Genetics Exam 1 & Final Material

The pairwise map distances for four linked genes are as follows: A-B = 22 m.u., B-C = 7 m.u., C-D = 9 m.u., B-D = 2 m.u., A-D = 20 m.u., A-C = 29 m.u. What is the order of these four genes?

ADBC

Purines

Adenine and Guanine

Initiation

After sliding along the DNA, σ factor recognizes a promoter, and RNA polymerase holoenzyme forms a closed complex. An open complex is formed, and a short RNA is made. σ factor is released, and the core enzyme is able to move down the DNA and make RNA.

Separating via Electrophoresis

Agarose: large nucleotides (>100 basepairs) Acrylamide: small nucleotides (<100 bp and proteins) DNA Standards are DNA fragments of known molecular weight (MW) measured in base pairs (bp). They are also called "markers" We refer to DNA fragments on a gel as "bands" If analyzing proteins, you'd use a protein ladder.

Hardy-Weinberg Equilibrium

Allele and genotype frequencies do not change over the course of many generations IF certain circumstances are present Five assumptions: Population size is infinite Individuals mate at random No new mutations appear No migration into or out of the population Genotypes have no effect on ability to survive and transmit alleles to the next generation

Why are organisms with an odd number of chromosome sets usually sterile?

Almost all gametes will have an unbalanced set of chromosomes.

What is the difference between a F factor and an F' factor?

An F' factor carries part of the bacterial genome whereas an F factor does not

How many promoters are in an operon?

1

There are ______________ usually found in the genetic code.

1 start codon and 3 stop codons

The kappa light chain of a mature immunoglobulin (protein) has

1 variable region, 1 joining region and 1 constant region

The four criteria if genetic material

1) Information: Must provide a blueprint to determine the inherited traits of an organism 2) Transmission: Genetic material must be passed from parent to offspring 3) Replication: Genetic material must be copied 4) Variation: Genetic material must vary in ways that can account for the known phenotypic differences within each species.

What is the correct order for the steps in transduction?

1) Phage infects cell 2) Host DNA digested into fragments 3) Some phage accidently carry host DNA fragment 4) Phage infects new cell 5) Phage transported DNA recombines with chromosome of new cell

Southern Blot Method

1.DNA is separated on by size (electrophoresis). 2.Transfer to a nylon membrane 3.Incubate membrane with labeled probe High Stringency - detects nearly identical sequences Low Stringency - detects similar sequences

About how many bases of DNA wrap around a histone complex?

146

When Mendel crossed two plants that were heterozygous for a single trait, what was the genotypic ratio of their offspring?

1:2:1

Adenine and thymine form ________ hydrogen bonds between them, while cytosine and guanine form ________ bonds.

2, 3

Which of the following ratios indicates a lethal gene?

2:1

Amplification of DNA by PCR

2^n

Which of following expressions denotes a trisomic organism?

2n+1

One strand of DNA is 5' - AGGCCTTA - 3'. What is the opposite strand?

3' - TCCGGAAT - 5'

Which of the following is NOT a modification made to pre-mRNAs? A) 5' Capping B) 3' Capping C) Base modification D) 3' polyA tailing E) Splicing

3' Capping

DNA polymerases are unable to replicate what areas of the chromosome?

3' ends

What RNA modification is important for mRNA stability?

3' polyA tailing

The zigzag and solenoid models are associated with the ________ level of DNA organization.

30 nm fiber

In a given population of Drosophila, curly wings (c) is recessive to the wild-type condition of straight wings (c+). You isolate a population of 35 curly winged flies, 70 flies that are heterozygous for straight wings, and 45 that are homozygous for straight wings. What is the TOTAL number of ALLELES in the gene pool?

300

When Mendel crossed two plants that were heterozygous for a single trait, what was the phenotypic ratio of their offspring?

3:1

In a given population of Drosophila, curly wings (c) is recessive to the wild-type condition of straight wings (c+). You isolate a population of 35 curly winged flies, 70 flies that are heterozygous for straight wings, and 45 that are homozygous for straight wings. What is the frequency of alleles in this population?

46.7% c; 53.3% c+

How many general transcription factors are needed for eukaryotic translation?

5

How many types of histone proteins are there?

5

The polarity of DNA synthesis is

5'→3'

Mapping and Genetic Markers

A "marker" is a specific DNA sequence that can be determined by various methods. At known sites in the genome. Can map via linkage to a marker instead of with a gene that produces a phenotype. Also useful in physical mapping. -Can also use markers to tell the differences between individuals in a population.

Nucleoside

A base and a sugar

Translation Elongation Stage (Bacteria)

A charged tRNA binds to the A site. EF-Tu facilitates tRNA binding. 16S rRNA (in the 30S subunit) detects incorrect tRNA bound at the A site Prevents elongation until mispaired tRNA is released Peptidyl transferase, (the 23S rRNA in the 50S subunit), catalyzes peptide bond between the polypeptide and the amino acid in the A site. The polypeptide is transferred to the A site. The ribosome translocates1 codon to the right. This translocation is promotedby EF-G. An uncharged tRNA is released from the E site. Cycle repeated, again and again, until a stop codon is reached.

You body has the ability to produce over 28 million different immunoglobulins (antibody proteins). What is the source of this diversity?

A few genes undergo site-specific recombination, which results in a large diversity of "mature" immunoglobulin genes

In a pedigree analysis, what does a black square represent?

A male with the trait or disease

DNA "dideoxy" sequencing

A mixture of nucleotides, both dideoxy and deoxy, are added to the sequencing reaction along with a primer and DNA polymerase The four dideoxy bases are labelled with different fluorescent dyes: ddA = green, ddT = red, ddG = yellow, ddC = blue PCR Produces fragments of varying lengths. Each fragment "ends" with a fluorescent dye. Resulting fragments are separated based on their length Automated Read Out

Balancing selection

A polymorphism may reach an equilibrium where opposing selective forces balance each other not evolving toward allele fixation or elimination 1. Negative frequency-dependent selection 2. Heterozygote advantage

Which of the following is TRUE about autosomes?

