Unit 3: Genetics & MB

researchers sequenced thousands of ____(approximately 1000 bp long) and tried to assemble the DNA in ____. the problem was many parts of the chromosome are ____

inserts; chromosomes; repetitive

repeats in the chromosome = intergenic repeats that include ______ elements and ______ repeats

transposable; tandem

researchers sequenced thousands of ____(approximately 1000 bp long) and tried to assemble the DNA in ____. the problem was many parts of the chromosome are ____

inserts; chromosomes; repetitive

repeats in the chromosome = intergenic repeats that include ______ elements and ______ repeats

transposable; tandem

solution to repetitive parts of the human chromosome: so-called ____ clones

• plasmids which contain ____ DNA fragments are sequenced from both sides

• this allowed researchers to integrate ____ reads and reconstruct the DNA sequence of all chromosomes

BAC; bigger; shorter

DNA can be read in ____ different reading frames. if we assume random distribution of nucleotides in the DNA, then a ____ codon should appear every 21 triplets (3 out of 64 triplets encode for it)

six; STOP

if there is a long stretch of nucleotides without interruptions by STOP codons, then it’s likely a ____ is in that location

gene

open reading frame (ORF) is a sequence of adjacent ____where, beginning from a specific starting point, the triplets are interrupted by a ____codon. long ORF signals the presence of a ____

nucleotides; stop; gene

conserved sequences

finding sequences of genes by comparison with close relatives

natural selection changes the DNA sequence between species by incorporating advantageous ____ and loosing deleterious ones

mutations

while genomes differ, some genes and their protein function are ____ across different ____

conserved; species

if sequence of DNA is similar to each other, it suggests there might be a ____ encoded in that area as DNA sequences have been ____ throughout evolution

gene; conserved

DNA homology is when two sequences of DNA have similar ____ sequences because they were derived from a ____ ____

nucleotide; common ancestor

only a small part of our DNA is coding for ____ and the central dogma applies to all ____ ____ ___genes. there are exceptions to the central dogma such as ____-____ ____

proteins; protein coding; non-coding RNAs

non-coding RNAs are important for 3D structure of ____, ____RNA’s are important for translation, ____-noncoding RNA’s and ____-noncoding RNAs are important for ____ expression

ribosomes (rRNA); tRNA’s; large; small; gene

retroviruses use ____ and not ____ as the information carrying material. retroviruses ____ a cell and incorporate the information for their building blocks into the ____ DNA. in order to do that, RNA must be transformed to ____ through a process called ____ ____

RNA; DNA; infect; host; DNA; reverse transcription

reverse transcription is done through the enzyme ____ ____

reverse transcriptase

magnetic beads carrying oligo-dT single stranded DNA can be used to isolate ____ molecules. since RNA has a poly-A tail, it can complementary ____ ____ with these beads and be bound. using a magnet, mRNA can be ____ from other RNAs. ____ ____ will then synthesize the DNA leading to a DNA-RNA hybrid

mRNA; base pair; separated; reverse transcriptase

after reverse transcription, a ____ stranded cDNA is synthesized. mRNA is digested with ____ and the ____’ end of the newly synthesized cDNA folds back and serves as a free 3’ ____ group for DNAP/primer. DNAP synthesizes the second DNA strand using the first as a template. ____ cuts the hairpin resulting in double stranded cDNA

double; RNase; 3; OH; nuclease

cDNA is a ____ copy of an ____ molecule made by reverse transcriptase which is a ____-dependent ____ polymerase. cDNA can be either ____ or ____ stranded

DNA; RNA; RNA; DNA; double; single

inserts and plasmids digested with the same ____ ____creating a library of bacteria is the old way of sequencing as its labor ____ and expensive. the next generation sequencing is ____

restriction enzyme; intensive; PCR

polymerase chain reaction (PCR) allows ____ of a specific fragment of DNA. makes use of ____ to synthesize a new strand with short DNA ____ that synthesized with the ____ sequence to the beginning and end of the area that is amplified

amplification; DNAP; primers; complementary

____ changes allow for amplification of DNA in PCR

• step 1: ____. temperature is ____ to ____ the DNA double helix into single strand DNA

