BIOL 3000 - Exam 3 - DNA Characteristics + Replication

How many PAIRS of homologous chromosomes must fit inside a nucleus? How many TOTAL chromsomes?

23 pairs, 46 chromosomes

What is the estimated amount of base pairs possible?

6 billion

There is approx. _____ meters of DNA packed inside one cell.

2 meters (6.5 ft)

A combination of DNA and proteins (histones) inside the cell

Chromatin

type of protein specifically involved in forming chromatin

Histones

List the two types of chromatin structures present within a chromosome.

1. euchromatin

2. heterochromatin

Euchromatin

Type of "active" chromatin with a loose structure. It is the most active chromatin pattern out of the two types because the DNA is easily accessible/readable by proteins and enzymes (ex. RNA polymerase).

Heterochromatin

Type of "silent" chromatin pattern with a tightly packed structure and genetically inactive sequences. Enzymes and proteins cannot access the DNA because of its tightly packed nature.

List the two types of heterochromatin.

1. constitutive heterochromatin

2. facultative heterochromatin

constitutive heterochromatin

Type of heterochromatin where the centromere is ALWAYS heterochromatic (tightly packed), therefore it cannot be accessed/read at ALL

facultative heterochromatin

Type of heterochromatin where the centromere can change between being heterochromatic (tightly packed) and euchromatic (loosely packed), so it can SOMETIMES be read (only when it is in a euchromatic state).

Which two models have been used to explain the association of DNA and protein (AKA chromatin as a whole)?

1. Folded Fiber Model

2. Nucleosome Model

folded fiber model

Proposed that there were whole mounts of white blood cells. It found few/no free fiber ends and concluded that each chromatid must consist of a single fiber (like a ball of string). Said that replication occurred from each end toward the centromere.

Proposed Type A and Type B DNA fibers.

Type A Fiber

Type of DNA fiber in the folded fiber model that was said to be 1-10 nm (ratio of 6:1)

Type B FIber

Type of DNA fiber in the folded fiber model that was said to be 20-25 nm (ratio of 10:1)

The folded fiber model said that extensive folding of Type ___ formed a chromatid.

Type B

Nucleosome Model

Proposed multiple levels of compaction, with DNA being wrapped around histones to form nucleosomes

Localized areas of transcription and was an overall better fit for protein biosynthesis.

Nucelosome

Type of structure made of DNA wrapping around core histones (proteins)

List the two classes of histones

1. core histones

2. Linker histones

Histone core

Histone cluster with DNA (1.5 turns) around it. Made of core histones and linker histones together

The histone core is very ________ charged, while DNA is very ________ charged.

positively, negatively

Core histones

Highly conserved during evolution. Combine to form the histone core. VERY BASIC in charge (approx. 25% lysine and arginine).

Which histone is referred to as a "housekeeping protein" and why?

Core histone. Called this bc H2A, H2B, H3 and H4 are always turned on and necessary for properly compacting DNA

What is meant by "core histones are highly conserved during evolution"?

They always have the same sequence and structure throughout the body

List the core histone proteins.

1. H2A

2. H2B

3. H3

4. H4

How many core histones are in each nucleosome? How many total proteins make up the core histone?

2 of each = 8 total proteins!

2 H2A, 2 H2B, 2 H3, 2 H4

Linker histone

Tissue specific expression and NOT highly conserved. Loosely associated with the histone core.

What proteins form the Linker histone?

H1

What is meant by "linker histones are NOT highly conserved"?

They have different sequences throughout the body

Is the linker histone part of the histone core?

No, it is NOT part of the histone core, but it is part of the nucleosome

How many base pairs of DNA wrap around the histone core to form the nucleosome?

146 base pairs

How many base pairs link one nucleosome to the next? What are these base pairs called?

54 base pairs. Linker DNA

What part of the histone core, in relation to core histones helps determines the structure of chromatin? How?

Histone tails. They they can make chromatin more relaxed (euchromatin) or more condensed (heterochromatin), thus regulating the accessibility of DNA for transcription, replication, etc.

