CHROMOSOME BANDING SF

In a non-dividing cell, why are chromosomes not visible by light microscopy

because chromatin spreads throughout the nucleus

When do chromatin condense and become visible as chromosomes

during the metaphase of cell division

At this time, what happens to each chromosome

it has been duplicated

What does a chromosome become after duplication

two sister chromatids attached at the centromere

What are the ends of the chromosome called

telomeres

If treated with chemical dyes, how will the chromosome appear

as a series of alternate dark and light bands

If Giemsa is used, what is the dark band called

G-band or G-positive band

If Giemsa is used, what is the light band called

G-negative band

What other dye can produce similar banding patterns

Quinacrine

What happens if chromosomes are treated in a hot alkaline solution before staining with Giemsa

a reverse pattern is observed, the original dark band becomes light and vice versa

What is another name for the G-negative band

R-band

Orig dark band becomes what

light band

Orig light band becomes what

dark band

How are the long and short arms of chromosomes labeled

q (queue) and p (petit), respectively

At the lowest resolution, how are the major bands labeled

q1, q2, q3; p1, p2, p3 etc., counting from the centromere

At higher resolution, how are sub-bands labeled

q11, q12, q13 etc., numbered from the centromere toward the telomere

At even higher resolution, how are sub-sub-bands labeled

q11.1, q11.2, q11.3 etc.

What is the cytogenetic map location of CFTR (cystic fibrosis transmembrane conductance regulator)

7q31.2

What does 7q31.2 indicate

chromosome 7, q arm, band 3, sub-band 1, sub-sub-band 2

How are the ends of the chromosomes labeled

ptel and qtel

What does the notation 7qtel refer to

the telomere (the end) of the long arm of chromosome 7

The haploid human genome (homo sapiens) occupies how many DNA base pairs

just over 3 billion DNA base pairs

What did the Human Genome Project (HGP) produce

a reference sequence of the euchromatic human genome, used worldwide in biomedical sciences

How many protein-coding genes does the haploid human genome contain

between 20,000 and 25,000 human protein-coding genes

What percent of the genome codes for proteins

about 1.5%

What does the rest of the genome consist of

thousands of RNA genes including tRNA, ribosomal RNA, microRNA and other non-coding RNA genes, regulatory sequences, introns, and “junk DNA”

How are human genes distributed across the chromosomes

unevenly

What do gene-rich and gene-poor regions correlate with

chromosome bands and GC-content (guanine-cytosine area of stronger hydrogen bond; 3 H-bonds)

What does the human genome contain that is crucial to controlling gene expression

many different regulatory sequences

Where do regulatory sequences typically appear

near or within genes

What do regulatory sequences control

switching on and off of gene expressions

What are some types of non-coding DNA that regulate gene expression

genetic “switches” that regulate when and where genes are expressed

Aside from genes and regulatory sequences, what else does the human genome contain

vast regions of DNA of unknown function

What percentage of the genome size may these (Other dna parts) regions comprise

by some estimates 97%

Much of these unknown regions are composed of what

repeat elements, transposons, and “junk” DNA

What are the two types of repeat elements

tandem repeats and interspersed repeats

Examples of tandem repeats

satellite DNA, minisatellite, microsatellite

Examples of interspersed repeats

SINEs (short interspersed nuclear elements), LINEs (long interspersed nuclear elements)

What are the two types of transposons

retrotransposons and DNA transposons

Examples of retrotransposons

LTR, Ty1-copia, Ty3-gypsy, and non-LTR, SINEs, LINEs

Another type of transposon

DNA transposons

What does DNA sequencing determine

the order of the nucleotide bases in a genome

What were the two projects that produced a haploid human genome sequence

Human Genome Project and Celera Genomics

What type of sequencing did these projects produce

composite sequencing of several individuals

What is personal sequencing

complete sequencing of the chemical base pairs that make up the DNA of a single person

What may personal sequencing lead to

personalized medical treatment based on individual genotypes

When was the fifth complete personal genome map announced

December 2008

Who own the 5th genome map that was mapped in December 2008

Korean researcher Seong-Jin Kim

Whose genome was completed in 2007

Craig Venter of the U.S.

Whose genome was completed in April 2008

James Watson of the U.S.

Whose genome was completed in November 2008

Yang Huanming of China

Whose genome was completed in January 2008

Dan Stoicescu

What was not sequenced in the Human Genome Project to protect volunteer identity

personal genomes

why was the personal genomes not sequenced in the Human Genome Project

to protect the identity of the volunteer who provided DNA Samples

From whom was the Human Genome Project sequence derived

several volunteers from a diverse population

What type of sequence is the HGP sequence

haploid

What type of sequence maps did Venter and Watson have

diploid, representing both sets of chromosomes

state the color codes of the nucleotide base (adenine, cytosine, guanine, thymine) during the sequencing

• adenine-green

• cytosine-blue

• guanine-black

• thymine-red

What does a genome sequence list

the order of every DNA base in a genome

What does a genome map identify

landmarks

How is a genome map described compared to a genome sequence

less detailed and aids in navigating around the genome

What does a genome map catalog

the patterns of small-scale variations in the genome that involve single DNA letters or bases

What is an example of a genome mapping project

HapMap (international HapMap Project)

What does HapMap describe

the common patterns of human DNA sequence variation

On what scales does genetic variation among individual humans occur

many different scales

Give examples of genetic variation scales

gross alterations in the human karyotypes to single nucleotide changes

it is the nucleotide diversity based on single mutations

single nucleotide polymorphisms (SNPs)

What is nucleotide diversity based on

single mutations called single nucleotide polymorphisms (SNPs)

What is the nucleotide diversity between humans

about 0.1%

How many differences per base pair is 0.1% diversity

1 difference per 1,000 base pairs

How many nucleotide differences does this amount to in the human genome

approximately 3 million nucleotide differences

How many nucleotides does the human genome have

about 3 billion nucleotides

What are most SNPs

neutral

What can some functional SNPs influence

phenotypic differences between humans through alleles

How many SNPs are estimated to exist in the human population

a total of 10 million SNPs

What percentage of SNPs are functional

at least 1%

What project studies SNPs

international HapMap Project

It is where, in full sequences of an individual's genome, the analysis of diploid sequences has shown that nonSNP variation accounts for much more human genetic variation than single nucleotide diversity.

COPY NUMBER VARIATION

what accounts for more human genetic variation than single nucleotide diversity

non-SNP variation

What does non-SNP variation include

copy number variation

What causes copy number variation

deletions, inversions, insertions, duplications

When copy number variation is included, how much is human to human genetic variation

at least 0.5% (99.5% similarity)

can the copy number variations  be inherited

inherited but can also arise during development

What is another type of genetic variation that arises from chemical tags that attach to DNA

epigenetics

What does epigenetics arise from

chemical tags that attach to DNA and affect how it gets read

What are the chemical tags called

epigenetic markings

What do epigenetic markings act as

switches that control how genes can be read

At some alleles, what can the epigenetic state of DNA and associated phenotype do

be inherited transgenerationally