• step 2: ____. temperature is ____ to allow short DNA ____ to base pair with the complementary sequence of the template DNA allowing a free 3’ OH group

• step 3: ____. DNAP binds to double stranded region of the ____ and adds nucleotides to the ____’OH

temperature

• denaturing; increased; separate

• annealing; lowered; primers

• extension; primers; 3

newly synthesized DNA fragments are also used as a____ for the next round of synthesis in PCR. given that the ends are defined by the ____, the intended DNA fragment gets more and more ____ after each cycle. PCR usually contains 35-40 cycles

template; primers; enriched

Sanger sequencing Chain termination sequencing of ____ ____ with PCR products or cloned DNA is highly ____

defined fragments; accurate

high-throughput sequencing is ____ sequencing of millions of random fragments of DNA. longer sequences are assembled based on ____ using bioinformatics

simultaneous; overlaps

high throughput sequencing:

____ stranded DNA isolated from species of interest and randomly fragmented. adapter fragments are ____ to fragments that can be used for hybridization purposes, as ____ for PCR, ____ for sequencing reactions, or ____ in subsequent bioinformatic analysis

double; ligated; primers; primers; identifiers

sequencing by synthesis is a commonly used method for next generation sequencing. after fragments were ____ amplified, they are added onto a chip (____). ____ sequences hybridized to chip-bound complementary sequences

PCR; flowcell; adapter

sequencing by synthesis:

• fragment genomic DNA is ligated with different ____ to each end using special ____ then PCR amplifies the fragments and the denatured fragments are added to flowcell

• complementary strands are synthesized using ____. denature and wash away the hybridized fragments

• prime PCR amplification of fragments through formation of ____ with flowcell ____. complementary strand is generated by bridge amplification with DNAP.

• ____ the complementary strands and repeat the bridge amplification several times. cleave one strand type from oligonucleotides and wash them away. the flowcell now has millions of different clusters of ____ fragments

• adapters; enzymes

• DNAP

• bridges; oligonucleotides

• denature

• identical

sequencing by synthesis adds one ____ at a time which causes a short ____ pulse. as different nucleotides are labeled with different dyes, this can be analyzed to obtain the DNA ____. ____ ____ are added to the sequence and ____’ ____blocked bases are added to the primers and fluorescence recorded. the blocks and flours are removed and second one is added and fluorescence recorded

nucleotide; fluorescent; sequence; hybridize primers; 3; OH

genomic DNA sequencing gives ____ results as cDNA sequencing

different

genomic DNA sequencing gives information about the whole ____ which includes ____. all parts of DNA should be ____ covered ideally

DNA; introns; equally

cDNA sequencing only gives ____ regions (5’ UTR, exons, and 3’ UTR). cDNA sequencing does not necessarily show every single ____that is expressed in the body. given that its derived from mRNA into cDNA, it represented ____ genes of that tissue

coding; gene; expressed

cDNA libraries can give us information about ____ ____

alternative splicing

combining info from gDNA and cDNA libraries allows the ____ of genes on specific ____ to be found

location; chromosomes

• gene rich regions are chromosomal regions that have more ____ than expected from average gene density over entire ____

• gene deserts are regions with no ____ genes

• genes; genome

• identifiable

anonymous DNA polymorphisms/DNA markers do not affect ____ but can be used to track specific regions of the ____ and is the most ____

phenotype; genome; common

non-anonymous DNA polymorphisms do affect ____ by altering ____ ____ such as frameshift, nonsense, or missense mutations

phenotype; gene function

DNA polymorphisms

sequence differences between individual genomes within species

genetic polymorphisms contribute to genome ____:

• includes: ____ ____ ____ (SNP), ____ ____ ____ (SSR), ____ ____ ____ (CNV), and ____/____ (DIP/InDel)

diversity; single nucleotide polymorphism; simple sequence repeat; copy number variant; insertion/deletion

