Mbb Lec 25 To Final

Front 1

Nuclear envelope

Back 1

Inner and outer membrane

Continuous with ER

Front 2

Nuclear lamina

Back 2

Sheet like network of intermediate filaments that line the inner membrane of nucleus

Provide structural and provide sites of chromatin attachment

Front 3

Nuclear pore complex

Back 3

Highly complex proteinaceous pore that regulates the entry/exit of proteins and exits of mRNA

Front 4

Nucleolus

Back 4

Ribosome-producing sub-compartment of the nucleus

Front 5

Nucleoplasm

Back 5

Chromatin/chromosomes containing region

Front 6

Chromatin

Back 6

Chromosomal material- is a protein-dna complex (plus some RNA)

Front 7

Histones function

Back 7

Package and order DNA into structured units

Front 8

When are histones made?

Back 8

G1 phase

Front 9

S phase

Back 9

DNA is replicated and histones and non histones proteins are deposited on the daughter dna molecules to produce chromatin structures

Front 10

G2 phase

Back 10

DNA content is doubled

Front 11

Mitosis

Back 11

Front 12

What does chromatin consist of?

Back 12

Dna, protein and small amount of rna

Front 13

Nucleosomes

Back 13

Histones package and order of DNA into structured units

Beads on a string

Front 14

5 types of histones

Back 14

H2a

H2b

H3

H4

Core histones - 2 copies of each form an octamer (8 subunits)

H1

Clamps DNA wrapped around nucleosomes

Front 15

Which type of histones is highly conserved?

Back 15

H3, H4

Front 16

What does histones contain?

Back 16

Small, basic proteins - contains 25% lys and arg

Why? Neutralize highly charged dna

Front 17

Nucleoplasmin

Back 17

Molecular chaperone

Assembly of histones with dna

Front 18

Nucleosomes are deposited in stepwise manner

Back 18

1) tetramer of two h3 and 2 h4 dimer are recruited first

2) followed by h2a-h2b dimer

3) h1 clamps DNA wrapped around nucleosomes (~1.65 loops)

Front 19

What digest the linker DNA?

Back 19

Nuclease

Front 20

Linker DNA

Back 20

Beads on a string form of chromatin

Front 21

What is the average length of linker DNA?

Back 21

~ 53 nt-pairs

Front 22

Diameter of nucleosomes

Back 22

11nm

Front 23

How to separate histones and DNA?

Back 23

High concentration of salt

Front 24

What is length of DNA after histones is taken off?

Back 24

147 nt pairs DNA double helix

Front 25

Lk is a _______ property of circular dna

Back 25

Topological

Doesn't change when dna is bent or deformed unless one or both strands is broken

Front 26

Left handed, solenoidal supercoil

Back 26

DNA wraps around the nucleosomes and changes lk by -1

Front 27

Left handed plectonemic supercoil

Back 27

Unbound positive supercoil and linking number (+1)

Front 28

What can relax the positive plectonemic supercoil causing a net negative supercoil?

Back 28

Topoisomerase 1

Front 29

In nucleosomes, what type of supercoil wraps around histones octamer?

Back 29

Left handed, solenoidal supercoil

Front 30

What is the 2nd level of chromatin organization?

Back 30

30nm fiber or solenoids

11nm chromatin fibers coil to form 30 nm fiber

Front 31

Wrapping the DNA around histones core compact the DNA ______

Back 31

~7 folds

Front 32

Where h1 located on the 30nm fiber ?

Back 32

Interior

Front 33

Does compaction occur throughout entire chromosome ?

Back 33

No. Regions in which gene are being actively transcribed are less orders and have little to no h1

Front 34

What does compaction make DNA inaccessible to ?

Back 34

Transcription and replication factors

Front 35

Where on DNA contains little h1?

Back 35

Regions that are Transcriptionally active- less order

Front 36

Does transcription occur in solenoid?

Back 36

No

Front 37

Scaffold

Back 37

Associated regions are separated by loops of dna

Front 38

Higher order chromatin

Back 38

Coils upon coils

Loops of DNA may contain related genes

Front 39

What are the three levels of DNA packing?

Back 39

1) nucleosomes

2) 30nm fiber

3) extended form of chromosome

Condensed section of chromosomes

Mitotic chromosomes

Front 40

Where does histones interact primarily with?

