BIOL 3000 Exam 3

Chromatin

DNA and protein complex that compacts DNA

T or F: Chromatin is only found in eukaryotes

True

Histones

Proteins found in chromatin, provides structure, shape and gene regulation of chromosomes

Euchromatin

Lightly packed chromatin rich in gene concentration. Is most often under active transcription

Heterochromatin

Tightly packed chromatin consisting mainly of genetically inactive sequences

In chromosomes, when gene transcription occurs, what is likely the chromatin formation?

Euchromatin

Facultative heterochromatin

Gene silencing; Barr bodies

The condensed, inactive X chromosomes found in females is an example of

Barr bodies

Constitutive heterochromatin

VERY gene poor; centromeres and telomeres

Folded fiber model

DNA and protein model that proposed a single, long chromatin fiber makes up each chromosome

Folded fiber model: Type A fiber

Chromatin fiber 1-10 nm. DNA packing ratio is 6:1

Folded fiber model: Type B fiber

Chromatin fiber 20-25 nm. DNA packing ratio 10:1

According to the folded fiber model, what type of fiber is folded more tightly?

Type B

According to the folded fiber model, extensive folding of Type __ forms a chromatid

B

Nucleosome model

Most accepted DNA packing model. Proposes nucleosomes to be the packing unit of eukaryotic chromatin, made up of a double DNA strand wrapped core histones.

Which DNA packing model is better fit for protein biosynthesis?

Nucleosome model

Which of the following statements is true regarding core histones? I. H2A, H2B, H3, and H4 are core histones II. They were highly conserved during evolution III. Have a very basic charge due to being made of cystine and arginine IV. Consist of approximately 120 amino acids each

I, II, and IV

Which of the following statements is true regarding linker histones? I. Consists of 200 animo acids II. They were highly conserved during evolution III. Tissue specific expression IV. Closely associated with core particle

I and III

H1 is in what histone class?

Linker histones

How many core histones are in a nucleosome?

8, two of each type

How many linker histones are in a nucleosome?

1

What is the importance of 10 nm fiber in nucleosome formation?

They are the primary packing of chromatin

Solenoid formation

Helical coiling of 10 nm fibers consisting of 6 nucleosomes

What histone is found in the center of a solenoid, and what is it used for?

H1, used for packing

How does H1 histone work?

Binds linker DNA and 146 bp portion of central core DNA, compacts up to 40x!

Zig Zag model formation

Due to the limited flexibility of DNA, straight linker DNA connects opposite nucleosomes

T or F: both solenoid and zig zag typologies may both simultaneously be present in chromatin fiber

True

Chromatin loops

Higher order of coiling with 300 nm chromatin fiber built around scaffold of topoisomerase II

Chromatin loops share the same level of compaction as...

Euchromatin

Metaphase chromosome

condensed chromatin loops looped around spiral scaffold composed of Topoisomerase II and about 15 non‐histone proteins.

Metaphase chromsosomes have the same level of compaction as...

Heterochromatin

2 nm-10 nm fibers are known as ___ and are found in the ___ phase

DNA and nucleosomes; G1

30 nm fibers are known as ___ and are found in the ___ phase

chromatin; early G2

300 nm fibers are known as ___ and are found in the ___ phase

Chromatin loops; late G2

700 nm fibers are known as __ and are found in the __ phase

condensed chromatin loops; beginning prophase

Chromosomes contain __ nm fibers, and are found in the ___ phase

700; metaphase

What are the phases of DNA condensation?

Nucleosomes > Solenoids > Chromatin Loops > Condensed Chromatin > Chromatin folded around protein scaffold

C value paradox

excess DNA present in genome that does not seem to be essential for development or evolutionary divergence of an organism

G value paradox

Number of genes does not correlate with organismal complexity

Types of DNA in the genome

Highly repetitive (HR), moderately repetitive sequence (MR), unique

Highly repetitive DNA sequences make up _% of the human genome

10

T or F: Highly repetitive DNA sequences are located in euchromatic regions around the centromere/telomere

False, heterochromatic

HR DNA function

Structural and organization to nothing more than junk

Where is HR DNA found?

Present at >10^6 copies per genome

What type of DNA sequence occurs as variable length motifs (5-100 bp) in long tracts of up to 100 Mb?

Highly repetitive

"noncoding/junk DNA" is known as what sequence type?