In human, they include all chromosomes except X and Y

Predicting change with directional selection

In subsequent generations, the HW equilibrium will be modified by directional selection: Frequency of AA: p2wAA Frequency of Aa: 2pqwAa Frequency of aa: q2waa mean fitness of the population

What is the term used to describe the situation in which an allele that is expected to cause a phenotype does not.

Incomplete penetrence

Gene flow

Individuals migrate between populations with different allele frequencies Can Occur in both directions Two important consequences: 1. It tends to reduce differences in allele frequencies between the populations 2. It can enhance genetic diversity within a population if a migrant introduces a new mutation

Key features of bacterial chromosomes

Most, but not all, species contain circular chromosomal DNA Usually a few million base pairs Most species contain a single type of chromosome, but it may be present in multiple copies. Several thousand different structural genes (protein-encoding) are interspersed throughout the chromosome. The short regions between adjacent genes are called intergenic regions (Play roles in DNA folding, replication, gene regulation, and genetic recombination). One origin of replication - required to initiate DNA replication. Repetitive sequences may be interspersed throughout the chromosome. Found in a region of the cell called the nucleoid - not surrounded by a membrane

Cap-binding proteins play roles in

Movement of some RNAs into cytoplasm Early stages of translation Splicing of introns

Site-Directed Mutagenesis

Mutations can arise spontaneously, or be induced by mutagens BUT they are difficult to isolate and predict Site directed = ENGINEERING A GENE -Change in designated nucleotide(s) (i.e. Substitution, Insertions, Deletions) by introducing mismatch/deletion in a primer. -Then test effect (i.e. expression, protein function or phenotype) of mutation in vitro or in vivo

A peptide bond is formed between the __________ of one amino acid and the __________ of the other

N-terminus (first amino acid), C-terminus (second amino acid)

Charge of the DNA backbone

Negative

The scientist(s) ________ developed the triplet-binding assay. Samples containing ribosomes and a particular RNA triplet were exposed to charged tRNAs with different radiolabeled amino acids. Only the amino acid whose tRNA matched the triplet would bind the ribosome. The triplet-binding assay established relationships between particular triplet sequences and specific amino acids.

Nirenberg and Leder

The building blocks of DNA are

Nucleotides

What enzyme is responsible for creating short RNA primers during DNA replication?

Primase

Recombinant DNA Technology

Produces new arrangements or combinations of DNA Used for -Sequencing the human genome -Cloning the open reading frames (ORFs) of genes for study -Cloning other fragments of DNA for study (promoters etc.) -Expressing proteins in cells to make therapeutic products (i.e. insulin)

What "rule" can we use to figure out the probability that two or more independent outcomes will occur?

Product Rule

Steps of gene cloning

Purify chromosomal DNA and the plasmid DNA Digest both with restriction endonuclease

cDNA is made using what as the starting material?

RNA

Initiation

RNA polymerase binds to DNA

Elongation

RNA polymerase slides along the DNA, creating an open complex as it moves. Template strand is used to make a complementary copy of RNA using same base-pairing rules except that U is substituted for T in the RNA (no proofreading) RNA pol moves along the template strand in a 3′ to 5′ direction, and RNA is synthesized 5′ to 3′ Nucleoside triphosphates as precursors.

Termination

RNA polymerase stops synthesizing RNA

Elongation

RNA polymerase synthesizes RNA

Which of the following is NOT part of the spliceosome? A) U4 snRNP B) U1 snRNP C) RNaseP D) U2 snRNP

RNaseP

Three features are found in most promoters (eukaryotes)

Regulatory elements - sequences bound by general transcription factors Enhancers and silencers TATA box Transcriptional start site

trans-acting factors

Regulatory proteins that bind to cis-acting elements and can effect multiple genes

Topoisomerase I

Relaxes negative supercoils and can introduce a break in one of the DNA strands

Physical mapping

Relies on DNA cloning techniques Genes are mapped relative to each other Distances in base pairs

Linkage mapping

Relies on genetic crosses Genes are mapped relative to each other and "markers" Distances in map units

Cytogenetic mapping

Relies on microscopy Genes are mapped relative to band locations FISH

Restriction Fragment Length Polymorphism (RFLP)

Restriction enzymes recognize specific DNA sequences and cleave the DNA at those sequences Along a long chromosome, a particular restriction enzyme will recognize many sites Some individuals have an extra site or lack a site due to sequence variations - In these individuals, a restriction enzyme will produce different sized fragments

What is the difference between a transposon and a retrotransposon?

Retrotransposon use an RNA intermediate, whereas transposons do not.

During this phase of the cell cycle, the sister chromatids are formed

S phase

Microsatellites

STR (Short, tandem repeats): simple sequences Abundantly dispersed throughout a species' genome Number of microsatellite repeats at a locus is variable Can determine how many microsatellites by amplifying with the PCR and analyzing length/size of product. Can be used to locate other genes for mapping. Also used in DNA fingerprinting for criminal investigation and paternity tests.

Which of the following is NOT an assumption of the Hardy-Weinberg equation?

Selection is favoring the dominant allele.

Mass spectrometry

Separates small peptides based on their size and charge Mass of protein correlates with its amino acid composition Amino acid composition can be used to compare to database of known sequences to determine sequence of protein isolated from gel Mass spectrometry can also be used to identify protein covalent modifications -Example: Mass of a phosphorylated protein increases by the mass of a phosphate

In bacteria, the sequence that facilitates the binding of the mRNA to the ribosome is called the

Shine-Dalgarno Sequence

Promoters

Site of RNA polymerase binding DNA sequences that "promote" gene expression Direct the exact location for the initiation of txn Typically located just before, "upstream" of the site where transcription of a gene actually begins The bases are numbered in relation to the transcription start site.

