Module 5 Flashcards by Josh Franco

 A simple polymer composed of four types of chemically related nucleotide subunits
 Carries the hereditary information of the cell

DNA Molecule

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Isolated nuclein in white blood
cell nuclei (1869)

Friedrich Miescher

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Transferred killing ability between types of bacteria (1928)

Frederick Griffith

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Discovered that DNA transmits killing ability in bacteria (1940)

Oswald Avery, Colin MacLeod, and Maclyn
McCarty

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Determined that the part of a virus that infects and replicates is its nucleic acid and not its protein (1950)

Alfred Hershey and Martha Chase

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Discovered DNA components, proportions, and positons (1909-early 1950s)

Phoebus Levene, Erwin Chargaff, Maurice
Wilkins, and Rosalind Franklin

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Elucidated DNA’s three dimensional structure (1953)

James Watson and Francis Crick

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Had his genome sequenced (2008)

James Watson

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 A section of a DNA molecule
 Sequence of building blocks that specifies the
sequence of amino acids in a particular protein

Gene

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Base + Sugar =

Nucleoside

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Base + Sugar + Phosphate =

Nucleotide

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Nucleosides containing ribose are known as

ribonucleotides

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Nucleosides containing deoxyribose are known as deoxyribonucleotides

deoxyribonucleotides

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What are the 3 components of a nucleotide

Deoxyribose sugar, a phosphate group and a nitrogenous base

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 The nitrogen-containing rings of nucleotides

Nitrogenous Bases

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What are the two categories of Nitrogenous Bases

Pyrimidines, Purines

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 have a six-membered pyrimidine ring
 Cytosine, Thymine, Uracil (for RNA)

Pyrimidines

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 Bear a second, five-membered ring fused to the six-membered ring
 Adenine, Guanine

Purines

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What is the proper base pairing for DNA

A pairs with T
G pairs with C

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What is the proper base pairing for RNA

A pairs with U
G pairs with C

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what bonds hold the base pairs together

Hydrogen bonds

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bonds formed between the deoxyribose sugars and the phosphates

Phosphodiester bonds

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 Nucleotides are joined into chains
 This creates a continuous sugar-phosphate
backbone.

Polynucleotide Chain

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has a free phosphate group

5’ end

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has a free hydroxyl group

3' end

The two strands are oriented with opposite polarities- that is they run antiparallel from each other this is also known as

antiparallelism

The twisting of the two strands together creates a wider gap called

the major groove

the narrower gap of two strands is called

the minor groove

important binding sites for CHONS that maintain DNA and regulate gene activity

grooves

thread-like structures inside the nucleus of a cell where DNA is packaged

Chromosomes

segments of DNA that contain the instructions for making a particular protein

Genes

large excess interspersed DNA

junk DNA

the bead part of chromatin

nucleosome

* The first and most fundamental level of chromatin packing *contains: 1. Core particle 2. Linker DNA

Nucleosome

Links nucleosome core particles

Linker DNA

DNA strand (147 nucleotides long) wrapped around a protein core of histone octamer (composed of 8 histone proteins)

Core Particle

helps pull nucleosomes together and pack them into a more compact chromatin fiber

Histone H1

brings together parts of the DNA sequence within the same long DNA molecule to form the overall “loop-ome” structure

CTCF

protein machines that use the energy of ATP hydrolysis to change the position of the DNA wrapped around nucleosomes, making the DNA either more accessible or less accessible to other proteins in the cell

Chromatin-remodeling complexes

* the most highly condensed form of interphase chromatin * about 10% of an interphase chromosome * concentrated around the centromere region and in the telomeres

Heterochromatin

* Has more decondensed state than heterochromatin

Euchromatin

* Aggregate of DNA and histone proteins * Makes up a eukaryotic chromosome

Chromatin

* Longitudinal subunit produced by chromosome replication

Chromatid

* AKA primary constriction * Constricted non-staining portion of a chromosome

Centromere

* Tip of a chromosome * Contains a DNA sequence required for stability of chromosome ends

Telomere

* Short arm of the chromosome * p for “petite”

p arm

* Long arm of the chromosome * q for “not-p” or queue (french for tail)

q arm

* Centromere is at the center * Both arms are of equal length

Metacentric

* Centromere is slightly offset from the center * Both arms are slightly asymmetrical

Submetacentric

* Centromere is severely offset from the center * One very long and one very short arm

Acrocentric

* Centromere is at the very end of the chromosome * Doesn’t exist in humans

Telocentric

* lacks a centromere

Acentric

* has 2 centromeres

Dicentric

permit smaller segments of each chromosome arm to be identified * The cytogenetic bands count from the centromere out toward the telomeres

G-bands

* Process by which a copy of a DNA molecule is made * Must occur before cell can divide to produce 2 identical daughter cells * Produces two complete double helices from the original DNA molecule * Duplication rate is as high as 1000 nucleotides/second

DNA Replication

 the parent DNA molecule remains intact after being copied and the daughter molecule would contain two entirely new DNA

Conservative

 DNA replication proceeds through a series of breaks and reunions; the resulting copies would be patchwork collections of old and new DNA

Dispersive

 Each parent strand serves as a template for the synthesis of a new daughter strand; the resulting helices each contains one strand from the original parent in addition to one newly synthesized strand

Semi-conservative

3 steps of DNA replication

Initiation, Elongation, Termination

pries the 2 DNA strands apart, breaking the hydrogen bonds between the bases

DNA Helicase

Y-shaped junctions where DNA synthesis occurs

Replication forks

prevent the separated strands from re-forming base pairs

Single-strand DNA-binding proteins

catalyzes the addition of nucleotides to a growing DNA strand using the original parent strand as template

DNA polymerase

is made up of a short chain of RNA that serves as a starting point for DNA polymerase

Primer

is an RNA polymerase that synthesizes the RNA primer

Primase

* Strand that grows in the normal 5’ to 3’ direction * DNA strand is synthesized continuously * RNA primer is needed only to start replication at a replication origin

Leading strand

* Strand that appears to grow in the incorrect 3ʹ-to 5ʹ direction * Backstitching imparts slight delay to the synthesis

Lagging strand

DNA is made discontinuously in successive, separate, small pieces of DNA called

Okazaki fragments

– Degrades RNA

Nuclease

– Replaces the degraded RNA with DNA

Repair polymerase

– Joins one DNA fragment to adjacent DNA fragment

DNA ligase

– Relieves tension on the other side of the replication fork made from the unwinding of the replication fork

DNA topoisomerases

– keeps DNA polymerase firmly attached to the template while it is synthesizing new strands of DNA

Sliding Clamp

– Facilitates assembly of sliding clamp around DNA

Clamp loader

A purine base from a nucleotide is removed giving rise to lesions that resemble missing teeth

Depurination

Spontaneous loss of an amino group from a cytosine in DNA to produce the base uracil

Deamination

promotes covalent linkage between two adjacent pyrimidine bases

UV Radiation

* “Clean” the broken ends and rejoin them by DNA ligation. * Rapidly repairs the damage but nucleotides are often lost at the site of repair

Nonhomologous end joining

* Flawless repair of the double-strand break, with no loss of genetic information * Most handy DNA repair mechanism available to the cell

Homologous Recombination