Structure & Function Of Genes And Genome - Aug 8

Front 1

What is a karyotype?

Back 1

Characteristic chromosome complement in terms of the numbers and morphology of the chromosomes in an organism's genome.

Front 2

What is a locus?

Back 2

The linear order position of a gene on a chromosome.

Front 3

What is cytogenetics?

Back 3

The study of chromosomes, their structure, and inheritance.

Front 4

What is a germline?

Back 4

The cell line from which gametes are derived.

Front 5

What are somatic cells?

Back 5

All cells in the body except those that develop into gametes.

Front 6

What are autosomes?

Back 6

All but the X/Y sex chromosomes.

Front 7

What are matching, paired chromosomes called?

Back 7

Homologous chromosomes or homologues

Front 8

What is an allele?

Back 8

One of several variations of a gene for a specific locus.

Front 9

Which bases are the pyramidines?

Back 9

Cytosine and Thymine

Front 10

Which bases are the puridines?

Back 10

Adenine and Guanine

Front 11

Which two bases pair to form 3 hydrogen bonds?

Back 11

Cytosine-Guanine (Adenine and Thymine form only 2 bonds)
http://en.wikipedia.org/wiki/GC-content

Front 12

What are the three units of a nucleic acid?

Back 12

Five carbon sugar (ribose or deoxyribose), a nitrogen containing base (C, G, A or T), and a phosphate

Front 13

What is the difference between deoxyribose and ribose sugars?

Back 13

2-deoxyribose has no -OH on the 2-carbon. Ribose does.

http://www.mun.ca/biology/scarr/Deoxyribose_versus_Ribose.html

Front 14

Which direction do nucleotides polymerize in? What type of bond is this?

Back 14

'5 to '3. Phosphodiester

Front 15

How is a phosphodiester bond made?

Back 15

Mg coordinates to an O on the 3' carbon. This O then bonds to the P of the phosphate (and displaces one of it's Os) attached to the 5' carbon of the next nucleic acid.

http://chemistry.gsu.edu/faculty/Huang/new_page_18.htm

Front 16

Is a DNA helix left or right-handed?

Back 16

Right

Front 17

How many DNA strands per chromosome?

Back 17

One

Front 18

What is chromatin?

Back 18

DNA + proteins that package it in a single chromosome

Front 19

What types of proteins organize DNA strands into chromatin?

Back 19

Histones and other heterogeneous, nonhistone proteins (that are still critical)

Front 20

How does histone organization work?

Back 20

http://online.vitalsource.com/books/978-1-4160-3080-5/id/fig2-f6

Front 21

What is a histone octamer?

Back 21

Two copies of each of the four core histones (five major types of histones altogether).

Front 22

How many base pairs are organized per histone octamer?

What is this structural unit called?

Back 22

146 bp

Nucleosome (146 bp wrapped twice around a histone octamer)

Front 23

What is a series of octamers with DNA wrapped around them called?

Back 23

Solenoid

Front 24

What is the area between nucleosomes called?

Back 24

Internucleosomal spacer region. Uses the fifth major histone. ~54 base pairs

Front 25

What is the histone code?

Back 25

A pattern of histone variants and post-translational modifications that determine specific properties of chromatin associated with epigenetics and differential gene expression.

Front 26

What is epigenetics?

Back 26

Any factor that can affect gene function without change in the genotype. Ex. DNA methylation, chromatin structure, chromatin structure, histone modifications, transcription factor binding - all affect gene expression without changing DNA sequence

Front 27

What is the phase of the cell cycle between two successive mitoses called?

Back 27

Interphase

Front 28

What structural units are solenoids organized into?

Back 28

Loops. 100 kilobase pairs (100,000 base pairs) per loop.

Front 29

What is the structure on which solenoids are stabilized called?

Back 29

Protein scaffold or matrix

Front 30

What is the relative size of the mitochondrial DNA molecules to a human chromosome?

Back 30

Mito DNA molecule is 16 kb (~37 genes).

Human DNA chromosomes 50,000 kb to 250,000 kb (100-2200 genes)

Front 31

What % of DNA encodes proteins?

Back 31

1.5%

Front 32

What % of DNA contains regulatory elements that influence or determine patterns of gene expression?

Back 32

5%

Front 33

How much of the genome is unique DNA?

What is unique/single-copy DNA?

Back 33

Half the DNA of the genome.

DNA whose nucleotide sequence is represented only once.

Most genes represented by unique DNA.

Front 34

What is repetitive DNA?

Back 34

DNA sequence present many times, either perfectly, or with variation.

Front 35

What is a centromere?

Back 35

Tandem repeat sections of DNA which is where sister chromatids are held together and where the kinetochore is formed. Necessary for normal segregation in mitosis/meiosis.

Front 36

What are segmental duplications?

How can they give rise to disease?

Back 36

Duplications of substantial segments of a chromosome.

