Cell Bio Genes

Front 1

how thick is a helical strand of nucleosomes?

Back 1

30-nm

Front 2

composition of nucleosome?

Back 2

core of 8 histones bound to DNA

Front 3

which histone is the linker histone?

Back 3

H1

Front 4

how thick is a nucleosome core?

Back 4

10nm

Front 5

how long is the linker strand of DNA b/w

Back 5

10-90nm

Front 6

Chromatin =

Back 6

DNA + proteins that produce chromosomes

Front 7

what histones make up an octomer?

Back 7

two of each:
1) H2A
2) H2B
3) H3
4) H4

Front 8

What are scaffold proteins?

Back 8

structural, non- histone proteins which help bind together the higher-order structure of chromosomes.

Front 9

how many chromosomes do humans have?

Back 9

46

44 autosomes and 2 sex chromosomes

Front 10

how many autosomes do humans have?

Back 10

44 (22 pairs)

Front 11

how many sex chromosomes do humans have?

Back 11

2 - X or Y

-male XY
-female XX

Front 12

Function of G (Giemsa) Banding of metaphase chromosomes?

Back 12

identify individual chromosomes
1) to assess the karyotype and
2) identify genetic abnormalities

Front 13

Dark bands of chromosomes are:

Back 13

A-T - rich regions

Front 14

define karyotype?

Back 14

the full set of 46 human chromosomes

Front 15

describe FISH:

Back 15

Fluorescence In Situ Hybridization

-chromosome painting via FISH provides a way to specifically identify chromosomal regions

Front 16

Function of Chromosomes?

Back 16

1) Provide a way to pack 2 meters of DNA into ~10 μm. ---10,000:1 packing ratio.

2) Provide a way of organizing genes so that their expression can be regulated.

3) Provide structures to assist DNA replication and partitioning during cell division
a. origin of DNA replication
b. centromere for mitotic segregation
c. telomere allows replication of linear DNA without loss of ends

4) Allow occasional transfers of genetic information and duplications of genes - evolution vs. genetic diseases.

Front 17

what is an autosome?

Back 17

-a chromosome that is not a sex chromosome
-exist in pairs
-both pairs always active

Front 18

what is a metaphase chromosome?

Back 18

- after replication and during cell division
- 2 sister chromatids
- chromatin is condensed
- gene expression is inhibited i think
-p arm (petite) and q arm

Front 19

what is interphase chromosome?

Back 19

-chromosomes in between cell division
-chromatin is dispersed
-gene expression proceeds
-no distinguishable chromosome structures!

Front 20

what is a centromere?

Back 20

-Point of contact between sister chromatids.

-composed of non-coding satellite DNA

-Centromeric chromatin is in the form of constitutive heterochromatin— has little expressed genes on it.

-kinetochore assembles here

Front 21

what is a kinetochore and where is it located?

Back 21

-where the spindle fibers connect to the sister chromatids to pull them apart

-assembled on the centromere

Front 22

What is satellite DNA?

Back 22

-the main component of functional centromeres
-non-coding

Front 23

what are spindle fibers?

Back 23

microtubules and protein that conenct to the kinetechore during mitosis and meiosis

Front 24

What is MTOC?

Back 24

-microtubule organizing center (MTOC)
-structure from which microtubules emerge.

Two functions:
1) organization of eukaryotic flagella and cilia
2) organization of the mitotic and meiotic spindle fibers,

Front 25

What are Telomeres?

Back 25

-Found at each end of chromosomes.

-contain repetitive oligomers of high G-C content for a few thousand bp: TTAGGG.

-protect ends chromosome from degradation by cellular nucleases.

-replaced each cell division by telomerase in germ cells and stem cells
----- shortening will make the cell non-viable.

Front 26

what is Telomerase?

Back 26

-a riboprotein (RNA-protein complex) reverse transcriptase that preserves chromosome ends

-adds DNA repeats ("TTAGGG") to 3' end of DNA in telomere regions

-uses RNA as a primer/template.

---Mutant mice which cannot repair telomeres can only reproduce a few generations.!