Regulatory sequences

Sites where proteins interact with the DNA to control transcription. Can be found in many locations relative to the coding sequence

Polymerase Chain Reaction (PCR)

Another way to make many copies of a particular DNA sequence Can copy DNA without the aid of vectors and host cells

-OH group of DNA

Attached to the 3' carbon; allows nucleotides to form covalent linkages with each other

Restriction enzymes

Bind specific DNA sequences and cleave the DNA at two defined locations, one on each strand

Gel Retardation Assay

Binding of a protein to a fragment of DNA retards (slows) its rate of movement through a gel. The band "shifts" sizes Must be performed under non-denaturing conditions -Unfolding of protein would cause it to release DNA -Separation of DNA strands would release protein Complexes are electrophoresed through a gel -Complexes that migrate more slowly indicate that DNA was bound by protein

A polyribosome can be found in which of the following types of cells? A) prokaryotic B) both C) eukaryotic

Both

Alternative splicing allows an organism to ________.

Carry fewer genes

Which of the following can be used to study DNA-protein interactions?

Chromatin Immunoprecipitations (ChIP), ChIP on chip, and Gel shift assay

What does CRISPR stand for?

Clustered Regulatory Interspaced Short Palindromic Repeats

Negative frequency-dependent selection

Common individuals lose fitness Rare individuals gain fitness No genotype becomes too rare or too common

Spliceosome

Composed of several snRNPs Each snRNP contains small nuclear RNA and a set of polypeptides Mechanism (similar chemistry as group II) 1.Binds to an intron sequence and precisely recognize the intron-exon boundaries 2.Holds the pre-mRNA in the correct configuration 3.Catalyzes the chemical reactions that remove introns and covalently link exons

For gene mapping in bacteria, which of the following is correct?

Conjugation is used to determine the relative order and distance of genes whereas cotransduction is used for accurate mapping of genes that are close together

5'UTR

Contains the Ribosome-binding site: site where ribosome binds Bacteria: translation begins near here. Eukaryotes, the ribosome scans the mRNA for a start codon

Negative supercoiling

Creates tension on the DNA strands that may be released by DNA strand separation.

________ uses the unique banding patterns of a chromosome to determine the general location of a gene.

Cytogenetic mapping

Which enzyme attaches adjacent Okazaki fragments, forming a continuous DNA strand?

DNA ligase

CpG islands are associated with

DNA methylation

What enzyme catalyzes the phosphodiester bond between two adjacent DNA nucleotides in DNA replication?

DNA polymerase I

Synthesizing a new DNA strand

DNA polymerase III uses a dNTP with 3 phosphate groups attached at the 5′ carbon. DNA pol catalyzes the formation of the phosphodiester bond between 3' -OH of last nucleotide and 5' -P of the new one, PPi is released.

cis-acting elements

DNA sequences that exert their effect only over a particular gene

Vector DNA

DNA that will replicate without integrating into host chromosome - plasmids and viruses Serves as the carrier of the DNA segment to be cloned

The process of interrupted mating may be used to do which of the following?

Determine the relative position of bacterial genes

What is the term used to describe a situation in which a gene's expression pattern is dependent upon the parent from which it was inherited?

Genomic imprinting

An octamer is composed of

H2A, H2B, H3, and H4: Contain many positively-charged amino acids. Amino acids in histone "tails" can me modified to affect nucleosome structure

What is the role of mediator in eukaryotic gene expression?

Help transition RNA polymerase form a closed conformation to an open conformation.

Supercoiling

Helps compact the bacterial chromosome.

What word is used to describe a gene on the X-chromosome in a male?

Hemizygous

CRISPR/Cas9 can be used to treat viral infections of

Herpes viruses since they are DNA viruses

What term is used to describe rapidly sequencing large amounts of DNA?

High throughput sequencing

Choose the statement that is most accurate concerning biochemical pathways. A) All enzymes in the pathway catalyze the same reaction. B) If an enzyme in a pathway is inactive, adding excessive amounts of its substrate will restore the normal phenotype. C) If an enzyme in a pathway is inactive, adding excessive amounts of its product will restore the normal phenotype. D) If the enzyme that catalyzes the final step in a pathway is inactive all the other enzymes will be inactivated as well. E) If the first enzyme in a pathway is inactivated, adding the final product will not restore the normal phenotype.

If an enzyme in a pathway is inactive, adding excessive amounts of its product will restore the normal phenotype.

What occurs during the annealing stage of a PCR reaction?

The primers bind to the template DNA

Molecular genetics

The study of DNA structure and function at a molecular level

What is true in both Temperate Phage and HIV infections?

There can be a long latent period where no sign of infection, such as cell death, is detectable.

Pyrimidines

Thymine, cytosine, and and uracil

Heterochromatin

Tightly compacted regions of chromosomes Transcriptionally inactive (in general) Radial loop domains compacted even further

What is the purpose of Okazaki fragments?

To allow DNA to be synthesized in the 5' to 3' direction on the lagging strand

What is the purpose of MARs and SARs?

To form loop structure, to condense DNA, and to bind to the nuclear matrix

RNA pol II

Transcribes all protein-encoding genes and some snRNA genes

RNA pol III

Transcribes all tRNA genes and 5S rRNA gene

RNA pol I

Transcribes most rRNA genes

What happens physically during the process of crossing over?

Two homologous chromatids break and rejoin at precisely the same site along the chromosome so that there is no loss or gain of material on either product.

What is a nucleosome composed of?