Genomic rearrangement of duplicated regions can result in the deletion of the region (and the genes) --> disease.

Front 37

What are the stages of the cell cycle?

What happens during each stage?

Back 37

http://en.wikipedia.org/wiki/Cell_cycle#Phases

Front 38

When are the checkpoints in the cell cycle?

Back 38

G1 g2

Front 39

What if damage to the genome is detected at a checkpoint?

Back 39

DnA repair or programmed cell death (aka apoptosis)

Front 40

What structural units of DNA mark the ends of chromosomes?

Back 40

Telomeres, repetitive sections of DNA.

Front 41

What enzyme maintains the ends of chromosomes, ensuring that DNA synthesis includes the ends of each chromosome?

Back 41

Telomerase

Front 42

What is the kinetochore?

Back 42

The centromere, the point at which two sister chromatids are held together, is associated to a number of proteins. This whole thing is known as a kinetochore, and is a structure which microtubules of the mitotic spindle can attach to.

Front 43

What is chromosome segregation?

Back 43

Giving each daughter cell one copy of a chromosome.

Front 44

What are the stages of mitosis? What happens during each stage?

Back 44

http://online.vitalsource.com/books/978-1-4160-3080-5/id/fig2-f10

Front 45

What is the chromosome spread?

Back 45

Visible, condensed chromosomes consisting of their sister chromatids. Happens during prophase, prometaphase, and metaphase.

Front 46

What are the structural names for the center of a chromosome? The short arm? The long arm?

Back 46

center = centromere = primary constriction

short arm = p (petit)

long arm = q

Front 47

How are chromosomes visualized?

Back 47

Treated with trypsin, then stained by the G-banding method. Darkness reflects amount of CG or AT.

Front 48

Which stage of meiosis does recombination occur during?

Back 48

Homologous sections of DNA exchanged between non-sister chromatids of a pair of homologous chromosomes during meiosis I. (Prometaphase)

Front 49

What are the stages of meiosis?

Back 49

http://online.vitalsource.com/books/978-1-4160-3080-5/id/fig2-f15

Front 50

What are the processes by which sperm and eggs are produced?

Back 50

http://online.vitalsource.com/books/978-1-4160-3080-5/id/fig2-f17

Front 51

What is an intron? Exon?

Back 51

Introns are noncoding regions in genes. Exons are the amino acid sequences that give rise to protein structures.

Front 52

What is the name of the sequence that is responsible for the initation of transcription in a DNA strand?

Back 52

The promoter region.

Front 53

Are introns transcribed?

Back 53

Yes, they are initially transcribed into RNA, but they are not found in the mature mRNA.

Front 54

Where does the polyA tail lie and what is its significance?

Back 54

The 3' end of a gene, the end of the mature mRNA sequence.

Front 55

What is the structure of a gene?

Back 55

http://online.vitalsource.com/books/978-1-4160-3080-5/id/fig3-f4

Front 56

What is a psuedogene?

Nonprocessed?

Processed?

Back 56

1. An inactive gene within a gene family, derived by mutation of an ancestral active gene and frequently located within the same region of the chromosome as its functional counterpart (nonprocessed pseudogene).

2. A DNA copy of an mRNA, created by retrotransposition and inserted randomly in the genome (processed pseudogene). Processed pseudogenes are probably never functional.

Front 57

What is the function of noncoding RNA genes and microRNA?

Back 57

The transcribed RNA is the final product of these DNA sequences. This RNA plays important roles in nuclear or cytoplasmic processes, and controls the expression/repression of other genes during development.

Front 58

What is a transcription factor?

Back 58

A large class of proteins that regulates transcription by forming complexes with other TFs and RNA polymerase; those larger complexes bind to the regulatory regions of genes to either promote/inhibit transcription.

Front 59

What direction is RNA synthesized in?

What direction is the template DNA strand read in?

Back 59

5' to 3'

3' to 5'

Front 60

What is the term to describe the transcribed, template DNA strand?

The other, nontranscribed DNA strand?

Back 60

Noncoding, antisense strand.

Coding, sense strand.

Front 61

What modifications are made before a transcribed RNA strand becomes mature mRNA?

Back 61

5' cap. Terminal 5' phosphate removed and GTP, then methyl group added. Protects from attach by ribonucleases.

Polyadenylation - addition of a poly(A) tail to the RNA molecule. Important for nuclear export, translation, and stability of mRNA.

Splicing can happen during transcription or after capping/polyadenylation. Cuts out introns. Allows alternative splicing, so one can make multiple proteins from one DNA sequence.

Front 62

Methionine code

Back 62

AUG - Start message for a ribosome to being translation. Often removed in post-translational modification.

Front 63

Stop codes

Back 63

UAA UAG UGA

Front 64

Degenerate code for codons?

Back 64

Yes. Coding sequence of 3 nucleic acids, each of which has 4 possibilities means 64 possibilities for 20 amino acids. Multiple codes correspond to 1 amino acid.