SNPs sometimes correlate with occurance of specific ____ and are common in the human ____

diseases; genome

the density of SNPs in the human genome average about 1 per 1000 bp. often just a single ____ that is changed within a population. these changes may be ____ or cause change in ____ sequence

nucleotide; silent; protein

SNP can be identified using ____ and ____ sequencing. PCR primers can be ____ in areas flanking the sequence that should be compared

• in homozygous state, Sanger sequencing gives one big ____ for the nucleotide

• in heterozygous state, Sanger gives a signal for ____ different nucleotides at the position

PCR; Sanger; designed; peak; two

deletion insertion polymorphisms are the ____ most common in human genomes and appear on average of once every 20 kb. size of deletions varies a lot with strong correlation with ____. the bigger bp, the ____ likely of the occurrence. this causes problems with DNA ____, ____, and DNA ____

second; size; less; replication; recombination; repair

simple sequence repeats (SSR) is a DNA ____ resulting from differences in ____ of copies of short DNA sequence that is repeated many times in a chromosome with common repeats of 1-,2-,or 3-base sequences found on average of every 30 kb of human DNA. commonly found outside ____ regions but can impact gene expression in some cases (Fragile X). frequency of new alleles much higher than normal ____ rate with many different ____ within the population with more than 10 for a single location.

polymorphism; number; coding; mutation; alleles

primers can be designed in genetic area adjacent to area of SSR due to ____base pairing. PCR amplifies region between ____ and ____ primers. if there are different number of repeats on two homologous chromosomes, PCR fragments will have different ____

complementary; forward; reverse; lengths

number of SSR defines the ____ of the band at a gel. given high frequency of mutations in SSRs, most individuals are ____ for the number of SSRs at a given location (two bands on gel)

size; heterozygous

several different regions of SSR are needed to have high probability of ____ the DNA. genotype is determined by PCR at many SSR ____. 13 pairs of PCR ____are labeled with fluorescent dyes. data is collected and matched from crime scenes

matching; loci; primers

copy number variation are tandem sequence ____more than 10 bp long caused by ____ during meiosis that leads to unequal ____ ____ . not common, so most are ____rather than being mutation

repeats; misalignment; crossing over; inherited

chromosomal rearrangements contribute to species ____. different chromosomes must have ____ DNA

evolution; exchanged

all chromosome rearrangements can be explained by two ____ ____ breaks. these breaks can be repaired using ____-____ ____ ____ (NHEJ) mechanism joining the ends together. if two breaks happen, the different end can be joined and cause ____ effects on chromosome arrangements

double stranded; non-homologous end joining; different

chromosomes undergo changes without affecting numbers through chromosome ____, chromosome ____(180 degree rotation), and ____ ____

deletions; inversions; reciprocal transversions

many regions on human chromosome can have very ____ sequences. during meiosis, chromosomes can arrange close together during prophase I and ____ occurs. some cases, recombination can happen within these ____ sequences. the aberrant recombinations change the ____ of chromosomes

deletions can have severe effects but can also be used to locate ____ alleles. homozygosity for deletions are often ____ as more than one gene is deleted

recessive; lethal

in combination with wildtype homologue (deletion ____), animals are often viable but several effects might be observed:

• can have some ____ due to reduced expression of genes in area of deletion

• increased risk of ____ due to mutation in other copy of the gene (on wildtype chromosome)

• may uncover existing ____alleles

• a deletion uncovers a ____mutation

heterozygous; phenotype; phenotype; recessive; recessive

big deletions can be directly observed by missing ____ on the chromosome

bands

deletions can be detected by crossing to all ____chromosome in the area

• the wildtype chromosome provides the gene its ____ missing in the deleted chromosome (shown through ____)

• ____ mutant for recessive allele of each genes a through f shows the phenotype as ____ for all genes and all ____ carry multiple recessive alleles

• a cross of wildtype chromosome and mutant chromosome shows ____ for all genes and the recessive alleles are ____ by the deletion mutation in another offspring as its a recessive mutation