Two turns of DNA wrapped around an octet core of histone proteins.

mRNA splicing with the spliceosome

U1 binds to 5′ splice site.U2 binds to branch site. U4/U6 and U5 trimer binds. Intron loops out and exons are brought closer together. 5′ splice site is cut. 5′ end of intron is connected to the A in the branch site to form a lariat. U1 and U4 are released. 3′ splice site is cut. Exon 1 is connected to exon 2. The intron (in the form of a lariat)is released along with U2, U5, and U6. The intron will be degraded

Thymine dimers are caused by

UV light

dideoxyribonucleotides (ddNTPs)

Uses DNA polymerase to copy a strand of DNA However, DNA synthesis is terminated at specific nucleotides by using nucleotide analogs Lack a 3' -OH group

Which procedure is used to identify a specific protein within a mixture of many different protein molecules?

Western blotting

The coat color of calico cats is a result of ________

X-inactivation

The genetic control of X-inactivation is governed by a short region on the X chromosome called the ________.

X-inactivation center (Xic)

If two genes are very close to each other on the same chromosome then____________

a crossover is unlikely to occur in the region between them you are likely to get a low % of recombinant offspring from a test cross.

Founder effects

a few individuals separate from a larger population and establish a new population

Monomorphic

a gene that predominately has only one allele. Not very common

Polymorphic

a gene with 2 or more alleles or a noncoding piece of DNA that shows variation in sequence

An allele that can cause the death of an organisms is called

a lethal allele

All viruses contain at least

a protein capsid and a nucleic acid

An auxotroph is

a strain that cannot grow in the absence of a specific nutrient

A temporary change in the structure of a nitrogenous base is called ________.

a tautomeric shift

Why should a selectable marker be present on a cloning vector?

allows the isolation of host cells that took up the cloning vector

tRNA processing

also made as large precursors cleaved at both 5' and 3' ends to produce mature, functional tRNAs Some nucleotides modified

Group I splicing of introns

also made as large precursors-cleaved at both 5' and 3' ends to produce mature, functional tRNAs-Some nucleotides modified

In nature, the CRISPR/Cas9 system has features of

an adaptive immune system

A testcross to determine genetic linkage is between

an individual that is heterozygous for 2 or 3 traits and an individuals that is homozygous recessive for the same genes.

Gene knockout

an organism that has a gene that has been specifically inactivated (completely deleted or disrupted)

Proteomics

analysis of the functional roles of proteins made

Select the phase when sister chromatids separate and head towards opposite poles of the cell.

anaphase

What is the term we use for a foreign molecule that can illicit an immune response in vertebrates?

antigen

The primary function of basal transcription factors is to

assist in associating RNA polymerase with the promoter element.

CRISPR was discovered in

bacteria and archaea

The prevalence of the allele for sickle cell anemia in some populations is an example of which of the following?

balancing selection

Which repair process uses enzymes called the DNA-N-glycosylases?

base excision repair

If a point mutation increases the chances to produce offspring, it would be called a ________ mutation.

beneficial

DnaA proteins

bind to the DnaA box sequences

Core enzyme

binds loosely to the DNA until promoter is reached. Composed of 5 subunits = a2bb'

Single-strand binding protein

binds to and stabilizes single-stranded DNA until it can be used as templat

Antisense RNA does which of the following?

binds to the mRNA and prevents translation

Chromatin immunoprecipitation (ChIP)

can determine if proteins can bind to a particular region of DNA -Proteins cross-linked to DNA -DNA isolated from cells and broken into small pieces -Antibody is used to precipitate the protein-DNA complexes -DNA is purified and amplified with PCR -Sequence of the amplified DNA can be identified by using it as a probe on a microarray

Reciprocal crosses

can reveal X-linked traits, is a set of two crosses: An affected male is crossed with an unaffected female AND an affected female is crossed with an unaffected male, and will give different results if the gene is X-linked

Chromosomal DNA

cellular, viral etc. Source of the DNA segment of interest DNA purified using a variety of biochemical techniques from tissues and cells of interest

What two diseases are caused by the varicella-zoster virus?

chicken pox and shingles

Bacterial cells that are able to take up DNA from the environment are described as

competent

Chromatin remodeling complexes alter nucleosomes, this occurs when

complexes of ATP-dependent proteins may reposition, evict, or change nucleosome composition

cDNA library

composed of cDNA inserts Should represent all of the mRNA in the cell

Genomic library

composed of chromosomal DNA fragments. Should represent all of the DNA of the cell

Bioinformatics

computer analysis generate insights into -Gene structure -Gene function -Relationships between genes and organisms -Protein function -Protein interactions -Predicting drug structure and function

Mutations that change the configuration of a protein at a specific temperature are called ________ mutations.

conditional

In _____________, their is a direct physical link between two bacteria that facilitate DNA transfer.

conjugation

The first generation of replication in the Meselson and Stahl experiment disproved which theory of replication?

conservative

Which describes the mechanism of DNA replication in which both parental strands remain together following replication?

conservative

Which of the following is NOT a way that a protein can be modified, which could affect its function?

consolidation

What is the purpose of phosphorylating the carboxy terminal domain (CTD) of RNA Polymerase II?

convert from the elimination to the elongation phase

Which of the following is not associated with positive transcriptional regulation?

corepressors

The conversion of cytosine to uracil in DNA is an example of ________.

deamination

Binding of an miRNA to a target mRNA can result in

degradation of the target mRNA.

Excision repair corrects DNA by

detecting, removing, and replacing damaged or incorrect nucleotides in a single strand of DNA.

Southern Blot

detects a specific DNA sequence Developed by E. M. Southern in 1975 Determine copy number of a gene in a genome Detect small gene deletions that cannot be detected in karotypes Identify gene families Identify homologous genes among different species •Uses a piece of "labeled" (e.g. radiolabeled) nucleic acid as a "probe" to detect the DNA by complementary annealing to it. Can use... •Whole or part of a gene •PCR product •Oligonucleotide

Western Blotting

detects a specific Protein Cell specific expression (at protein level) - Red blood cells vs. brain cells Developmental stage specific expression (at protein level) - Fetal vs. adult cells Starts out similar to Southern and northern blotting separating proteins by size (under denaturing conditions) and transferring to a membrane. But can't detect proteins using nucleic acids!