Front 27

how do cancers affect telomerase?

Back 27

turned back on again in cancers – a possible target of treatment.

Front 28

How does HIV affect CD8+ T lymphocytes?

Back 28

causes them to over-replicate and lose telomere length, contributing to immune dysfunction.

Front 29

In what cells are telomeres inactive?

Back 29

1) cells that divide a limited number of times (most cells in the body)
2) cells that never need to replicate again – post-mitotic cells.

Front 30

What is the function and mechanism of histone acetylation?

Back 30

-activates transcription by opening chromatin
-generates EUCHROMATIN
-unlinks HI

1) positive charge to neutral
2) dissociation from DNA
3) opening of chromatin 30 nm fibers to 10nm fibers
4) transcription can begin.

Front 31

What is the function of histone methylation?

Back 31

inhibits transcription by condensing chromatin.
-generates HETEROCHROMATIN

Front 32

Describe transcriptional control by histones:

Back 32

-Epigenetic mechanism to control gene expression

1) Acetylation of histones - genes ON - it’s the tails that are acetylated and deacetylated!

2) Methylation of histones - genes OFF (usually)!

Front 33

What are Histone Acetyltransferases (HATs)?

Back 33

enzymes that acetylate histones
-HATs act in competition with methylation

Front 34

what recruits HATs during transcription?

Back 34

transcription factors

Front 35

What is the Histone Code?

Back 35

transcription of DNA partly regulated by chemical modifications to histones.

Front 36

what are histone methylases?

Back 36

enzymes that perform histone methylation

Front 37

describe euchromatin

Back 37

-Light staining
-Transcriptionally available
-Acetylated
-10 nM fibers
-Not complexed to histone 1

Front 38

describe heterochromatin

Back 38

Dark staining
Transcriptionally repressed
Highly methylated
condensed 30 nM strands
Complexed to histone 1

Front 39

What is a Barr body

Back 39

inactive X chromosome
highly methylated
condensed and located away from active transcription areas of the nucleus.

Front 40

What is dosage compensation in regards to the X-chromosome?

Back 40

keeps the number of expressed X-linked genes equal for males and females

Front 41

what is a chromatid?

Back 41

one copy of a duplicated chromosome, which generally is joined to the other copy by a centromere

Front 42

what is an allele?

Back 42

Variations in DNA sequence among copies of a gene

Front 43

What are the elements of a coding gene?

Back 43

1) A promoter
2) usually an enhancer - can be far away from the promoter - position independence!

3) Coding region.
----Open Reading Frames, or “ORFs” are the coding part.
--------Exons contain ORF and any untranslated regions (UTRs)

4) often introns
5) a poly(A) signal

Front 44

what is a simple gene?

Back 44

-simple transcription unit
-no introns
-1 version

Front 45

what is a complex gene?

Back 45

-complex transcription unit
-can be spliced into variant mRNA b/c of introns
-allows use of less DNA to make protein variations

Front 46

how does a complex gene promote evolution?

Back 46

-allows evolution to generate new forms by exon duplication.

Front 47

what are solitary genes

Back 47

-represented by only one copy!
-25-50% of all genes are single copy!

Front 48

what are tandem arrays of genes?

Back 48

-gene cluster of multiple copies of the same exact gene
-purpose of increasing the total output of that product (protein or RNA)

-a SPACER separates the genes from each other!

Front 49

what is a spacer?

Back 49

-separates the genes from each other in tandem arrays

Front 50

what is a gene family?

Back 50

-a set of several similar genes
-formed by duplication of a single original gene
---crossovers may be involved
-result in slightly different protein functions

Front 51

define hnRNA

Back 51

heterogeneous nuclear RNA
-RNA before processing

Front 52

define mRNA

Back 52

Mitochondrial RNA
-RNA after processing
-used for translation into proteins

Front 53

define tRNA

Back 53

Transfer RNA
-bring amino acids to ribosomes

Front 54

define rRNA

Back 54

Ribosomal RNA
-part of the ribosome

Front 55

define snRNA

Back 55

Small Nuclear RNA
-variety of RNA that are part of ribonuclear protein complexes that perform various nuclear jobs such as RNA splicing and maintaining telomeres

Front 56

define miRNA

Back 56

Micro RNA
-made by cells to silence genes by destroying mRNA
-are a natural part of the cell’s gene regulation

Front 57

define siRNA

Back 57

Small Interfering RNA
- 20-24 bp double stranded RNA
-RNA Interference!!
---- complementary to specific mRNA, prevent their translation into proteins

Front 58

what % of genome do Exons make?

