1. List the basic steps in how a genotype determines a phenotype.
genotypea different
alleles are composed of different BP
Sequences all of which may for may not)
proteins
functionally different
code for different
,
making
ribosome
Gent
DNA
phenotypes
RNA
-
a
protein
Explain the difference between phenotypes determined by genetics, and phenotypes that are not
genetically based. List ways that the environment can influence phenotypes.
determined by genetics :
protein function
-
not determined
-
-
by genetics :
socioeconomics
personal desires
Define the following terms: gene, allele, mutant allele, polymorphism, wild-type
Gene w a
protein
segment of DNA that codes for
allele - a variation of a
gene
that
mutant alleles an unatural allele
a
was
specific
changed
Polymorphismadversion of an allele present in 21% of
the population
Wis most commonly
occuring version not necessarily
,
dominant
Explain what we mean by “forward genetics” and why one would want to perform such an
experiment.
Forward
genetics :
-examining phenotypes to understand their relationship
genotypes (ex : GWAS)
more ethical to do in humans as it doesn't necessarily
-
require mutations
,
,
also
helps
you
gauge the roles of loci
to
Use pedigree information to determine whether a trait is likely genetic. Infer whether the trait is
genetic, recessive, or dominant, and what the likely genotypes of individuals shown are.
Dominant every gen
Recessives
skips gens
Know how mutations can arise from biological or chemical processes. Again, you do not need to
know actual mechanisms! But we do want you to know the implications for genetics.
mutations
-
come
from :
intercolating agents
I
-
chemicals
-
-
V
polymerase mistakes
Calculate the likelihood that an individual on a pedigree will have a given genotype or
phenotype.
-for offspring , always reference most recent
ancestor if possible , also use
-
context
always
assume unrelated people are unaffected
List genetic similarities and differences between mitosis and meiosis.
mitosis - exact copies of daughter cells duplicates
,
genome and divides only 1x
mitosis :
2n
2n
I'll
-
Sister
-
chromatics
-
I1
divide
2n
Il 02 identical daughter
isomatic
cells
meoisis !
-
-
-
germline
occurs in
m1
and
mil
daughter cells are not genetically identical
un(x)
IIII
In
-
I
In
Il
/
-
nnnn
I
I
Igermline
List important genetic differences between meiosis I and meiosis II.
meiosis
-
-
1:
homologous chromosome pairs divide
leaves 2 copies of
maternal/ paternal in each cell
-
recombination
M2 :
-
-
sister chromatids divide
should leave I
copy of maternal , paternal ,
or
recombinant in each cell
Given an individual’s genotype, determine the genotypes of gametes that individual can make
-
-
-
linkage dictates crossing
watch out for
independent
over
map distance
assortment
lead to genetic
and
-
diversity
crossing over
Explain the consequences of non-disjunction during meiosis.
M1 :
I
11
I
Y
M2 :
end up
with a paternal
and maternal
Sister chromatic
in each cell and
2
empty
cells
IIII
Il
Il
7
end duplicate
upe
Sister chromatids
in one cell and
1 empty cell
Match diagrams or cell images to mitosis, meiosis I, meiosis II.
mitosis
IIII
I
11
M2 :
M1 :
Il
11
Il
I
I
11
Suggest a pattern of inheritance (autosomal dominant, autosomal recessive, X-linked dominant,
X-linked recessive, Y-linked, mitochondrial) that matches a pedigree or a description of
phenotypes after crosses.
-
Choose the BEST ANSWER .
Given phenotypic ratios, map distances between genes. Or, given map distances, calculate the
probability of obtaining a given genotype.
-
# of recombinant
+ o+al
-
1y
each
%
(100) = map distance
each
%
=
1 - (mb)
2
=
mix
Z
Diagram or recognize how chromosomes (including sex chromosomes) and alleles are
segregated at the end of meiosis I, meiosis II, and mitosis.
-
sex
chromosomes do
pair up as homlogous
during meiosis due topseudoautosomal regions
Describe a test cross and explain when/how it would be useful in a genetic study.
Test
Cross :
Dominant
phenotype
x
double recessive
A-B-Xaabb
-
determines the
genotype of the
dominant
Po
Calculate genetic distances given information about parental phenotypes and test cross offspring.