Northern Blot

detects a specific RNA Procedure is similar to Southern blotting RNA is electrophoresed, transferred to membrane, and probed Used to identify a specific RNA within a mixture of many RNA moleculesNorthern Blotting41 Cell specific expression - Nerve vs. muscle cells Developmental stage specific expression - Fetal vs. adult cells Differentiate between alternatively spliced mRNAs

Bioinformatisists

develop programs to analyze DNA and protein sequences/structures Programs to organize data and make it accessible to researchers.

DNA sequencing uses special type of nucleotides called __________, in which no additional nucleotides can be added to the 3' end.

dideoxyribonucleotides

In animals, somatic cells are ________ and gametes are ________.

diploid ; haploid

All transposable elements are flanked by

direct repeats in the host genome

Which of the following types of selection favors one extreme of a phenotypic distribution?

directional selection

A true-breeding line of green pod pea plants is crossed with a true-breeding line of yellow pod plants. All of their offspring have green pods. From this information, it can be stated that the green color is ________ to the yellow color.

dominant

Dispersive model

each strand is a mix of old and new

The step in DNA replication in which the proteins connect the correct sequence of nucleotides into a continuous new strand is called

elongation

Proteome

entire collection of a species' proteins

aminoacyl-tRNA synthetases

enzymes that attach amino acids to tRNAs

Helicases

enzymes that unwind the double helix at the replication forks. Breaks H-bonds between nucleotide

When the absence of a specific protein results in a lethal phentype, the gene that encodes for the protein is

essential

Proteomics

examines the functional roles of the proteins that a species can make Analyze all the proteins a cell produces at one time...Depends on -Cell type -Stage of development -Environmental conditions Genomic data can provide important information about the proteome, but have to be followed up with protein studies Sequencing and analysis of an entire genome can identify all the genes that a given species contains but it can not identify all of the proteins

A functional protein is made up of the information contained within what region of DNA?

exons

What is the general term for an enzyme that cleaves the phosphodiester bond between the last nucleotide and the 2nd-to-last nucleotide in a nucleic acid strand?

exonuclease

Disruptive selection

favors the survival of two or more different genotypes with different phenotypes. Can lead to speciation

Enzymes involved in metabolism are most likely regulated via ________.

feedback inhibition

An XXY Drosophila fly is

female because sex in flies is determined by the ratio of X chromosomes to autosomes

Wobble rules

first two positions pair strictly according to the AU /GC rule third position can tolerate certain types of mismatches

FISH technology depends on

fluorecently-labeled pieces of DNA that can bind to a sequence of interest by complementary-base pairing

What do both the rho-dependent and rho-independent mechanisms of termination have in common?

formation of a stem-loop structure

Acetylation of histones results in

formation of an open chromatin structure

Which of the following involve the movement of a population from one location to another?

founder effect

Histone 1

functions in the linker region between nucleosomes and helps regulate "closeness" of the nucleosomes

ALL the alleles of EVERY gene in a population make the _____________

gene pool

In a Punnett square diagram, the outside of the box represents the ________

haploid gametes

Areas of the chromosome that are highly condensed and transcriptionally inactive are called

heterochromatin.

When two sequences are similar because they are derived from a common ancestor they are _____________; and when the sequences are from genes of different species, the genes are considered _______________.

homologous; orthologs

During sexual reproduction, each parent contributes one set of chromosomes. Similar chromosomes from each parent are called ________.

homologs

When one gene can compensate for the loss of another gene (i.e. gene redundancy), an individual needs to be __________________ to have the mutant phenotype

homozygous recessive for both genes

When the phenotypic ratio is the same as the genotypic ratio, the trait mostly likely exhibits

incomplete dominance

Fitness

individual's relative ability to survive and transmit its genes to the next generation (a statistical measurement) measured in all individuals of the same genotype in a population Two basic components: viability and reproductive success

rRNA processing

initially transcribed as a large RNA in nucleolus This large RNA transcript is enzymatically cleaved into smaller functional pieces

Which of the following steps is NOT done by all viruses during their viral reproductive cycle?

integration

A loss of an internal portion of a chromosome is called a(n)

interstitial deletion

Given the following sequence of genes on a chromosome, determine what change in chromosome structure occurred. The asterisk (*) indicates the centromere. Before: A B C D * E F G H After: A C D * E F G H

interstitial deletion

In chickens and many other birds, the male

is the homogametic sex

DNA ligase

joins Okazaki fragments

A DNA microarray is a slide that is dotted with

known sequences of DNA

The experiment by Noll, 1974, supported the observation that histones were regularly spaced on chromosomes because

limited digestion with DNase I resulted in DNA fragments that differed in size by approximately 200 bp.

Chromosomes are sometimes called __________ because it contains a group of genes are physically linked together.

linkage groups

Which of the following procedures best determines the relative order, but not precise location, of a series of genes on a chromosome?

linkage mapping

"In situ" hybridization

locate the position of a gene or other unique DNA segment in a chromosome

The location of a gene on a chromosome is called its ________.

locus

A codon is a three-base sequence of

mRNA that codes for an amino acid.

In eukaryotic cells, replication proceeds from ____ origin(s) of replication.

many

High-throughput sequencing

many sequences run in parallel

The _____________ is defined as the number of recombinant offspring divided by the by the total number of offspring, multiplied by 100. The units are _________________.

map distance; map units (mu)

Protein synthesis begins with the amino acid ___________ as its codon is the one used as the "start codon" by nearly all organisms.

methionine

Genomics

molecular analysis of the entire genome of a species

The correct order of compaction from least compacted to most compacted would be

naked DNA, nucleosome, 30 nm fiber, radial loop, metaphase chromosome.

