BIOL 3301 - Exam 4 Lin/Daane (COMBINED SET)

What is the central dogma of biology?

DNA -> RNA -> Protein

What is the central dogma of biology in terms of genomics?

genome -> transcriptome -> proteome

What does the term genome mean?

the total genetic composition of an organism

What does the term genomics refer to?

the molecular analysis of the entire genome of a species

What two things does genomics typically involve?

Mapping and DNA sequencing

What is mapping?

determining the locations of sites, such as genes, along a chromosome

What is DNA sequencing?

determining the entire base sequence of a genome which is usually millions to billions of base pairs in length.

Genomes ______ _________ in size, and they may consist of __________ DNA molecules or __________ of chromosomes

size, single, hundreds

Gene number generally _______ with organismal complexity, but genomes alsy vary with respect to the proportions of noncoding sequences

increases

To sequence an entire genome... ?

genomes must be broken into small fragments and the pieces sequenced in parallel

What are the two approaches to sequencing an entire genome?

clone-by-clone sequencing, whole-genome shotgun (WGS) sequencing

What is clone-by-clone sequencing?

chromosomes are broken into overlapping fragments that are then arranged in linear order to produce a map

What is whole-genome shotgun (WGS) sequencing?

DNA of entire genome is fragmented and pieces chosen at random sequenced

"High-throughput"

robotics and automation

"comprehensive"

informatics

"Highly parallel"

miniaturization

In ______ researches _______ ______ amd ______ ________ obtained the first complte DNA sequence of an organism

1995, Craig Venter and Hamilton Smith

What bacterium did Craig Venter and Hamilton Smith obtain the DNA sequence of?

Haemophilus influenzae

In 1996, the genome of which eukaryote was completed?

Saccharomyces cerevisiae (baker's yeast)

Saccharomyces cerevisiae (baker's yeast) consisted of how many linear chromosomes

16

The Human Genome Project with James Watson as the director was... ?

largest internationally coordinated undertaking in the history of biological research; great benefit is ability to identify and study the sequences of our genes

Human genome requires how many sequencing runs?

42,000,000 sequencing runs

The U.S. human genome project offiicially began in.... ?

1990

The HGP started as a ___________ project and began by developing a ______ ______.

clone-by-clone; physical map

HGP had which 7 goals?

1. obtain genetic linkage map of human genome
2. obtain physical map of human genome
3. obtain DNA sequence of entire human genome
4. develop tech for management of human genome info
5. analyze genomes of model organisms
6. develop programs focused on understanding and addressing ethical, legal, and social implications
7. develop tech advances

In ______. the 1000 genomes project was launched to establish a detailed under human genetic variation

2008

The goal of the Genomes project was to

determine the DNA sequence of at least 1000 anonymous participants from around the globe

rapidly sequencing large amounts of DNA is called

high-throughput sequencing

parallel sequencing is?

simultaneously perform many (96) sequencings runs in multiple gel-filled capillary tubes

next-generation sequencing technologies is?

ability to process thousands or even millions of sequence reads in parallel

mizture of single-stranded DNA fragments with adaptors called

sample library

fragments are attached to beads that are

PCR amplified

How do researchers decide which genomes to sequence?

1. basic research
2. medicine
3. agriculture
4. evolution

comparative genomics shows

relationships among living species

What is the goal of functional genomics?

to elucidate the roles of genetic sequences in a given species, aims to understand gene function

What is the proteome?

the entire collection of proteins that an organism can make

What is the goal of proteomics?

to understand the functional roles of the proteins of a species

What is bioinformatics?

the analysis of biological information using a mathematical/computational appraoch, aimed at extracting information from genetic and genomic datas

RNA sequencing used to study...?

simultaneous transcription of many genes

RNA-seq used to compare transcription in

* diff cell types
* healthy vs diseased cells
*diff stages of development
* response to diff environmental agents such as hormones or toxic chemicals

rna-seq

1. isolate rna from a sample of cells
2. break RNAs into small fragments
3. attach short oligonucleotide linkers to ends of RNAs
4. synthesize cDNAs ivia reverse transcriptase PCR, using RNAs as templates
5. sequence cDNAs using next-gen sequencing tech
6. using computer tech, align cDNA sequencing along genomic sequence

What are the advantages of using RNA-seq over microarrays?

* more accurate at quantifying amount of each RNA transcript
* superior at detecting RNA transcripts that are in low abundance
* identifies exact boundaries between exons and introns
* identifies splice variants
* identifies the 5' and 3' ends of RNA transcripts

Ways to generate collections of knockouts?

* transposable element jumps
* crispr-cas technically

computer analysis of genetic sequences usually relies on what three basic components?

computer, computer program, some type of data

a computer program is ...?

a defined series of operations that can analyze data in a desired way

* first step in computer analysis is a data file

computer program TRANSLATION

can translate a genetic sequence into six reading frames

What is sequence recognition?

the program has the information that a specific sequence of symbols has a specialized meaning

What is pattern recognition?

does not rely on specialized sequence info

What is gene prediction?

refers to the [process of identifying regions of genomic DNA that encode genes

* protein-encoding genes
* genes for non-coding RNAs

search by signal computer program ?

program tries to locate an organization of known sequence elements that are normaly found within a gene (promoter, start/stop codonts, etc.)

search by content computer program?

program tries to identify sequences that differ significantly between from a random distribution due to codon bias within protein-encoding genes

first, second, and third nucleotides also called

reading frames 1, 2, and 3

what is an open reading frame (ORF)?

nucleotide sequence that does not contain any stop codons

how many reading frames are possibly in a newly discovered sequence?