-
-
check for
recombinance 2
alleles& a time
if 3 alleles are involved look
for double
recombinants. Check w/ parentals allele
that is never parental is in the
,
,
middle
Predict offspring ratios given parental phenotypes, genotypes, and map distances between sites.
Describe and interpret the results of mapping crosses
mapping crosses in
crossing
C
Elegans
mutants with
.
:
mapping strains
on each chromosome until
you don't get any MAB's .
the
-keep
mutation is on this
chromosome.
-
look for
"a-only"
them Whichever ones
.
the
mutants
produce MA/MB
.
Self-cross
are further from
locus.
M
eX !
"b-only"
and
A-only :
a
- makes m
3
a + m
B- only :
F
bm
so
> makes no m
-
Explain complementation
-complementation occurs when2 genes
that confer similar phenotypes when
mutated are crossed , and WT is restored
-
these
genes complement
each
other
m Interpret or suggest experiments to investigate complementation between alleles.
you have two mutants /similar
phenotypes and unknown mutations , cross them
- if
IF :
Mixmz
=
NT ,
the
mutations complement and are not on
same
gene
m , xmz = m , mutations do not complement and
are on the same gene
Describe how genotypes can be determined using PCR and gel electrophoresis.
-
-
Place
primers
You
must
difference
-
on
either side of the alleles.
know that
(2100 +
there
will
be a
s
BP) between A + B
amplify + run get
Heterozygote
(big + small
=
-homozygote
call
small
-
Describe the typical eukaryotic protein-encoding gene, list important elements of this
type of gene.
ORF
II
"enhancer
-
-
-
↳ promoter
looping
TF
-
binding site for polymerase
binding
-TF
binding
activator protein
binding
ORF :
-read by RNA
-
-
polymerase
START o STOP
-
exons
leave nucleus
expressed
as
proteins
Describe the effects cytosine methylation, histone modification, X-inactivation, and
imprinting have on gene expression.
cytosine methylation :
physically prevents proteins from binding to
promoter/enhancer/ORE
reduces/stops transcriptions expression
Histone modification:
charged tail domains
can
tighten/loosen nucleosome ,
Dua expression
allowing for more/less
-
-
-
-
E
-
-
-
-
-
Imprinting - sex-specific methylation occuring during gametoPredict the genotypes and phenotypes over multiple generations of an imprinted gene. genesis
X-inactivation :
happens in XX (or more
methylation
mix of
occurs
for XXX +) individuals
and condensing into heterochromatin
randomly during embryonic development
maintained throughout mitoses
reset each
maternal :
generation
gene from
mom silenced
3 regardless
of
genotype
paternal : gene from dad silenced
Explain in your own words the molecular basis for epistatic interactions between genes.
Epistasis when 2 genes interact within a bathway
-
I
complementary : (9 : 7)
A-B- Phenotype
dominant - (12 : 3 : 1)
>
-
A - Bu
phenotype
recessive : 19 : 3 : 4)
1x
a
B- C
-
find
POXPO = WT (F1)
gene
interactions
F(xF)-F2
Dy
4
Observe
crosses
doing dinybrid
and
recording phenotype
ratios of
offspring
Define synonymous and non-synonymous mutations
Synonymous codon
nonsynonymous diff
selection type :
amino
creates same
AA
w=
acid
S (100)
S
1
Purifying (W(I)
-
Directional (w)])
A
Compare and contrast different animal models and their use as in genetics experiments
(Drosophila, elegans, yeast, mice, other animals)
yeast :
good
-
for complementation
can be
-
haploid + reproduce
and reproduce
-not
C
.