The lac operon is under what type of control?

negative control

The failure of chromosomes to separate during anaphase is called

nondisjunction

Which DNA repair process often leads to deletion in chromosome sequence?

nonhomologous end joining (NHEJ)

What does physical mapping provide that the other types of genetic mapping do not?

number of nucleotide base pairs between genes

Positive assortative mating

occurs when individuals are more likely to mate due to similar phenotypic characteristics. How "pure-breeding" lines were created in the lab. And what dog breeders do.

Negative assortative mating

occurs when individuals with dissimilar phenotypes mate preferentially = Opposites attract.

An inversion heterozygote contains which of the following?

one normal chromosome and one chromosome with an inversion

Coding Strand

opposite DNA strand; has the same base sequence as RNA transcript

Metagenomics allows researchers to study the genomes of

organisms that can not be grown in a lab, organisms that have never been isolated before, and a bunch of organisms all at once

Which enzyme forms peptide bonds between adjacent amino acids during polypeptide synthesis?

peptidyl transferase

During complementary base pairing, enzymes join the base's nucleotide to the preceding nucleotide by a(n) __________bond

phosphodiester

Which of the following is not an example of translational regulation in prokaryotes? A) altering the structure of the mRNA B) phosphorylation of an enzyme C) incorporation of antisense RNA D) sterically blocking the ribosome

phosphorylation of an enzyme

Chromosome walking is used in

physical mapping

Small circular pieces of DNA that are not associated with the bacterial chromosome are called

plasmids

Small circular pieces of bacterial DNA that are used as vectors in cloning experiments are called

plasmids

A single gene that effects many phenotypes is called

pleiotropy

The multiple effects of a single gene on the phenotype of an organism is called

pleiotropy

If a gene has more than one allele and each allele has a frequency that is less than 99%, then the gene is considered to be

polymorphic

The term for a group of individuals from the same species that can interbreed with one another is

population

Translocations and inversions may cause which of the following?

position effect

What types of amino acids are most responsible for the binding of DNA to histones?

positively charged amino acids

What is the name of the sequence that indicates the transcription start site?

promoter

Archibald Garrod (1857 - 1936)

proposed a relationship between genes and protein production Studied alkaptonuria-Patients' bodies accumulate abnormal levels of homogentisic acid proposed it was due to a missing enzyme, namely homogentisic acid oxidase recessive pattern of inheritance

2D gel electrophoresis separates

proteins based on size and charge

This area of research tries to describe the roles of and interactions between every protein expressed in a cell or tissue.

proteomics

The results of the replica plating experiments by the Lederbergs supported which of the following mutation theories?

random mutation theory

A translocation cross may occur in an individual which has which of the following?

reciprocal translocation

Sigma factor (s)

recognizes both the -35 and -10 regions. Contains a helix-turn-helix motif gives tighter binding to the DNA

Gene cloning

refers to isolating, and then making many copies of a particular sequence of DNA

The cellular organelle responsible for protein synthesis is the

ribosome

tRNA structure

secondary structure exhibits cloverleaf pattern-Three stem-loop structures Variable regions (shown in blue) acceptor stem with a 3' single-stranded region Anticodon (orange) is different between the tRNAs tertiary structure involves additional folding tRNAs commonly contain modified nucleotides

DNA replication occurs through a _________process.

semiconservative

Which describes the mechanism of DNA replication in which the newly made double-stranded DNA contains one parental strand and one daughter strand?

semiconservative

2D Gel Electrophoresis

separates by SIZE and CHARGE Can resolve two proteins that differ by a single charged amino acid

What aspect of meiosis best explains Mendel's law of segregation?

separation of homologous chromosomes during Meiosis I

Repetitive sequences

short (a few bases to a few thousand bp) sequences repeated many times in a genome -Can originate with transposable elements -Can be microsatellites, aka short tandem repeats (STRs) •Repeat of 1-6 bp sequence•Usually repeated 5-50 times •Minisatellite: 6-80 bp repeat covering 1,000-20,000 bp

The method of sequencing genomic fragments cloned straight from the genome is

shotgun sequencing

Protein microarrays

similar concept to DNA microarrays More challenging because proteins are more easily damaged during microarray fabrication Synthesis and purification of proteins more difficult

Chromosomes may be identified based on which of the following characteristics?

size of the chromosome, banding patterns, and location of the centromere

Genetic drift has the greatest influence on allele frequencies for which population size?

small

Site-directed mutagenesis allows researchers to produce a mutation at a ________ within a cloned DNA segment.

specific site

AUG (methionine)

start codon AND codes for methionine within protein

primase

starts an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template

Shotgun sequencing

state of the technology No extensive physical map needed Clones from a genomic library isolated randomly & sequenced Overlapping sequences matched using computers

UAA, UAG and UGA

stop codons

poly-A tails

string of adenine nucleotides at 3' end of mature mRNA added enzymatically after gene is transcribed (Polyadenylation)• **Not encoded in gene sequence** important for the stability of mRNA and the translation of the polypeptide Length varies between species

Metagenomics

study of a complex mixture of genetic material obtained from an environmental sample

Leading strand

synthesized continuously, towards the replication fork

Lagging strand

synthesized discontinuously, away from the replication fork (toward the origin

Which molecule contains an anticodon? A) mRNA B) rRNA C)snRNA D) DNA E) tRNA

tRNA

What method is used to identify proteins by weighing the amino acids that compose peptide fragments?

tandem mass spectometry

Which of the following would have the shortest p arm of the chromosome?

telocentric

Which of the following is found at the end of a eukaryotic chromosome?

telomeres

RF1 and RF2 are active during ________.

termination

Group II splicing of introns

the 2'-OH on an endogenous alanine "attacks" the phosphodiester bond at the 5' splice site. Then the free 3' - OH links to the 3' splice site

What causes gene duplications?

the crossing over of misaligned chromosomes

The primary structure of a protein refers to

the linear sequence of the amino acids.