Back 40

Sugar phosphate backbone

Interaction not sequence specific

Front 41

Why cant ~70 % DNA surface exposed and available to interact with DNA binding protein?

Back 41

Inaccessible due to dna/nucleosomes binding

Front 42

What does n-terminal tails protrude from?

Back 42

Octamers

Front 43

Structural organization of histones

Back 43

Front 44

Handshake interaction

Back 44

Histone 2a and 2b form a dimer

Front 45

What interaction does a h3 and h4 form?

Back 45

Dimer

All together to form tetramer

Front 46

H3/h4 or h2a/h2b forms a scafford?

Forms a octamer?

Back 46

H3/h4

h2a/h2b onto H3/h4

Front 47

Why are n terminals important?

Back 47

Assembly for 30 nm fiber and gene regulation

Front 48

Why in xray crystal structure are most histones n terminals not visible?

Back 48

Suggests they are flexible

Front 49

Properties of n terminals tails of histones (4)

Back 49

Protrude from octameric disk

Highly conserved between histones

Positively charged

- lys and are

Highly flexible

Front 50

What does n terminal histones tails mediate?

Back 50

30 nm fiber assembly

Front 51

How do histones tails help pack nucleosomes into 30 nm fiber?

Back 51

+ charged n termini bind - sugar-phosphate backbone on DNA of neighboring nucleosomes

Front 52

Chromatin remodeling

Back 52

Increase or decrease its accessibility to proteins in cell

Can change nucleosomes structure and modify histones

Front 53

What does chromatin remodeling complexes require?

Back 53

Atp

Front 54

Exposed DNA can accessed by enzymes involved in? (4)

Back 54

Gene expression, DNA replication , recombination and repair

Front 55

What n terminal histones tails are subject to covalent modification?

Back 55

Reversible acetylation of lysines (-coch3), phosphorylation of serines (-po4), methylation of lysines (-ch3)

Front 56

Acetylation of lysines

Back 56

Acetylation core histones (h3/h4)

Neutralizes positive charge of lysine residues which reduce binding to DNA and destabilizes chromatin

Likely facilitates the of extended regions consisting of the 11nm fiber

Front 57

Methylation of lysines

Back 57

Three different level of lysine methylation can occur

- all results in lysine positively charged

Depending on which residue is modified, methylation can be associated with gene activation or gene silencing

Front 58

Serine phosphorylation

Back 58

Add a neg charge to histones

Impact of histones phosphorylation in terms of chromatin stricture/gene expression is somewhat less well defined

Front 59

Histone code

Back 59

Front 60

Heterochromatin

Back 60

Tightly packed form of DNA

Stains darker

Some regions of DNA are consistently compacted as heterochromatin (constitutive heterochromatin)

Commonly found near centrosomes and telomeres

Front 61

Euchromatin

Back 61

Lightly packed form of DNA

Stains lighter

Often under active transcription

Predominant form during interphase

Front 62

What happens in chromosome remodeling during DNA replication ?

Back 62

As replication fork approaches a stretch of chromatin, nucleosomes on parental duplex is displaced with new ones on reformed on newly synthesized daughter duplexes

Front 63

What 3 kinds of DNA sequences within the chromosomes is controlled for replication?

Back 63

Replication origin

Centromere

Telomere

Front 64

Kinteochore

Back 64

Serves as attachment site for mitotic spindle (protiens complex)

Front 65

Centromere

Back 65

Part of a chromosome that link two sister chromatid

Allows one copy of each duplicated and condensed chromosome to be pulled to each daughter cell during cell division.

Front 66

Operon

Back 66

Genes that encode protiens that are involved in the same process

Front 67

Structural genes

Back 67

Gene that codes for any RNA or protiens product other than a regulatory factor

Front 68

What does a operon encompass?

Back 68

Promoter, operator and structural genes

Front 69

Polycistronic mrna

Back 69

Genes are transcribed together onto a single mRNA

Front 70

Cistron

Back 70

Each section of these mRNA may then be translated independently

Front 71

Effector molecules

Back 71

Transcription of operon can be induced or repressed

Front 72

Negative regulation

Back 72

Repressor protiens binds to DNA at a site or near promoter and blocks transcription by RNA pol

Front 73

Positive regulation

Back 73

An activator protein binds to DNA at activator binding sites and enhances the activity of RNA pol

Front 74

Where are repressors and activator protiens bound for turning promoter on and off?

Back 74

Operator and activator binding sites