-
sexually (a + a)
lots of
diploid
mice :
elegans :
-
easily visible phenotypes
Flieswew
1x0/ meiosis
-
or
observed phenotypes
easily
simple
-
a sexually
offspringtself fertilization so no need for
Use the Hardy-Weinberg equation to predict genotype frequencies in a population at F(xF)
equilibrium
D q= 1
+
p2 + 2pq + q2 = 1
J
conditions that
-
-
-
Large Pop
no new
mutations
random
mating
no
-
-
migration
no natural
[
Hwe means that allele
frequencies do not change from gen to gen
Being in
support HWE !
in Ov out
selection
&
impossible ,
is
good
but equation
for
predicting
behavior of LG populations
Note the limits of the Hardy-Weinberg equilibrium and discuss how a real population
may fail to satisfy some or all assumptions
like
always
Predict how the likelihood of allele fixation in a population changes with selection for
(directional) or against (purifying) a given allele
Directional :
-
if allele
is
being selected against
Alfixation) goes down
-
VV
if
is
allele
being selected for
Purifying :
-
against new mutations
Compare and contrast directional, stabilizing, and disruptive selection; Explain how they
affect allele frequencies over time
disruptive:
Directional Stabilizing :
:
A -2 M
one allele is
favored
-
-
Frequency shifts
-
least extreme
-
phenotype is favored
whatever alleles confer
from twBovertime
Explain the ideas of introgression and admixtures this rise
extremes are
favored
-
-
can
2
for
lead to
populations
Introgression : 2 separate species making viable
Offspring (F1s)
Admixture : 2 PO's from the same species
from different populations
reproduce
but
Describe adaptive radiation
when
a
species encounters
With many open niches and
a new
environment
explodes
Illumina :
sanger :
reads
-
-
reads ~100
1000 BP
short reads, accurate
-cheap for short
-
-
of DNA
amt
-
requires lots(ish)
OF
-
:
300 BP
LOTs of reads
-cheap if
-very
sequencing
a LOT
Of DNA
accurate
-millions of reads/run
DNA
Compare and contrast DNA sequencing techniques in terms of read length, accuracy,
and efficiency.
Nanopore
PacBic
reads
-
-
-MB's
-
accuracy is ok but
-
samples
are
bad
not
resequenced
so
cheap
Portable
-long reads
-
inaccurate
-gold standard for long reads
-
can detect structural
modifications
Evaluate different techniques in terms of advantages and disadvantages for applications
in genome sequencing. Techniques: Sanger, Oxford Nanopore, Illumina, PacBio, SNP
genotyping, PCR.
PCR :
-
length of your sequence
can only tell you
,
difference
must be30 BP
SNP :
-
only
uses
known
SNPs , no new SNPs
Define the following in terms of DNA sequencing: read, run, contig, length.
Read Run -
a
one
group
of
BP continuously
sequenced
full run
Contigo assembled from overlapping reads
length -# of BPs
Discuss the challenges of genome assembly and describe ways that genomes are
assembled from sequencing reads.
Challenges :
heterozygosity in haplotypes, makes correct aligment
difficult (Double-Stranded ID)
-
How :
short reads
-
-repeating regions
-
-
SNPS
-
Long
reads
W/PacBio
short reads
willumina
assemble illumina
reads
into
DaCBiC
-
contigs using
for reference
Predict the relative length of contiguous tract of sequence over multiple generations
The more
shared
distantly
related , the shorter the
sequence tracts
will be
.
Describe the DNA sequence diversity of humans compared to that of other animals
Humans are much less diverse than other species , mostly
homozygous wISNPs 1/1000 BD
-
likely due to a bottleneck when a population emigrated
out of Africa
years ago
Suggest strategies to determine whether an observed SNV is a result of a sequencing
error, individual (private) variation, or a particular lineage
error:
-
present in only
·
one
read
real:
-
present in appropriate
proportions of reads
(212 for hetero ,1 for homo)
Reference with
lineages
-resequence
families/
Use information from the Integrative Genomics Viewer (igv.org) and the Geography of
Genetic Variants Browser (popgen.uchicago.edu/ggv) and similar data displays to
understand allelic frequencies in populations
Describe evidence that modern humans contain sequences from ancient lineages
including Neanderthals and Denisovans
-
have
we
likely
heanderthat and Denisovan
all 3
SNPs ,
introgressed when early
species
modern humans left Africa
-non-African humans
-
Southeast
SNPS
have these
SNPs
Asian humans have more
Denisovan
Describe basic steps in identifying genes in human populations that are associated with
traits of interest
GWAS :
choose a trait of
-
-
choose
populations and
trait of
interest.