Nucleosomes reduce DNA length by _____ times.

7

Describe the arrangement of nucleosomes.

Linear. They look like beads on a string.

What is the approximate fiber diameter of each length of nucleosomes ("string of beads") that packs into the next chromatin structure?

10 nm fiber

Solenoid Model

Supercoiling DNA model where a structure of multiple strings of nucleosomes packed together to form chromatine. Uses helical coiling of 10 nm fibers consisting of 6 nucleosomes stacked on top of each other in a helical arrangement to form one turn of this model. Nucleosomes have a uniform orientation. DNA has a 30 nm nucleosomal arrangement overall.

Considered the next step of chromosome formation after nucleosome formation.

What structures of the nucleosome/which histone allows the nucleosomes to pack together in a ring-like formation to form the solenoid structure?

H1 histone/Linker histone

How does the H1 histone/Linker histone work to bind nucleosomes together and form the solenoid? How much does it compact the DNA?

H1 binds to both linker DNA and the DNA wrapping around the histone (146 base pairs) and induces tighter DNA wrapping around histones to form the solenoid complex.

Compacts it by 40x.

Adding ___________ induces compaction of DNA into the solenoid structure.

Histone H1

Zigzag model

Forms a chromatin structure using nucleosomes. Nucleosomes appear to be stacked in an nonuniform, zigzag pattern.

The DNA backbone is not flexible enough to bend between nucleosomes, so DNA CANNOT BEND in this structure. Allows more compaction than solenoid model.

Uses straight linker DNA to connect opposite nucleosomes.

T/F: experimental results show that both solenoid and zigzag topologies may both simultaneously be present in chromatin fiber

True

Condensed chromatin loops

Last stage of chromosome formation. Has a metaphase chromosome structure. DNA is 700 nm. Spiral scaffold composed of topoisomerase II and 15 non-histone proteins. Heterochromatin is most present and compact here.

List the different phases of the cell cycle.

1. G1 Phase (cell grows)

2. S Phase (cell replicates)

3. G2 Phase (cell grows prepares for mitosis)

4. Mitosis

Karyotype

A display of the chromosome pairs of a cell. Arranged by chromosome size, centromere position, and whether the chromatin is heterochromatin vs euchromatin.

Complexity

the intricate ways in which genetic information is organized, regulated, and expressed, leading to the diverse traits and functions seen in organisms.

What defines complexity within organisms?

The number and type of cells and the degree of cellular organization.

Organisms have a _________ building of complexity. They build upon each other from atoms to cells to living things.

hierarchial

Does the amount of DNA in a genome correlate with the complexity of the organism?

he size of the genome is unrelated to the metabolic, developmental, and behavioral complexity of an organism

SO, they are NOT correlated

WHY does genome size alone not correlate with complexity?

Bc of "junk DNA". A majority of organisms with a large amount of DNA use very little of it, while the majority of it goes to waste.

Ex. flatworms

C-value paradox

States that genome size (INCLUDES "junk DNA" AND coding DNA) does not correlate with organismal complexity.

the Onion Test

Test that showed that onion has 5x more DNA than humans, but that does not make it more complex than humans.

G-value Paradox

The number of protein-coding genes ALONE does not correlate with organismal complexity.

Does NOT include junk DNA

Why are humans actually considered to be more advanced than an onion?

While onions may have more DNA, than humans, we can do more with our DNA than onions (ex. have the ability to splice our genes, can make more proteins with fewer material), so we are more advanced

List the 3 types of DNA in the genome

1. Highly repetitive DNA sequence (HR)

2. Moderately repetitive DNA sequence (MR)

3. Single Copy DNA sequence (Unique)

What percentage of the human genome is comprised of highly repetitive DNA sequences (HR)?

10%

In which regions of the genome is highly repetitive DNA typically found?

Heterochromatin/'non-coding' DNA regions

What is an example of highly repetitive DNA?

Alpha satellite DNA

What is alpha satellite DNA?

Type of repetitive DNA with a high order of repeated base pair sequences.

What is formed when repeated base pair monomers come together in alpha satellite DNA?

