Nucleic Acids and Chromatin

Replication

the duplication of DNA

Transcription

copying of the DNA sequence information into RNA

Translation

information in mRNA molecules is translated during polypeptide chain synthesis

Genome

the complete set of an organism’s DNA
is the same in every cell of an organism

Transcriptome

the complete set of mRNA molecules that are produced from the genome within a cell at a particular time

varies tremendously over time and between cells in an organism

Proteome

the complete set of proteins produced within a cell
varies over time and between cells in an organism

linear polymers of nucleotides

What are nucleic acids?

storage of information

What is the purpose of Deoxyribonucleic acid (DNA)?

transmission of information

What is the purpose of Ribonucleic acid (RNA)?

polymers; nucleotides

DNA and RNA are _____ whose monomer units are called ______.

a five carbon sugar (ribose or deoxyribose)
a weakly basic nitrogen base
at leas on phosphate group

What are the three components of a nucleotide?

a base covalently linked to a (deoxy)ribose = base + sugar

What is a nucleoSide?

a nucleoside esterified to one or more phosphate groups = base + sugar + phosphate

What is a nucleotide?

purines and pyrimidines

What are the two major classifications of bases?

Adenine and Guanin

Which bases are purines?

Cytosine, Thymine, Uracil

Which bases are pyrimidines?

nucleoside monophosphate

What does NMP stand for?

nucleoside diphosphate

What does NDP stand for?

nucleoside triphosphate

What does NTP stand for?

the 5’ end

the nucleotide with a free 5’-phosphoryl group is called:

the 3’ end

the nucleotide with a free 3’-hydroxyl group is called:

nucleases

enzymes that cleave the phosphodiester bonds between the nucleotide subunits of nucleic acids

• DNases (DNA substrates)

• RNases (RNA substrates)

exonucleases

nucleases that cleave nucleotides from the end (exo) of a polynucleotide chain

endonucleases

nucleases that cleave internal phosphodiester linkages

Watson and Crick in 1953

Who proposed the 3D model of DNA and when?

a right-handed double helix

What is the overall shape of DNA?

two helical chains

How many strands make up DNA?

they are complementary to each other

How are the two DNA strands related?

they run in opposite directions (one 5’ to 3’ and the other 3’ to 5’)

What does it mean that DNA strands are antiparallel?

inside the helix

Where are the nitrogenous bases located in DNA?

they are stacked with planar rings close together and perpendicular to the axis

How are the bases arranged inside the helix?

guanine pairs with cytosine an adenine pairs with thymine

Which base pairs are found in DNA?

three hydrogen bonds

How many hydrogen bonds are between G and C?

two hydrogen bonds

How many hydrogen bonds are between A and T?

on the outside of the helix

Where is the sugar-phosphate backbone located?

it is hydrophilic so it interacts with the aqueous environment

Why is the DNA backbone on the outside of the helix?

unequal; the major; the minor

Stacking of the base pairs creates two groves of ____ width on the surface of the duplex, ___ _____ and ___ _____ grooves

hydrophobic interactions

burying purina and pyrimidine rings in the double helix interior

van der Waals forces

stacked base pairs

hydrogen bonds

hydrogen bonding between base pairs

charge-charge interactions

electrostatic repulsion of negatively charged phosphate groups is relived by interaction with cations and cationic proteins

it wraps around the histone octamer

How is DNA arranged around a nucleosome?

about one and two-thirds turns

How many turns does DNA make around the histone octamer?

DNA between nucleosomes

What is linker DNA?

no, it is variable

Is the length of linker DNA constant?

about 20-60 base pairs

What is the typical length range of linker DNA?

nucleosome “bead”

DNA-hitsone complexes found along a string of double-stranded DNA

double-stranded DNA

What does the “string” in the nucleosome model represent?

histones H2A, H2B, H3, and H4

What proteins make up a nucleosome core?

two copies of each (H2A, H2B, H3, H4)

How many copies of each histone are in a nucleosome?

approximately 147 base pairs

How much DNA is wrapped around each nucleosome?

histones

DN is coiled around proteins called":

Nucleosome

a core of eight histone molecules around which the DNA helix is wrapped

chromatins

Nucleosomes are further condenses into:

Chromosomes

Chromatin fibers are organized into loops that provide the superstructure of:

Chromosomes

darkly stained, rod-shaped bodies in the nuclei of dividing cells

a very long DNA molecule and its associated proteins; it stores and transmits genetic information

Chromatin

the complex of DNA and proteins that comprises the eukaryotic chromosomes

the structural building block of chromosomes

What is chromatin in simplified terms?

23

How many pairs of chromosomes do human cells contain?

Messenger RNAs (mRNAs)

carry genetic information from the gene to a ribosome, where the corresponding protein can be synthesized

Ribosomal RNAs (rRNAs)

a class of RNA molecules serving as components of ribosomes, accounts for ~80% of RNA in cells

Transfer RNAs (tRNAs)

carry activated amino acids to ribosomes for polypeptide synthesis (73-95 nucelotides long)

Small Nuclear RNAs (snRNAs)

a class of short RNAs (100-200 nucleotides long), present in the nucleus and involved in pre-mRNA splicing

long non-coding RNAs (lncRNAs)

non-protein coding RNAs longer than 200 nucleotides that may function in gene regulation

Small interfering RNAs (siRNAs)

a class of double-stranded RNA molecules, 20-25 base pairs in length, interfering with the expression of specific genes

MicroRNAs (miRNAs)

small non-protein coding RNA molecules (about 22 nucleotides in length) that function in regulation of gene expression

5’ 7-methylguanine cap of mRNA

7-methylguanine is joined to the 5’ of eukaryotic mRNA in a 5’-5’ triphosphate linkage by a capping enzyme