-
map their SNPS
-
see if
-use
interest
any
SNPs
classify
correlate
people based on that
to traits
Sequencing tech to see if any surrounding genes are
expressed in relevant tissues
-use model
systems worthologs , Kos
,
causation
to establish
or human
versions
Suggest experiments designed to test a hypothesis that a given candidate gene is
involved in a trait of interest
-
mica
use
and 42 other
-give 1/2 one version of human gene
track relevant phenotypes
-
Define QTL.
-
quantitative trait locus, a place
within
the DNA that correlates with variance in a
trait
List conditions that are needed to perform QTL analysis
-
species with
SNPs & every locus that differ from
polymorphic
homozygous
strains of a
the other species
1) mutate species 1
2) cross species 1 and species 2
and then cross FIs
3) collect mutants
4) do SNP analysis on them and note
any regions 100 %
for either strain
5) examine surrounding genes
Describe caveats that must be considered when performing QTL analysis
SNPs
are
not
necessarily causative for
they are likely just linked to the gene
BUT
-
-
-
they could affect regulation
or even the actual
ORF
mutations,
of interest
Suggest approaches to identify QTLs or interpret results from these experiments
look for
-
-
100 %
regions
one
strain
only look& mutants. All other regions
Should be so/so
Suggest experiments designed to test a hypothesis that a given candidate gene is
involved in a trait of interest
-
introduce a gene on a plasmid and see if
that
-use
restores Wit
model
systems
or
stem
cells
Compare and contrast genome-wide association studies (GWAS)
CWAs millions of individuals , completely
Forward genetics and
natural variance
to
genes)
occuring complex
traits
-
using
attempt
connect sups (and then
to naturally
to
categorize each
person for that
complex trait and perform statistical
analysis
Briefly describe how CRISPR works; Name key components and their functions (guide
RNA, Cas proteins, target sequences)
guide RNA- BPs to target DNA and recruits CAS9
CAS9- makes
a
double-stranded
cut
& locus
target sequencess are Bed to by guide RNA and
cut
cell must
be in S
-external
or G2 for
thist o
occur
Via
-
HDR
sequences
no external
can be
introduced to cut DNA
sequence , gene is broken by
NHEJ
Design a CRISPR/Cas-based experiment to edit a gene
-
-
>
nonspecific
cuts
CASa is not perfect
would require embryonic
change in all cells
-
-
editing to see
cost , only available to the rich
2. Describe technical and ethical issues that arise in designing gene editing therapies
List challenges in sequencing ancient samples
DNA
-
-
-
-
-
fragmentation
carefulabio
human Dua contamination- sult up/enrich
bacterial contamination zenrich,
mutation from chemicals/UV
small sample size
I
target eukaryote
specific
3 enrich then
PCR
Explain the roles of related species in studying ancient DNA sequences
-related species can act as
reference
genomes to allow for shorter
be
aligned more easily
reads to
Identify duplicated and deleted regions using data from an SNP array
Dup :
deleted
:
-
-
-
-
-
-
genes
Discuss the limitations of using SNP arrays to identify important sequence variations
including translocations or inversions
-SNP arrays
can
literally only
individual has an sup
or
tell if an
not
. If
it but it's been moved around SNP
,
won't know.
they have
arrays
Describe differences between tumor suppressors and (proto-) oncogenes
suppressors o natural function is to
prevent unhealthy cell division , cause Cancer via
Tumor
LOF mutations
(proto) oncogenes - natural functions include
-
cell growth and division
encouraging
via
GOF mutations
*
,
cause cancer
Interpret experiments designed to distinguish between tumor suppressors and (proto-)
oncogenes
Connect pedigrees showing patterns of cancer to gene functions and cancer
development phenotypes
cancer traits
-
but are
sometimes
appear dominant
actually recessive this
,
is due to Lot
3. List challenges in using engineered immune cells to target cancer
-
teaching T-cells to target cancer-specific
antigens can be detrimental , because tumors
&
likely are not the only
these
-
-
cells
antigens
expressing
target glycolic ?)
immunoengineered T cell therapy can cause
Cytokine release syndrome