• mutant

• function; +

• homozygous; mutant; gametes

• wildtype; uncovered

in deletion heterozygotes, there is no ____in the area of deleted genes. this can only happen between homologs at regions of ____ and cannot occur within a ____ ____, so genetic map distances in deletion heterozygotes will not be accurate

recombination; similarity; deletion loop

gene deletions and duplications are due to ____ ____ ____ during meiosis. this requires similar sequences in the same ____. if sequences are similar, ____ of the homologue chromosome can happen. once they recombine in this mispaired location, one chromosome will have a ____ and the other a gene ____

unequal crossing over; orientation; mispairing; deletion; insertion

unequal crossing over can cause ____ ____ variation and can lead to changes in gene expression. changes in copy numbers (how many ____ of a specific gene) can lead to increased or decreased ____ ____ of the affected genes. the more copies the more ____ produced and these changes usually happen during ____ over any generations

copy number; copies; gene expression; mRNA; evolution

____: segment of DNA that resembles a gene but is not capable of coding for a ____. most often derived from genes that have lost their ____-____ ability due to accumulated mutations over evolution

pseudogene; protein; protein-coding

____ is when duplicate genes from duplicated events diverge and form different aspects of gene’s original function

subfunctionalization

____: diversification of one member of a duplicate pair for new function

neofunctionalization

unequal crossing over example:____ ____

• genes for red and green pigments are ____ on the X chromosome

• green pigment may be present in multiple ____ on the chromosome due to ____ and unequal ____ ____ during meiotic recombination resulting in gene ____ and ____ ____

• color blindness

• close

• copies; mispairing; crossing over; deletion; color blindness

most chromosome inversions don’t result in abnormal ____, but can occur if:

• inversion disrupts a ____

• inversion places a gene near ____ ____for other genes or near highly expressed noncoding DNA ____

phenotype

• gene

• regulatory sequences; heterochromatin

inversions can act as crossover ____. in inversion heterozygotes, no viable ____ are produced that carry chromosomes resulting from recombination in inverted region

suppressors; offspring

inversions are genetic rearrangements where order of genes in chromosome segment is ____ and do not alter genetic ____. in an inversion heterozygote, chromosomes twist into a ____ in the region where gene order is inverted (two different ____)

reversed; content; loop; loops

inversions can happen in different parts of the ____

• ____ inversion is when the centromere is within the inverted segment

• ____ inversion is when the centromere is not within the inverted segment

chromosome

• pericentric

• paracentric

crossing over within a paracentric inversion loop during recombination produces one ____ (no centromere), which is very unstable and gets degraded, and one ____ (two centromere) chromosome, which breaks randomly into ____ pieces without all genes present and not viable after ____. only gametes that didn’t ____ in inversion were able to survive with suppression of recombination in area

acentric; dicentric; monocentric; fertilization; recombine

crossing over within pericentric inversion of heterozygote results in ____ and ____ of genetic information. half the gametes will have large ____ and ____ and are not viable. this inversion suppresses ____ in the area of inversion since these are not ____

deletions; duplications; deletions; duplications; recombination; viable

geneticists make use of recombination suppression by developing ____ chromosomes that carry many different ____ and ____that change the phenotype so they can be tracked. no viable ____ can be produced when normal homolog recombines with balance chromosome. normal chromosome stays the ____ over many generations

balancer; inversions; alleles; offspring; same

____ ____ leads to exchange of genetic information of non-homologous chromosomes.

reciprocal translocation

____ occurs from the interchange of parts between nonhomologous chromosomes and there is no loss of ____ information but the ____ may be altered.