Back 58

1.5%

98.5% of genome is non-coding

Front 59

What % of the genome is Transposable Elements?

Back 59

45%

Front 60

What are Transposable Elements?

Back 60

DNA that can change its position within the genome

-parasitic DNA
-non-coding
-retroviral origin
-can make new genes by introducing new DNA

Front 61

what are the 2 types of Transposable Elements?

Back 61

1) DNA transposons
-move as DNA
-leave one site and enter another.
-“cut and paste”



2) Retrotransposons
- RNA intermediate
-reverse transcriptase
-original copy remains in original location.
-“copy and paste”!

Front 62

What are the 2 types of Retrotransposons?

Back 62

1) Endogenous Retroviruses
----are genetically structured like retroviruses
----443,000 in humans

2) Non-Retrovirus-Like Retrotransposons
- lack the structure of retroviruses
- most abundant mobile DNA elements in mammals -21% of human DNA

Front 63

what % of DNA is non-retrovirus-like retrotransposons?

Back 63

21%

Front 64

types of Non-Retrovirus-Like Retrotransposons:

Back 64

LINEs – Long Interspersed Elements ~6 kb each
SINEs – Short Interspersed Elements ~100-400 bp each

Front 65

What is Microsatellite DNA?

Back 65

a type of Simple Sequence Repeats

-1-13 bp repeated ≤150 times
- caused by backwards slippage during DNA replication
-interfere with other DNAs/RNAs

Front 66

Why is Microsatellite DNA important?

Back 66

b/c they can cause genetic defects when they occur within genes

Front 67

What is Satellite DNA?

Back 67

-Mostly repeats of 14-500 bp in 20-100 bp arrays
-often in centromeres and telomeres

Front 68

What is DNA fingerprinting?

Back 68

-an assay to identify individuals based on their unique pattern of satellite or ! microsatellite DNA

steps:

1) PCR w/ mix of primers
2) electrophoresis - bands based on variable lengths of the regions between the primer binding sites
3) Some bands match if the DNA donors are related.

Front 69

Why do we care about transposable DNA?

Back 69

1) Disease

---Can inactivate genes or products by disrupting them.
---Can activate genes or their products by inserting near them.

---------Hemophilia can be caused by insertion into clotting factor IX. X-linked: males get this
---------Cancer - inactivation of tumor suppressor genes or activation of oncogenes by insertional mutagenesis

2) Evolution

can duplicate genes and products and modify existing ones.

Front 70

What is RNA Interference?

Back 70

a way to regulate gene expression and defend against viruses
-we use siRNA

Front 71

What are Pseudogenes?

Back 71

non-functional gene family members

Front 72

what are Protein Isoforms?

Back 72

variations of the same protein by splicing

Front 73

What is the human genome project?

Back 73

Large scale sequencing of entire genomes of humans and animals. Uses computers to predict where genes are, how they are organized and how they evolve based on comparative genomics

Front 74

What is NIH ENCODE Project?

Back 74

-Seeks to know map non-coding gene elements, the regulatory sequences - exons, introns, promoters, enhancers, transcription binding sites and histone modifications associated with transcription activation and repression.
-Like the HGP, it’s a large scale project.

It’s rewriting our understanding of genes by showing:

1) Splicing can occur between genes, creating proteins of unexpected structure

2) >80% of the genome contains promoters, enhancers, regions encoding
non-translated RNA.

3) 75% of the genome is transcribed at some point or other.

4) Many DNA variants associated with diseases lie within or near non-coding functional DNA elements.