II: DNA DOUBLE HELIX

SAS 6 TOPIC (BIOCHEMISTRY)

TRUE

TRUE OR FALSE

Only pairs involving one small base (a pyrimidine) and one large base (a purine) correctly “fit” within the helix interior

A–T (2 H-bond) and G–C (3 H-bond)

hydrogen-bonding possibilities are most favorable for the _________________ pairings, and these two combinations are the only two that normally occur in DNA.

complementary

The pairing of A with T and that of G with C are said to be _________________.

3’ A- C- G- T- T- C 5’

5’ T- G- C- A- A- G 3’

WHAT IS THE COMPLEMENTARY BASE STRAND OF DNA?

3’ A- C- G- T- T- C 5’

5’ U- G- C- A- A- G 3’

WHAT IS THE COMPLEMENTARY BASE STRAND OF RNA?

hydrophobic in nature

. Purine and pyrimidine bases are ___________________.

London forces

Purine and pyrimidine bases are hydrophobic in nature, so their stacking interactions are those associated with hydrophobic molecules—mainly _________________.

B-DNA

- the most common or prinicipal form of the DNA double helix that occurs in nature.

A-DNA

a form of a DNA double helix characterized by having fewer residues per turn and major and minor grooves with dimensions that are more similar to each other than those of B-DNA. Found as artifact of DNA preparation or dehydrated B-DNA samples

Z-DNA

has been seen to occur naturally under certain circumstances. Has zigzag look of the phosphodiester backbone when viewed from the side.

RIHT HANDED

Helix turns OF BOTH of A-DNA & B-DNA

LEFT-HANDED

Helix turns of Z-DNA (ZIGZAG)

Narrow and Deep

Major grove A-DNA

Wide and Deep

Major grove B-DNA

Flat

Major grove Z-DNA

Wide and Shallow

Minor grove A-DNA

Narrow and deep

Minor of groove of BOTH B-DNA & Z-DNA

11

Number of base pairs per helical turn A-DNA

10

Number of base pairs per helical turn of B-DNA

12

Number of base pairs per helical turn of Z-DNA

A-DNA

present mostly In DNA-RNA hybrids or RNA-RNA double stranded regions

B-DNA

present mostly In Chromosomal DNA

Z-DNA

PRESENT MOSLY IN In sequence of alternating purines and pyrimidines (ex. polyGC like dCpGpCpGpCpG)

chromatin

Each chromosome in the nucleus of a eukaryote contains one long, linear molecule of dsDNA, which is bound to a complex mixture of proteins (histone and non-histone) to form __________________.

Prokaryotic organism

typically contains a single, double-stranded, supercoiled, circular chromosome.

nucleoid

Each prokaryotic chromosome is associated with non-histone proteins that can condense the DNA to form a ________________________.

plasmids

species of bacteria (prokaryotes) also contain small, circular, extrachromosomal DNA molecules called __________________.

Plasmid DNA

carries genetic information and undergoes replication that may or may not be synchronized to chromosomal division.

circular

Prokaryotic DNA is __________________.

negative supercoils

If the strands are underwound they form

positive supercoils

If they are overwound, they form

TOPOISOMERASE

Enzymes that are involved in changing the supercoiled state of DNA.

Class I topoisomerases

cut the phosphodiester backbone of one strand of DNA, pass the other end through, and then reseal the backbone.

Class II topoisomerase

cut both strands of DNA, pass some of the remaining DNA helix between the cut ends, and then reseal.

DNA gyrase

is a bacterial topoisomerase that introduces negative supercoils into DNA

NEGATIVE SUPERCOILING IN RIGHT-HANDED HELIX SUCH B-DNA

LEFT HANDANDED (COUNTERCLOCKWISE) ANALOGOUS TO _______________________.

POSITIVE SUPERCOILING IN RIGHT-HANDED HELIX SUCH B-DNA

RIGHT HANDANDED (CLOCKWISE) ANALOGOUS TO _______________________.

Eukaryotic DNA

complexed with a number of proteins, especially with basic proteins that have abundant positively charged side chains at physiological (neutral) pH.

histones

The principal proteins in chromatin are the _____________________.

lysine and arginine

H1, H2A, H2B, H3, and H4. All these proteins contain large numbers of basic amino acid residues, such as ____________________.

H1

In the chromatin structure, the DNA is tightly bound to all the types of histones except__________.

Chromatin

a complex of DNA and protein found in eukaryotic nuclei

Histones

basic proteins found complexed to eukaryotic DNA

Nucleosome

a globular structure in chromatin in which DNA is wrapped around an aggregate of histone molecules

Chromosomes

is an individual DNA molecule bound to a group of proteins.

75% BY MASS DNA

85% BY MASS PROTEINS

CHROMOSOMES: Typically, ____ by mass DNA and ______by mass proteins

TELOMERE

complexes of DNA plus proteins (collectively known as shelterin) located at the end s of. linear chromosomes. Used to maintain structural integrity that protect the chromosomes.