translocation; genetic; function

translocations may produce ____ ____ which changes the gene function due to repositioning of a gene. gene expression may be ____ or ____ in translocated gene

position effects; elevated; decreased

____ is an example of reciprocal translocation where chromosome 9 and 22 get exchanged. this fuses a ____ which is misexpressed and can lead to cancer

leukemia; protein

due to exchange of DNA, the homologous chromosomes and the chromosome with exchanged DNA will ____ during meiosis in translocation ____

align; heterozygote

chromosomes can be separated in ____ different ways during meiosis I depending on which ____/____ the spindle fibers attach. its important for survival that gametes are____ as each part of the chromosomes should be present exactly ____

three; centromere; kinetochore; balanced; once

semisterility

reduced fertility from having non viable offspring

acrocentric

centromere on one side of the chromosome leading to long and short arms

nonreciprocal translocation is the fusion of two ____chromosomes in the centromere region resulting in loss of one ____ in karyotype analysis. genetic information is lost in the ____ of the translocated acrocentric chromosomes

acrocentric; chromosome; tips

when chromosome 21 is one of the ____ in a robertsonian translocation, the rearrangement leads to inherited type of ____ ____. the ____ carrier is phenotypically normal, but high risk occurs due to ____ segregation in meiosis

acrocentrics; down syndrome; heterozygous; aberrant

euploid

cells with complete set of chromosomes

for proper gene expression, the correct ____of chromosomes must be within the cell. except for sex chromosomes, genes of both ____ chromosomes are expressed

number; homologue

aneuploidy

describes the loss of a chromosome or gain of additional chromosome

monosomy vs trisomy (types of aneuploidy)

missing one chromosome; extra chromosome is present in addition to two complete sets

autosomal monosomy is usually ____. most trisomies are as well except chromosomes ____,____,____

lethal; 13; 18; 21

extra copies of chromosomes can have severe effects such as ____ and ____ disabilities, disruption in ____ or delays

physical; intellectual; development

aneuploidy for sex chromosome often has less severe ____. symptoms include ____ and ____ abnormalities

consequences; infertility; skeletal

turner syndrome occurs in females who are ____. the phenotype includes ____ height and sterility due to lower than normal doses of ____ linked genes

XO; short; X

klinefelter syndrome occurs in males with more than one ____ chromosome (____). the phenotype includes usually ____ height and sterility due to abnormally high X linked gene dosages

X; XXY; tall

what is the likely reason there is less severe effects of aneuploidy of sex chromosomes?

X chromosome inactivation

most genes of the inactivated X chromosome are not transcribed, but genes on the tips called ____ genes are still expressed even from the silenced chromosome. this leads to a ____-____ of these genes which are the likely cause of skeletal abnormalities

SHOX; mis-regulation

meiotic nondisjunction is the failure of ____ to separate during meiosis I, or the failure of ____ ____to separate during meiosis II resulting in ____ meiotic products

homologs; sister chromatids; aneuploidy

nondisjunction during first meiotic division results in two n____1 and two n____1 gametes. the zygotes with fertilization with normal gamete create two ____ (2n+1) and two ____(2n-1)

+; -; trisomic; monosomic

nondisjunction during second meiotic division creates two aneuploid gametes one n____1 and one n____1 and two n gametes that are ____. zygotes with fertilization creates one ____ (2n-1), one ____(2n+1), and two ____(2n)

+; -; haploid; monosomic; trisomic; diploid

risk of down syndrome increases with ____ of the mother. recombination studies suggest many ____ events happen during meiosis I

age; disjunction

individuals with down syndrome can have ____ kids. trisomic chromosomes undergo abnormal ____ due to the formation of ____ and ____

healthy; segregation; trivalents; univalents

trivalent is the abnormal pairing of ____chromosomes in cell division with two homologues and certain arms are facing away from the normal crossing over bivalents

trisomic

univalent is an ____ chromosome in trisomy that is ____in cell division (two bivalents and one univalent)

extra; unpaired

there is a ____/____ chance a person with down syndrome will have a child with/without it

50;50

two characteristics for euploid organisms:

• n= number of chromosomes in ____

• x= number of chromosomes in ____, complete set

gamete; single

____ plants can be generated to identify genes for fitness. geneticists use ____pollen and induce growth of a plant by treating embryoids with plant hormones and nutrients. these plants are often ____ (homologue chromosomes can’t be ____)

monoploid; haploid; sterile