DNA, chromosomes, and the nucleus. DNA Packaging (cell biology, ch. 18)

Medel 1866

-worked with pea plants
-proposed that "discrete factors" were responsible for inheritance of traits
-factors work in pairs and separate during meiosis

Friederich Meischer 1868

-documented the presence of "nuclein" later known as nucleic acid

Griffith 1928

-worked with Pneumococcus and documented transformation in bacteria
-called the unknown substance "transformation principle

Avery and McLeod and McCathy 1944

used proteases, DNase and RNase to show that DNA was the transformation principle

Erwin Chargaff 1944-52

-studied base composition of DNA from various sources
-showed that the ratio A=T and C=G known as the Chargaff rules

Harshey and Chase 1952

used Bacteriohage to confirm DNA as the genetic material

Watson and Crick 1953

-built a model for DNA structure
-used X-ray diffraction data from Wilkins, Rosalind and date from Chargaff
-offered insight into how DNA replicates itself

DNA is a polymer of units called


Composition of a nucleotide

-nitrogen base
-phosphate group

Nitrogen Bases of DNA

-The Pyrimidines:
-Thymine (found in DNA only)
-Uracil (found in RNA only)

The Structure of DNA

The Sugar-Phosphate Backbone and DNA Double Strand

The sugar phosphate backbone

-3' OH of sugar is linked to 5' PO4 of the next nucleotide by a phosphodiester bond
-The bases are on the inside linked to the 1' OH of the sugar
-This forms a linear strand molecule of DNA

DNA double strand

-two strands side by side held by H-bonds
-base pairs are C=G and A=T
-double strand DNA is coiled into a double helix (coiled staircase)

The groves of DNA

-Major Grove- twisting of DNA. They are the sites for binding of regulatory proteins
-Minor Grove- space between the two strands in the double helix

Forms of DNA



left handed conformation and is the main form of DNA


right-handed conformation and is shorter and thicker than B-DNA


left-handed conformation and has a zig-zag pattern

Genetic Information in DNA

sequence of bases (ATCATTG�) on the DNA is the actual code of the genetic information

Genetic information is organized into

units called genes

In eukaryotes, genes are located on

the chromosomes


portion of DNA that code for specific polypeptide or RNA


the total complement of genes in a cell or living organism

Mechanism of DNA synthesis

-copying of two strands
-two strands must separate to provide template for the synthesis of sister strands
-new strand stays together with the template strand

What is the enzyme for DNA synthesis?

DNA polymerase

What was used to differentiate new DNA from old DNA?

Heavy N15 and light N14 nitrogen

In prokaryotic DNA, replication begins at

only one origin of replication

In eukaryotes, replication starts at

multiple sites

Bidirectional Replication

DNA replication progresses in both directions

The proteins/enzymes of DNA replication

1. Helicase
2. Topoisomerase
3. Single-strand-binding proteins
4. DNA polymerase
5. Primase
6. Ligase

Why do cells replicate their DNA?

to pass the genetic information to new cells during cell division

When do cells replicate their DNA?

just before cell division

UV absorption properties of DNA

-max absorption is at wavelength 260nm
-ssDNA absorbs more than dsDNA

Thermal properties of DNA

-When DNA is heated, it denatures or melts causing the two strands to separate
-When cooled, it renatures or anneals
-Tm is the melting temperature

Why do eukaryotes have lots of DNA?

most of it (40%) consists of repeated sequences

Britten and Kohne 1960s

used DNA renaturation studies to show the presence of two kinds of DNA

Types of DNA

-single copy DNA
-tandemly repeated DNA

Single copy DNA

sequences that occur as one copy in the genome (mostly protein coding genes)

Tenderly Repeated DNA

type of DNA multiple copies are arranged next to each other in rows

Simple Repeat Units

-short, about 10 base pairs
-located around the centromere

Minisatellite DNA

the number of repeats per site is 10^2 to 10^5

Microsatellite DNA

the repeat until is 1-4 bp and the number of repeats is 10-100 per site

Satellite DNA is used for

DNA fingerprinting

Interspersed Repeated DNA is located

scattered around the genome

DNA Length and Size of Nuclei

the total length of DNA is many times the diameter of the nucleus

In human cells, DNA can wrap

15,000 times around the cell

In E.Coli, DNA can wrap

400 times around the cell

Packaging of DNA in prokaryotes

-bacteria chromosomes (single circular DNA molecule in nucleoid)
-plasmid DNA (small circular DNA molecules in bacterial cells)
-histone-like proteins

Packaging of DNA in eukaryotes

-chromatin (diffused in non-dividing cells)

Nuclear Proteins

-non-histone nuclear proteins
-histone proteins

Non-Histone Nuclear Proteins

-found in the nucleus
-regulate the functions of the DNA

Histone Proteins

-organize and package the DNA in the nucleus

Types of Histones

-H2A and H2B

What is a nucleosome?

-beadlike chromatin structure with a diameter of about 10nm
-basic unit of chromatin structure
-short DNA segment wound 2.5 times around histone octamer

What is a histone octamer?

it is an octamer of histones found at the center of nucleosome core particle
-consists of 2 copies of each of the four core histone proteins (H2A, H2B, H3, H4)

Linker DNA

segment of DNA linking individual nucleosomes

What is the importance of the nucleosome?

helps to pack the DNA in a small space

What is the hierarchical level of chromatin organization?

-nucleosome strings
-looped domains

What are the non-histone proteins?

-regulatory proteins (control gene activity)
-enzymes (transcription and recombination, for DNA repair)

Examples of non-histone proteins

-Helix-turn-Helix Motif
-Zinc-Finger Motif
-The Leucine Zipper

Types of Chromatin



-dense staining areas of the nucleus with tightly packaged DNA
-genes are inactive


-lightly stained are of the nucleus
-rich in active genes

DNA Supercoiling

helps to compact the DNA in a small space
-consists of loops

What is Toposiomerase?

an enzyme that induces supercoiling of DNA during replication

What is relaxed DNA?

DNA that is not supercoiled

Organization of Chromatin in a Cell

-the chromosome
-chromosome numbers

A man has how many chromosomes?

46 chromosomes
-22 pairs of autosomes
-X/Y chromosomes