Highly repetitive

Alpha satellite DNA

consists of 2-30+ repeats of 171 bp tandem repeats, HR DNA

moderately repetitive sequences make up about ____% of the human genome

30

T or F: MR sequences are found throughout the euchromatin

True

Where are Moderately Repetitive sequences present?

Between 10-10^5 copies per genome

MR sequences are about __ bp in size

300

'redundant' genes for histones, and ribosomal RNA and proteins is a trait of which DNA sequence type?

Moderately repetitive

Microsatellite DNA

Variable number of tandem repeats typically occurring in non-coding regions of the genome

Interspersed repetitive DNA

Transposable elements

What are two examples of MR sequences?

Interspersed repetitive DNA and microsatellite DNA

Microsatellites occur through what type of mutation?

Slippage recognition

___ are useful genetic markers because they tend to be highly polymorphic

Microsatellites

Microsatellites are uses as genetic markers for what purposes?

To sequence the human genome, to marker certain disease/conditions, markers for DNA testing in forensic cases

Unique DNA makes up ___% of the human genome

1-5

T or F, Unique DNA sequences are found throughout the heterochromatin around centromeres/telomeres

False, they are found throughout euchromatin (not near centromeres and telomeres!)

"coding DNA regions = GENES" describe what DNA sequence type?

Unique sequences

T or F: about 40,000 protein coding genes can be found in Unique sequences

False, only about 20,000 can be found

Where are unique sequences present?

Single or low copy number per genome

Gene

Sequence of unique nucleotides (GENOTYPE) that carry the genetic information which is to be expressed (PHENOTYPE)

Molecular genes contain which of the following: I. Promoter II. Operator III. Terminator IV. Transcribed Region V. Regulatory Sequence

I, III, IV, and V

Promoter

DNA sequence onto which the transcription machinery binds and initiates transcription

transcribed region

Contains the information that specifies an amino acid sequence

Regulatory sequence

Binding site for regulatory proteins that regulate rate of transcription

Exon

Expressed sequence of DNA; codes for a protein

Intron

Sequence of DNA that is not involved in coding for a protein

Flanking regions

5' untranslated region and 3' untranslated region

5' untranslated region

mRNA that is directly upstream from the initiation codon.

3' untranslated region

section of messenger RNA (mRNA) that immediately follows the translation termination codon

TATA box

highly conserved sequence in DNA serving as the binding site for transcription factor binding.

Which of the following is a core DNA sequence

5'‐TATAAA‐3'

Do promoters or enhancers have a basal level of transcription?

Promoters

Enhancer sequences

CAAT box and GC box

CAAT box

(5'‐GGCCAATCT‐3') consensus sequence that occurs upstream by 60‐100 bases to the initial transcription site

GC box

region of DNA that can be bound with proteins (activators)to activate transcription of a gene or genes

Do promoters or enhancers have a ramped up level of transcription?

Enhancers

Terminators

section of nucleic acid sequence that marks the end of agene or operon in genomic DNA during transcription

What are the types of genes?

Solitary Genes (Unique), Duplicated Genes, Multigene Families, Pseudogenes, and Repeated Genes

Solitary genes (unique)

A single copy of a gene (in haploids, 2 copies in diploids), comprises the bulk of euchromatin

Duplicated genes

Process by which a portion of a chromosome is duplicated resulting in an additional copy of a gene (paralog gene

Paralog gene

A copy of the original gene

In Duplicated Genes, _____ of the two genes may mutate and change the original function of the gene

Either

T or F: Duplicated genes usually occur due to an error during Meiosis

True

Multigene families

Set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions

What gene type(s) are most often located in similar regions of the chromosome?

Multigene families

T or F: Multigene Families are most often used or synthesized at different times

True

Pseudogenes

Dysfunctional relatives of genes that have lost their protein‐coding ability, often the result of multiple mutations within a gene

Repeated genes

Multiple copies of small genes clustered throughout the genome at specific sites

What gene type(s) are present in high copy number?

Repeated genes

T or F: Repeated genes are few times present in a "head‐to‐tail" configuration

False, they are many times present

What are two examples of repeated genes?

genes for tRNA and rRNA

Central Dogma of Molecular Biology

1 GENE (genotype) -> 1 mRNA (intermediate) -> 1 "PROTEIN" (phenotype)

DNA to mRNA is called

transcription

Where does transcription occur?

Cell nucleus in eukaryotes

When does transcription occur?

Either G1/S or G2/M

Template strand

DNA strand that mRNA is built from