Inbreeding

the mating between genetically-related individuals

Outbreeding

the mating between genetically-unrelated individuals

In a 3-point cross, the parental genotypes will always be

the most abundent

Fluorescence in situ hybridization (FISH)

the probe is fluorescently labeled DNA complementary to the sequence of interest.

Natural selection

the process that progressively eliminates individuals whose fitness is lower Individuals whose fitness is higher become the parents of the next generation

During Western blotting, the primary antibody recognizes

the protein of interest

conglomerate.

the recipient population

A DNA microarray (or gene chip) is used to measure

the relative amount of RNA transcribed from thousands of different genes

One definition of epigenetics would be

the study of reversible mechanisms that lead to changes in gene expression that do not involve changes in DNA sequence.

Following transcription, the RNA has a complementary sequence to

the template strand of DNA

In a cloning experiment with chromosomal DNA, you use a vector that contains a lacZ gene as a selectable marker. If the competent cells are grown on X-Gal and IPTG, which colonies would contain cloned chromosomal DNA?

the white colonies

The group of enzymes able to relax supercoils in DNA is called

topoisomerases

Genome

total genetic composition of an organism

Polysomes

transcripts with multiple ribosomes translating simultaneously

Regulation of gene expression may occur at which of the following levels?

translation, posttranslation, and transcription

The term for when a piece of one chromosome attaches to another chromosome is

translocation

Which of the following does not usually show a problem during meiosis?

translocation homozygote

What are sometimes referred to as "jumping genes"? because there are inherently mobile

transposable elements

What enzyme is responsible for excising a transposable element out of DNA?

transposase

In the following sequence of DNA, the italicized base has been mutated. What type of mutation is this? 5' - G A T C T C C G A A T T - 3' original strand 5' - G A T C T C C C A A T T - 3' mutated strand

transversion

Which type of plant would usually be a seedless variety?

triploid

How many replication forks depart from an origin of replication?

two

The majority of the nonrepetitive genes in an organism are found in which of the following?

unique sequences

DNA helicase

unwind DNA, separating the strands in both directions beyond the origin Helicase travels in the 5' to 3' direction Use ATP for energy to drive strand separation

A cytogeneticist would primarily do which of the following?

use a karyotype analysis to examination chromosomal structure

Key Features of Eukaryotic Chromosomes

usually linear 10,000,000 - 100,000,000 bp in length. Occur in sets (homologous chromosomes) Genes are interspersed throughout the chromosome. Each chromosome contains many origins of replication, about every 100,000 base pairs. Contains a centromerethat forms a recognition site for kinetochoreproteins (pull apart chromatids in mitosis/meiosis). Telomeres- specialized sequences located at ends of linear chromosome Repetitive sequences are commonly found near centromeric and telomeric regions, but they may also be interspersed throughout the chromosome.

Genetic variation is ultimately based upon which of the following?

variations in nucleotide sequence of the DNA

A ________ uses the lytic cycle to begin the immediate manufacture of new phages in the host cells.

virulent phage

Epistasis is

when one gene can mask the expression of a second gene

Polymorphisms are caused by changes such as

Small deletion/insertions (indels) Single nucleotide polymorphism (SNP)

Detecting proteins in Western Blotting

Specific proteins are detected by antibodies. Antibodies are produced in mammals (rabbits, goats, etc) that are specific to protein of interest "Primary antibody" recognizes and binds to protein of interest. "Secondary antibody" recognizes the primary antibody as an antigen the 1o and 2o antibodies are from different mammals. 2o is attached to alkaline phosphatase, which cleaves a colorless molecule into a black one that can be detected

What was the outcome of the experiment that reconstituted two different strains of tobacco mosaic viruses that had different infection characteristics?

The differences in infection characteristics depended only on the RNA sequence of the virus strain.

Suppose that an arctic fox has white fur in the winter and brown fur in the summer. Which of the following explanations is most likely?

The environment has an effect on the phenotype

Heterozygote advantage

The higher fitness of the heterozygote is balanced by the lower fitness of both corresponding homozygotes

Bacterial Initiation

The mRNA, initiator tRNA, and small ribosomal subunits associate to form an initiation complex. 16S rRNA is complementary to the Shine-Delgarno requires three Initiation Factors: IF1, IF2, and IF3 (proteins) The initiator tRNA recognizes the start codon (AUG) in mRNA-In bacteria, this tRNA is designated tRNAfmet(methionine that has been covalently modified to N-formylmethionine) Initiation factors are released and the large (50S) subunit binds forming the entire 70S ribosome

Z DNA

Left-handed conformation, helical back-bone, looks like it zig zags as it winds around the helical structure, 12 base pairs per 360 degree turn. Bases are substantially tilted relative to the central axis Evidence suggests that this type of DNA is used in the process of transcription

Euchromatin

Less condensed regions of chromosomes Transcriptionally active Regions where 30-nm fiber forms radial loop domains

Bottleneck effect

Dramatic reduction in population size, population re-established by only a few individuals

Functional sites of ribosomes

During bacterial translation, mRNA lies on the surface of 30S subunit As a polypeptide is being synthesized, it exits through a hole within the 50S subunit Peptidyl site (P site) Aminoacyl site (A site) Exit site (E site)

What ribosome site does a "used" tRNA move to just before it leaves the ribosome?

E

Why do researchers think that CRISPR was more effective at treating EBV infection than HSV-1?

EBV infects cell types that are actively dividing so the viral genome is accessible when the nuclear membrane breaks down during mitosis

Horizontal gene transfer

Exchange of genetic materials among different species

Stabilizing selection

Extreme phenotypes are selected against and the intermediate phenotypes have the highest fitness values

Dominant alleles typically have which of the following mechanisms

Gain of function - the mutation causes the protein or gene product to have a different function than the wild type Dominant-negative: The mutation causes the protein or gene product to inhibit the function of the normal protein Haploinsufficiency: 1 copy of the normal/functional gene is not enough maintain the "normal" or wild type phenotype

What is a major difference between the general and regulatory transcription factors?