6

what are orthologs?

found in different species and have been derived from the same ancestral gene

what are paralogs?

two homologous genes found in a single organism

what is a gene family?

consists of two or more copies of homologous genes within the genome of a single organism

BLAST

Basic Local Alignment Search Tool

What does BLAST do?

relationship between the query sequence and each matching sequence is given an e-value - represents number of times that the match would be expected to occur purely by random chance in the entire database

BLAST starts with a _______ _______ and then locates ________ ________ in a large database

genetic sequence; homologous sequences

amino acid sequence used as a query sequence by BLAST program

human phenylalanine hydroxylase

what does a small e-value mean?

similarity is unlikely to be due to random events, genes are likely to be homologous

multiple sequence alignment proposed by

Saul Needleman and Chirstian Wunsch in 1970, demonstrates whale myoglobin and human b-hemoglobin have similar sequences

what is a conserved site?

site that is identical or similar across multiple homologs

The use of information about a patient's genotype and other clinical fata in order to select medication, therapy, or preventative measure called...?

personalized medicine

many genetic diseases are the result of ?

mutation in one gene

genes play roles in development of diseases that have complex patterns of inheritance

true

The study of human genetic diseases provides insights regarding

our traits

ex. analyzing hemophilia, researchers identified genes that participate in blood clotting

diseases in family pedigrees often obey

simple mendelian inheritance patterns

several observations are consistent w/ idea that a disease is caused (some part) by...?

genes

when individual exhibits a disease, the disorder is more likely to occur

in genetic relatives than in the general population

identical twins share the disease more often than

fraternal twins

identical twins called

monozygotic twins

fraternal twins called

dizygotic twins

What is the concordance of a disorder?

the degree to which it is inherited

concordance refers to percentage of...?

twin pairs in which both twins exhibit disorder or trait

* identical twins concordance is 1

genetic basis for a human disease includes

1. disease does not spread to individuals in same environment
2. diff populations tend to have diff frequencies of disesase
3. disease tends to develop at specific age

age of onset?

the age at which first exhibit characteristics of disease

Inheritance patterns of human disease may be determined via...?

pedigree analysis

pattern of inheritance of a human disorder...

caused by a mutation in a single gene can be deduced by analyzing human pedigrees

Tay-Sachs Disease

* autosomal recessive inheritance

* affected individuals appear healthy at birth but then develop neurodegenerative symptoms at 4 to 6 months

* typically die at 3 or 4 years

* 100x more frequent in Ashkenazi Jewish populations than in others

TSD is the result of a mutation in the gene that encodes...?

enzyme hexosaminidase A

* excessive accumulation of this lipid in cells of the CNS causes symptoms

What are the 4 common features of autosomal recessive inheritance?

1. affected offspring will have 2 unaffected parents

2. 2 unaffected heterozygotes have children, percentage of affected children is 25%

3. 2 affected individuals have 100% affected children

4. trait occurs w/ same frequency in both sexes

Disorders that involve defective enzymes typically have what kind of mode of inheritance ?

autosomal recessive

In autosomal recessive, the heterozygote carrier has 50% functional enzyme.

this is sufficient for a healthy unaffected phenotype

What is the major symptom of Huntington Disease?

degeneration of certain types of neurons in the brain, leads to personality changes/dementia/death

HD is a result of a mutation in a gene that encodes a protein named...?

huntingtin, mutation adds a polyglutamine tract to the protein

HD is inherited in an...?

autosomal dominant manner

What are the 5 common features of autosomal dom inheritance?

1. affected offspring usually have one or both affected parents
2. affected individual w. 1 affected parent expected to produce 50% affected offspring
3. 2 affected heterozygous individuals will have 25% unaffected offspring
4. trait occurs w/ same frequenci in both sexes
5. for most dom disease-causing alleles, homozygote more severely affected w/ disorder

3 common explanations for dom disoroders?

haploinsufficiency, gain-of-function mutations, and dom neg mutations

what is haploinsufficiency?

heterozygote has 50% of the functional protein, this is not sufficient for a healthy (unaffected) phenotype

what is a gain-of-function mutation?

mutation changes protein so it gains a new function

what is a dominant negative mutation?

mutant gene product acts antagonistically to the wild-type gene product

What type of inheritance poses a special problem for males?

x-linked recessive inheritance

* males are hemizygous

A female heterozygous for an X-linked recessive allele will pass this trait to

half of her sons

What is the major symptom of hemophilia?

blood cannot clot properly when a wound occurs

Hemophilia A is caused by a defect in?

an X-linked gene that enocdes a clotting protein called Factor VIII

What disease is known as the "royal disease"?

hemophilia

3 common features of X-linked recessive inheritance?

1. males more likely to exhibit trait
2. mothers of affected males often have affected brothers/father
3. daughters of affected males will produce 50% affected sons

What type of disease inheritance is rare?

x-linked dominant