base pairs
7. 5' end is extended and a short single stranded region remains after primer removal
97
How is SAMENESS inherited?
- complementary base pairs
- DNA synthesis relies on template strand
- exonuclease activity of DNA polymerase III PROOFREADS
98
What are sources of DNA DAMAGE?
EXOGENOUS: outside cell
--> radioactivity, chemicals, UV light
ENDOGENOUS: inside cell
--> mitochondria, DNA replication, unstable electrons
99
DNA DAMAGE vs MUTATION
- DNA damage: single strand change
- Mutation: double strand change
100
What are the steps to repair DNA DAMAGE?
1. Proofreading - immediate
2. Mismatch repair - checkpoint
3. Excision repair
101
How does PROOFREADING work?
DNA polymerase III reverses and uses 3'-5' exonuclease to remove mismatched pair
102
How does MISMATCH REPAIR work?
1. Repair protein scans and cleaves backbone on each end of the mismatch taking several bases
2. Gap is filled by repair DNA polymerase
3. DNA ligase fills gap on 3' end
103
How does BASE EXCISION REPAIR work?
Non bulky DNA damage is recognized and removed by specific protein. DNA polymerase and Ligase replace and seal DNA strand
104
What are THYMINE DIMERS?
adjacent thymine crease bulky distortion of backbone stopping DNA polymerase
--> not a mismatch
--> caused by UV light
--> repaired by excision repair
105
How are REACTIVE OXYGEN SPECIES created?
Ionizing radiation split water molecules apart creating free radicals that travel unpaired
106
Why are ROS dangerous?
highly electronegative and unstable so it will damage DNA to reach stability
--> want to be paired electrons so they pair with proteins (impacting function) RNA or DNA (cut backbone and gets electron from phosphate group)
107
What is the OXYGEN PARADOX?
oxygen necessary for survival but its free radicals come from UV radiation, small, diet, toxins. Free radicals cause damage protein in the mitochondria and detoxification proteins get overwhelmed
108
How are DOUBLE STRAND BREAKS repaired?
Non-Homologous End Joining - cell in panic state, tries to piece DNA together without template and might cause mutation in DNA.
- deletion
- insertion
- inversion
- return to normal sequence
109
What causes DOUBLE STRAND BREAKS
radiation!
110
How much of the DNA sequence is essential?
10% - 2% is coding
- the rest is transposons, unknown, introns, or unnecessary
111
What are types of POINT MUTATION?
Silent, Nonsense, Missense
112
What is a SILENT MUTATION?
- type of point mutation
- change in base makes a different codon that codes for the same amino acid = no difference to protein
113
What is a NONSENSE MUTATION?
- type of point mutation
-change in base makes a stop codon = shorter polypeptide
114
What is a MISSENSE MUTATION?
- type of point mutation
- change in base makes change in amino acid (might be no difference to significant difference)
115
What are SINGLE NUCLEOTIDE POLYMORPHISMS?
- single nucleotide difference in DNA sequence
- common type of genetic variation among people
- used for prediction of health issues
- most have no affect
116
What happens during DNA polymerase SLIPPAGE?
Backwards: insertion of the same sequence = one longer strand
Forwards: skips sequence = one shorter strand
117
What is TAUTOMERIZATION?
base shifts to its tautomer form and changes its preferential base pair, causing DNA DAMAGE or MUTATION in future replications
+ base pairing with preferential base is NOT damage
118
What are TRANSITION mutations? What are TRANSVERSION mutations?
Transition: purine -> purine or pyrimidine -> pyrimidine
Transversion: pyrimidine -> purine or purine -> pyrimidine
119
What are TRANSPOSABLE ELEMENTS?
- genes that can jump from one loci in the genome to another
- usually to introns (non coding regions) but it can jump to coding regions
120
What to TEs cause?
- increased genome size
- effect varies from negligible to disease
121
How have TEs evolved?
active TEs insert into safe havens in the genome, but most TEs are inactive due to mutation
122
What happens when TE lands in a protein-coding gene?
- disease causing mutation
- when excising, it might take a piece of the genome with in and add it to a different section, under a different promoter
123
What was the Blending Theory of Inheritance?
1800s - offspring have characteristics of both parents, so offspring must be a blend of the parent generation
124
What were Mendel's conclusions?
- variation in traits in due to different alleles
- alleles segregate randomly into gametes
- organisms inherit two alleles for each trait
- appearance of heterozygotes is determined by dominant alleles
125
What is the OCA2 gene?
gene coding for P protein a surplus of which produces melanosomes which produce a large amount of melanin to make darker eye colour
126
How are the the alleles in dihybrid crosses assorted?
independently of each other
127
What is the ratio of two heterozygous being dihybridly crossed?
9:3:3:1
128
What is Incomplete dominance?
alleles produce intermediate expression
129
How is Tay Sachs Disease an example of incomplete dominance?
No Tay Sachs = homozygous dominant = HEX A enzyme produced = fatty structures broken down properly
Mild Tay Sachs = heterozygous = some HEX A enzyme produced = some fatty structures broken down
Severe Tay Sachs = homozygous recessive = no HEX A = no fatty structures broken down
130
What is Codominance?
alleles are EQUALLY expressed in heterozygotes
131
How is Blood Type an example of Codominance?
Type AB has equally expressed type A and type B
Type A: Antigen A on RBC and Anti-B antibody in plasma
Type B: Antigen B on RBC and Anti-A antibody in plasma
Type AB: Antigens A+B
Type O: Anti-A and Anti-B antibodies
132
What happens in incompatible blood transfusion?
surface antigens and opposing antibodies cause haemolysis (destruction of RBC)
133
What are glycoproteins? How do they relate to blood type?
