Molecular Exam 2

10 nm fiber

-DNA winds around histones to form nucleosome "beads" -Nucleosomes are strung together like beads on a string by linker DNA

300 nm loops

30 nm gets folded onto scaffold proteins

Helicase

An enzyme that untwists the double helix of DNA at the replication forks. a. - unzips DNA b. - moves along leading strand in Eukaryotes

Explain why DNA replication is said to be semi-discontinuous

Because the leading strand is synthesized discontinuously, the overall process is described as semi-discontinuous

Explain how DNA is packaged within the cell and the function of histones:

DNA is packaged tightly into the nucleus of each cell with the help of histones. The DNA wraps around the histone that then form into nucleosomes.

core DNA

DNA most tightly associated with the nucleosome

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule a- ONLY ADD nucleotides to the 3' END b- catalyzes in 5' to 3' c- cannot synthesize DNA de-novo d- can proofread e- moves to exonuclease active site during termination of bacterial replication: 3' - 5' EXONUCLEASE REMOVES UNPAIRED BASE f- monitors the ability to form a base pair only when the correct pair is formed are the chemical groups.

Nucleosome remodeling complexes

Large, multiprotein complex that uses the energy released by ATP hydrolysis to alter the position or structure of nucleosomes, thereby remodeling chromatin structure.

How are nucleosomes arranged in condensed 30 nm fiber?

Nucleosomes in condensed 30 nm fiber cause the thinner fiber to coil or fold to become thicker. Based on interactions between H1 Histones proteins.

cohesins

Proteins that hold sister chromatids together until anaphase

origin of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides. a. where DNA synthesis begins b. eukaryotes have multiple, prokaryotes have one or two

What role do histones play in nucleosomes?

The core histones (H2A, H2B, H3, H4) help make up the nucleosome while the linker histone (H1) that helps seal the DNA to the histone core. They help package the DNA into nucleosomes. The histones are the chief components of chromatin.

Phosphorylation

The metabolic process of introducing a phosphate group into an organic molecule.

DnaA protein

a protein that binds to the dnaA box sequence at the origin of replication in bacteria and initiates DNA replication A. - recognizes and binds DNaA boxes/sequences

postive supercoils

circular DNA with more than the normal number of turns of the helix

semiconservative replication

in each new DNA double helix, one strand is from original molecule, and one strand is new

ter sequences

locate on the opposite side of the oriC

HDACs (histone deactyletransferases)

remove acetyl groups, eraser protein

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication a. removed by RNase H during elongation

RNase H

the enzyme that helps to remove the RNA primer during DNA replication

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

Chromatin

A complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells

trombone model

DNA replication occurs within a fork structure in which the lagging strand loops around in proposed "trombone model" to help orient the replication enzymes for repeated synthesis and joining.

DNA polymerase III

In charge of synthesizing nucleotides onto the leading end in the classic 5' to 3' direction. a. majority of chromosomal replication b. MAIN REPLICATIVE ENZYME c. 10 diff proteins d. only 1 subunit has catalytic function e. can synthesize a very long stretch of DNA f. processive - sliding clamp and clamp loader g. stay attached for 1000s of nucleotides

polymerase switching

In eukaryotes, the switch that occurs from DNA synthesis by the polymerase alpha-primase complex to DNA synthesis by the processive replicative polymerase that carries out the bulk of DNA elongation

sliding clamp

protein that moves DNA pol III along the DNA as it adds nucleotides to the 3' end of the new strand a. prevent the DNA polymerase from falling b. ring shape that encloses DNA- highly stable and stays associated with DNA once loaded c. ADD THOUSANDS OF BASES AT A TIME

Nucleosome

repeating subunit of chromatin fibers, consisting of DNA coiled around histones, unit of chromatin, single histone complex

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication a. removed by RNase H during elongation

SSBs

single stranded binding proteins: the proteins that bind to the outside of the two single template strands and prevent the separated strands of DNA from reattaching a. bind regions of single stranded DNA b. keep DNA open

DNA primase

synthesizes a short RNA primer to provide a 3'-OH group for the attachment of DNA nucleotides a. - DNA dependent RNA polymerase b. - REMOVED EVENTUALLY

parental strand

the DNA strand acting as a template to direct the synthesis of a new daughter strand of DNA

bidirectional replication

the process in which DNA replication proceeds outward from the origin in opposite directions

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork. a. discontinuous replication b. AWAY from replication fork c. MANY RNA primers

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain. a.- ligation is an energy dependent process requiring ATP b. - MAKES PHOSPHODIESTER BONDS IN ELONGATION

Explain what a nucleosome is:

A nucleosome is a repeating subunit of chromatin fibers that consists of DNA coiled around histones. It is a single histone complex. The tail moves around to be accessible to enzymes. Nucleosomes that are tightly put together are then known as chromatin.