Front 65

How is mitochondrial DNA processed?

Back 65

RNA polymerase encoded in nucleus sent to mitochondria. Two promoter sequences, one on each strand of the circular genome, initiate transcription. Modified after to generate mRNA, tRNA, and rRNA.

Front 66

CAAT Box

Back 66

Singals the binding site for RNA transcription factor.

Front 67

TATA Box

Back 67

Core promoter sequence. Binding site of general transcription factors or histones (mutually exclusive) and is involved in transcription by RNA polymerase. Mutations --> Reduced transcription.

Front 68

What is an enhancer?

Back 68

A sequence element that can act as a distant (can be several kbs or more) from a gene to stimulate transcription.

Front 69

LCR

Back 69

Locus control region - a DNA domain, situated outside a cluster of structural genes, responsible for the appropriate expression of the genes within the cluster.

Front 70

What dinucleotide pattern signals for splicing?

Is it in the intron, or the exon?

Back 70

GT/GU in the intron are the start of splicing.

AG in the end of the intron at the end of splicing.

Front 71

What sequence signals for a poly-A tail?

Back 71

AAUAAA 20 bp upstream of the polyadenylation site.

Front 72

What is somatic rearrangment?

What is its purpose?

Back 72

Rearrangement of DNA sequences in the chromosomes of lymphocyte precursor cells.

Generates antibody and T-cell receptor diversity. (Can generate 10^11 antibodies from our genome)

Front 73

What is an immunoglobin?

Back 73

Antibodies.

Two heavy (H) chains. Two light (L) chains. Each chain has a constant (C) and a variable (V) region. C region determines type of antibody. V region forms the antigen-binding site and determines specificity.

Front 74

What is allelic exclusion?

Back 74

In immunogenetics, the observation that only one of the pair of parental alleles for each H chain and L chain of an immunoglobulin molecule is expressed within a single cell

Front 75

What is chromosomal aneuploidy?

Back 75

Having an abnormal number of chromosomes. (an extra one, or being deficient one)

Front 76

What are the two causes of gene mutations?

Back 76

Error introduced during DNA replication and mutations arising from a failure to repair DNA after damage.

Front 77

How common are base pair mutations during replication under normal scenarios?

Back 77

Less than one base pair mutation per cell division. (6*10^9 base pairs of DNA / 10^-10 errors per bp during replication)

Front 78

What are the three types of mutations?

Back 78

Substitution (point mutation)

Insertion/deletion (frameshift mutations)

Front 79

What is the most common type of mutation in human genetic disease?

Least common types?

Back 79

http://online.vitalsource.com/books/978-1-4160-3080-5/id/B9781416030805_tbl0001

Front 80

What is the difference between a missense and a nonsense mutation?

Back 80

Both are single nucleotide substitutions (point mutations).

Missense mutations alter the 'sense' of the coding strand of a gene by specifying a different amino acid.

Nonsense mutations introduce stop codons in place of normal codons, yielding highly unstable mRNA, and if translated, a protein so unstable that it is quickly degraded.

Front 81

What is a transition substitution?

Back 81

Substituting one purine for another, "A for G". Can be done with pyrimidines as well.

Front 82

What is a transversion substitution?

Back 82

Substituting a purine for a pyrimidine, or vice versa.

Front 83

Why is the CG doublet a hotspot for mutation?

Back 83

C is methylated for DNA repair, especially when it is 5' to G. When C undergoes spontaneous deamination and becomes T, C-->T or G-->A transition mutations will be overlooked by DNA proofreading.

More than 30% of single nucleotide substitutions are of this type, 25x more common than any other type.

Front 84

What is the cause of contiguous gene syndrome?

Back 84

The microdeletion of chromosomal DNA extending over 2 or more genes/loci.

Front 85

What is a LINE sequence?

Back 85

A family of interspersed, repetitive sequences that may be transcribed into a special RNA. This RNA, when reverse transcribed, generates a DNA sequence that can insert itself into different sites in the genome.

Front 86

What does 'unequal crossing over' refer to?

Back 86

A type of gene duplication even that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in meiosis. The homologous sequences are not paired precisely, leading to mutations.

Front 87

What is a dynamic mutation?

Back 87

A simple trinucleotide repeat which is transcribed, but not translated is expanded during gametogenesis. This portion of the gene interferes with transcription, mRNA processing, or translation.

Front 88

How to determine the frequency of mutation per locus per generation?

Back 88

Measure the incidence of new, sporadic cases of an autosomal dominant, or x-linked genetic disease that has an easily identifiable phenotype.

Front 89

What is genetic polymorphism?

Back 89

One interbreeding population.
Discrete, different genetic forms.
Not maintained by mutation.

>1% genetic polymorphism
<1% rare variant

Front 90

What is allelic heterogeneity?

Back 90

The presence of multiple alleles at one locus.