- found on RBC membrane made of sugars, the terminal of which determines which antigen and therefore blood type
- terminal sugar is added by glycotransferase which are different for each blood type
(Type O is nonfunctional glycotransferase)
134
How do sex-linked characteristic differ in males and females?
different inheritance patterns -- males have a higher chance because they only need one while females can be a carrier
135
How does autosomal recessive disorders compare with sex-linked disorders?
autosomal-males can be carriers
higher chance of sex-linked disorders
136
What is a polygenic trait?
continuous variation in a population of a phenotype because there are so many genes involved (fur/skin)
137
What is an epistatic gene?
Interferes with gene expression
138
Why was the blending theory not plausible?
--> "factors" are always intermediate
--> doesn't explain evolution of traits (how genes can skip a generation)
139
How did Mendel use the scientific method?
- pea plant experiment
- controlled test crosses (rr with dominant phenotype)
- observable analysis
- high reproduction rate
140
How is epistasis different from Mendelian genetics?
epistasis: the genes expressed can be masked by another gene in a continuum (9:3:4)
Mendelian genetics is dominant masks the recessive for a single gene (9:3:3:1)
141
What is microevolution?
changes in allele frequencies that occur form one generation to the next
142
What is macroevolution?
large scale evolutionary patterns
143
How can you calculate observed phenotype frequency?
sum of species with the phenotype/total population (total phenotype frequency should add to 1)
144
How can you calculate observed genotype frequency?
of species with the genotype/total population
145
How can you calculate observed allele frequency?
total number of one allele type/total number of alleles
if there is 36 BB, then 72 alleles
if there is 100 in population, there is 200 alleles
146
What is the Hardy Weinberg Principle?
no evolutionary agents and random mating
expected frequencies = observed frequencies
allele frequencies DO NOT change over generations, no evolution at that locus
147
How can you calculate expected genotype frequency (no EA and random mating)?
p^2 -- BB
2pq -- BR
q^2 -- RR
where p and q are the allele frequencies
148
What are evolutionary agents?
- selection
- mutation
- immigration/migration
- genetic drift
149
What is fitness?
contribution of offspring (of their alleles) to future generations
--> fitness depends on how many offspring is being produced by others of the same species
150
What is absolute fitness?
of offspring that survive to reproductive age
151
What is relative fitness?
compare absolute fitness to the maximum fitness in the species:
absolute fitness/absolute fitness of the most successful genotype
152
What is genotypic fixation?
100% frequency of a genotype
153
Selection against the dominant phenotype?
BB = BR < RR
--> frequency of B allele, BB, and BR genotypes would reach 0
--> frequency of R allele and RR phenotype would reach 100 (fixation)
154
Selection against recessive phenotype?
BB = BR > RR
--> BR doesn't allow for fixation (R allele is still present)
--> dominant allele reaches a high value - not 100%
--> frequency of recessive would reach >0%
155
Is it possible to completely remove recessive phenotypes?
No -- selection acts of phenotypes, so recessive genotype can hide in heterozygous genes
156
What is a distribution of phenotypes?
range of phenotypes from many alleles/loci (ex. height)
157
Selection in a distribution of phenotypes?
--> reduces genetic diversity
--> result in DIRECTIONAL selection, shifting towards one end of the distribution
158
What is heterozygous advantage?
SS < NS > NN
--> codominance and incomplete dominance only
159
What is stabilizing selection?
result of heterozygous advantage
--> mean phenotype favoured
160
What is heterozygous disadvantage?
WW > WS < SS
--> codominance and incomplete dominance only
161
Why does starting allele frequency matter in heterozygous disadvantage?
the one that is more common to start will reach fixation
rare allele will decrease and might disappear because the rare alleles will most likely be found in heterozygotes
162
What is the affect of heterozygous advantage on diversity?
increases genetic variation --> common alleles become less common, rare alleles become more common, and extreme alleles possible
--> no fixation
163
What is the affect of heterozygous disadvantage on diversity?
decreases genetic variation --> more common allele becomes more common
164
What is disruptive selection? What does it cause?
extreme phenotypes favoured so the two extremes can evolve to two different populations
165
What is gene flow?
any movement of individuals or genetic material from one population to another (immigration and emigration)
166
What is genetic drift?
by chance not all alleles of parents is passed to offspring, occurring as long as the population is not infinitely large
--> rare alleles more likely to be lost
--> greater impact on smaller populations
--> reduces genetic variation
167
What is the bottleneck effect?
change in allele frequency due to random sampling of a very small number of individuals due to large reduction in population
--> reduction of diversity
168
What is the founder effect?
population reduction is due to a small number of individuals starting a new population
--> loss of alleles by chance
169
What is assortative mating?
mating between similar phenotypes
--> increases homozygosity
--> if this is across the genome this is INBREEDING
170
What are the consequences of INBREEDING?
--> exposes harmful recessive alleles --> inbreeding depression --> health issues
171
What is non random mating?
individuals select mate based on phenotype but this doesn't change allele frequencies, so it is not an evolutionary agent
172
What is disassortative mating?
mating with dissimilar phenotypes which increases heterozygosity (inbreeding avoidance aka outcrossing)
173
What is binary fission?
asexual reproduction in prokaryotic cell
174
What are the steps of binary fission?
B period = bacterial cell birth and growth
C period = circular chromosome replication begins in the middle of the cell and the replicated oris move to opposite poles
D period = replication complete; plasma membrane grows inward and cell wall synthesized