Define the roles of modifying amino acid side chains in altering nucleosome structure and how the structure of chromatin can be used for regulating gene expression:

A. Lysine: modification (methylation and acetylation) i. Methylation: have a neutral effect on overall charge of histones ii. Makes histones hydrophobic (package more tightly) iii. (not always) B.Arginines: modification (methylation) C.Serines: modification (phosphorylation) i.Histones are basic and have a large number of lys and arg

Explain what form of chromatin is present during interphase:

Chromatin is in its least condensed state and appears loosely distributed throughout the cell.

negative supercoils

DNA is underwound so right-handed supercoil compensates

DNA gyrase

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix a. unwind overwound or rewind underwound DNA b. diff types: IA and IB c. work by breaking one or 2 DNA strands and passing the same number through the break d. makes positive supercoils into negative supercoils to allow strand separation e. ahead of helicase

Why do eukaryotes need telomeres, but prokaryotes do not?

Eukaryotes need telomeres because it helps keep the ends of the chromosomes from becoming degraded, but prokaryotes are circular chromosomes, so telomeres are not necessary.

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. ALL DNA DURING MITOSIS, darkly stained, no space for DNA for gene expression, TRANSCRIPTIONALLY INACTIVE, TELOMERES, HIGHLY REPETITIVE DNA SEQUENCES.

core histones

H2A, H2B, H3, H4, make up the nucleosome

Histones (types)

Protein molecules around which DNA is tightly coiled in chromatin, H1, H2A, H2B, H3, H4, core and linker, chief protein component of chromatin

know when DNA replication occurs during the cell cycle

S phase for eukaryotes

Linker Histones (H1)

Seals DNA to histone core, binds to linker DNA between successive nucleosomes, helping compaction

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription. Lightly stained. Genes that need to be expressed.

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction. a. - continuous replication b. - requires ONE RNA primer c. - TOWARDS replication fork

daughter strand

The strand of DNA that is newly replicated from an existing template strand of DNA.

Linker DNA

The string between beads of DNA on histones. Stretch of DNA separating two nucleosomes.

DnaA boxes

a DNA sequence that serves as a recognition site for the binding of the DnaA protein, which is involved in the initiation of bacterial DNA replication

replication bubble

a region of DNA, in front of the replication fork, where helicase has unwound the double helix

Be able to explain why DNA replication is semiconservative

a. DNA replication is said to be semi-conservative because of this process of replication, where the resulting double helix is composed of both an old strand and new strand. Due to complimentary based pairings on the template strand the new DNA has one old strand and one new strand. The two DNA molecules produced will be identical to each other/ and/ the original parent molecule.

HMTs (histone methyltransferases)

add methyl groups, eraser protein

Methylation

addition of a methyl group, neutral effect on overall charge, locks in positive charge, most hydrophobic, package more tightly in nucleus, recognized by chromodomain

Acetylation

addition of acetyl group, amino acid chain with no charge changes interaction with DNA, makes it lose charge, reduce affinity of tails, recognized by bromodomain

Condensins

assemble into complexes on the DNA when phosphorylated by M-Cdk

TaUS (protein)

binds terminus and blocks progress of the replication fork

DNA pol I

enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule a. ONLY ADD nucleotides to the 3' END b. catalyzes in 5' to 3' c. cannot synthesize DNA de-novo d. can proofread e. moves to exonuclease active site during termination of bacterial replication: 3' - 5' EXONUCLEASE REMOVES UNPAIRED BASE f. monitors the ability to form a base pair only when the correct pair is formed are the chemical groups

origin recognition complex (ORC)

initiator protein in eukaryotes; binds to the replicator and recruits proteins

30 nm fiber

interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber

Exonuclease (3'-5', 5'-3')

nucleases that cut DNA from the ends

HATs (histone acetyltransferases)

open up the chromatin, makes DNA more easily transcribed, writer protein, adds acetyl groups

scaffold proteins

organize groups of intracellular signaling molecules into signaling complexes, where 30nm fiber forms looped domains

Ori C

origin of replication in E. coli a. three types of sequences: five 9bp sites or DNaA boxes, AT rich regions, GATC methylation sites

Interphase

period of the cell cycle between cell divisions in which the cell grows, S phase important for eukaryotic replication

Metaphase

phase of mitosis in which the chromosomes line up across the center of the cell

clamp loader

places sliding clamp onto DNA a. high affinity with primer template junction

chromatin remodeling complexes

protein machines that use the energy of ATP hydrolysis to change the position of the DNA wrapped around nucleosomes