General transcription factors are essential for any transcription for all genes while regulatory transcription factors regulate transcription of specific genes.

During conjugation, one gene (A) is found to transfer to the recipient bacteria 26 minutes following the start of conjugation, while a second gene (M) is found to transfer 37 minutes following the start of conjugation. A third gene (T) transfers 45 minutes following the start of conjugation. Based on this information, which of the following is true?

Genes A and M have a genetic distance of 11 minutes Genes A and T have a genetic distance of 19 minutes Genes M and t have a genetic distance of 8 minutes The order of the genes is A M T

Beadle and Tatum's Experiments

Interested in the relationship among genes, enzymes and traits Is it one gene-one enzyme or one gene-many enzymes? Model organism was Neurospora crassa Wild-type cells grew on minimal media - prototrophs Mutants could not grow on minimal media alone - auxotrophs Mutants could be separated into different groups depending on whether or not they grew on media supplemented with biosynthetic intermediates One gene-one enzyme hypothesis: A single gene controlled the synthesis of a single enzyme

DNA Gyrase (Topoisomerase II)

Introduces negative supercoils using energy from ATP and can untangle DNA molecules

What are the four major classes of chromosomal rearrangements?

Inversions, duplications, translocations, deletions

How does tryptophan, the end product of the trp operon, function in the regulation of the operon?

It binds to the repressor and only then can this complex bind to DNA preventing transcription of the operon.

Which of the following is true about a strain that is met- bio- thr+ leu+ thi+?

It can grow in media that contains biotin

Which of the following is TRUE about horizontal gene transfer?

It can occur between bacteria of different species It includes transformation, transduction and conjugation It is the cause of the spread of antibiotic resistance in bacteria

A cDNA library differs from a genomic library in which way?

It contains only coding sequences, not introns

The wild-type eye color of Drosophila is red. A single-base mutation occurs that produces a white eye color. Which of the following is correct regarding this mutation?

It is an example of a mutation that alters protein function.

Which of the following is correct concerning F factors?

It may integrate into the host chromosome It stands for fertility factor It allows conjugation to occur F+ bacteria act as donor strains in conjugation

How is glucose involved in the catabolite repression of the lactose operon?

It results in decreased cAMP levels, which in turn leads to decreased CAP binding; thus the lac operon is repressed even if lactose is present along with the glucose.

Hershey/Chase

Knew that bacteriophages could genetically alter bacteria but didn't know how. They incubated the bacteria and phages under two conditions: S35 P32 They found that most of the S35 isotope was found in the supernatant, meaning that the empty phages contain primarily protein.

Ribosome structure and assembly

Large macromolecular complex made of rRNA and protein Bacterial cells have one type of ribosome in cytoplasm Eukaryotic cells have two types of ribosomes * One in cytoplasm * Other in organelles (Mitochondria and Chloroplasts)

What principle says that "Two different genes randomly assort their alleles during the formation of haploid cells."?

Law of Independent Assortment

What type of transposable element makes up over 20% of our genome?

Long interspersed elements (LINEs)

The recent study that was published in Nature in August 2017 used CRISPR to repair a mutation in the ____________gene in human ____________.

MYBPC3; embryos

What does the enzyme reverse transcriptase do?

Makes a DNA strand complementary to a RNA template strand

Three main phases of genomic analysis

Mapping Sequencing Functional genomics

Selection coefficient

Measures the degree to which a genotype is selected against s = 1 - w

Telomeric sequences consist of

Moderately repetitive tandem arrays 3' overhang that is 12-16 nucleotides long Each species has a variation of the sequence Several guanine nucleotides Often many thymine nucleotides

Microarrays (Gene Chips)

Monitors the mRNA expression of thousands of genes simultaneously Can be used for -Finding genetic variations -Cell-specific gene expression -Gene regulation -Tumor profiling -Microbial strain identification

7-mG 5'Cap

Most mature mRNAs have a 7-methyl guanosine covalently attached at their 5' end Capping occurs during transcription when transcript is ~20 - 25 bases Cap is recognized by cap-binding proteins

What happens when viruses have a latent infection, which is also called lysogenic infection in bacteriophages?

Most of the viral genes are silent

Termination stage

Occurs when stop codon is reached in mRNA These codons are not recognized by tRNAs, Instead recognized by proteins called release factors (RFs) 3D structure of release factors mimics tRNAs Bacteria: RF1, RF2 and RF3 Eukaryotes: eRF1, eRF3 Polypeptide is cleaved from the last tRNA in the P-site. Complex falls apart

Plasmids and viruses used as vectors contain

Origin of replication- can be replicated in host organism Selectable marker - isolation of hosts that carry the vector. Any cell that doesn't have the plasmid will die. Polylinker - Site for joining vector DNA to DNA segment to be cloned May have additional features such as sequences to allow expression of the cloned DNA

Why are pig organs suitable for transplant into humans?

Pig organs are about the same size as human organs

Alternate mRNA splicing

Pre-mRNA with multiple introns can be spliced different ways-generates mature mRNAs with different combinations of exons Regulated Different mature mRNAs in different cell types or during different stages of development 2+ polypeptides can be derived from a single gene Differential expression of snRNA's determine splicing

B DNA

Predominant form of DNA in living cells. Right-handed helix, 10 base pairs per 360 degree turn. Bases tend to be centrally located, and hydrogen bonds tend to be relatively perpendicular to the central axis.

What is one reason why an amphibian, such as a salamander, might have a larger genome than a mammal, such as a chimpanzee?

The amphibian has more repetitive sequences than the mammal.