A higher order repeat (HOR).

How many monomers might a higher order repeat (HOR) consist of?

10-20 monomers.

How many times can a higher order repeat (HOR) be repeated?

Hundreds or thousands of times.

What do multiple higher order repeats (HORs) form in alpha satellite DNA?

An HOR alpha satellite array.

Anything not in the repeated base pair sequence of alpha satellite DNA is _________

monomeric

What is the range of functions for HR DNA?

Ranges from structural and organizational roles to junk DNA

T/F: HR DNA is mostly found around telomeres and centromeres, but can be found anywhere in the chromosome

true

What percentage of the human genome is comprised of moderately repetitive DNA (MR)?

30%

Where is moderately repetitive DNA (MR) primarily located in the human genome?

Scattered throughout euchromatin/'coding' areas.

What is the average size of moderately repetitive DNA (MR) sequences?

300 bp

How many copies of moderately repetitive DNA (MR) can be present in a genome?

Between 10 and 10^5 copies

What type of genes does moderately repetitive DNA (MR) include?

'Redundant' genes

What is an example of moderately repetitive DNA?

Microsatellites

Genes that you need in MASS quantities to operate the cell, ex. histones, RNA, proteins.

Redundant genes

Type of DNA strand with short repeated sequences. Has useful genetic markers as they tend to be highly polymorphic.

Microsatellites

List the 3 types of microsatellites.

1. di

2. tri

3. tetra

Microsatellites occur through a mutation known as?

Slippage recognition

List 3 functions of microsatellites in research.

1. used to sequence human genomes

2. used as markers for certain disease conditions

3. primary markers for DNA testing in forensic cases

What is another name for single copy DNA?

Unique DNA

What percentage of the human genome does single copy DNA comprise?

1-5%

Where is single copy DNA primarily found?

In euchromatin/'coding' areas

What do single copy DNA sequences code for?

Proteins that are not always needed

How many protein-coding genes are contained in single copy DNA?

20,000

What is the copy number of single copy DNA per gene?

Single or low copy number

If HR, MR, and Unique DNA add up to form 45% of the genome, what is the other 55% made from?

It is unknown

Gene

The basic and functional unit of heredity. Sequence of unique nucleotides (genotype) that carry the genetic information which is to be expressed (phenotype).

"Instruction manuals for our bodies"

Every person has ____ copies of each gene - one from mom, one from dad

2

> ______% of the number of genes are the same in ALL people. < _____% of the total number of genes contribute to each person's unique physical features

> 99%, < 1%

DNA sequence that gives rise to an RNA molecule

Molecular level gene

transcriptional unit

A segment of DNA that is transcribed into RNA as a single molecule. It encompasses all the necessary elements required for the transcription process, including promoters, terminators, coding sequences, and regulatory sequences.

What are the two coding areas of the transcribed region of RNA (not mRNA)?

1. exons

2. introns

Exon

"Coding sequence" of RNA = phenotype. They are both transcribed and translated.

Intron

"Intervening sequence" of RNA = do NOT code for phenotypes. They are transcribed from DNA, but not translated because they are removed from RNA --> mRNA

List the flanking regions of the transcribed region of RNA

1. 5' untranslated region

2. 3' untranslated region

5' untranslated region

Flanking region where mRNA is directly upstream from the initiation codon, so it is not translated to mRNA

3' untranslated region

Flanking region where mRNA immediately follows the translation termination codon

Promoter

DNA sequence onto which transcription machinery binds and initiates transcription. Includes TATA box.

TATA Box

Highly conserved DNA sequence of TATA base pairs that serves as the binding site for transcription factors to turn translation on/off. Located about 25-30 bases upstream of transcription site. Part of the promoter region.

Enhancer

A segment of eukaryotic DNA containing multiple control elements. They function by binding specific proteins, such as transcription factors, to increase the transcription of a target gene, often located at a significant distance from the enhancer itself.

List two types of enhancers primarily found on DNA within eukaryotes.

1. CAAT box

2. CG box

CAAT box

Typically required for inducible genes to be produced in large amounts.