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BIOL 308 Molecular Biology > Proteins and Chromatin Structure > Flashcards

Proteins and Chromatin Structure Flashcards

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1
Q

amino acid side chain (R group) properties

A
  • shape, folding
  • protein charge (local and overall)
  • enzymatic properties
  • modification sites
  • H bonding properties
  • hydrophilic vs hydrophobic
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2
Q

general amino acid structure

A

amine group (+ve)
alpha carbon (connected to R group)
carboxylic acid carbon (functional carbon)

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3
Q

proteins sorted by R group: categories:

A
  • acidic
  • basic
  • nonpolar
  • polar (uncharged): H bonds
  • aromatic
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4
Q

which protein/gene always at start of protein seq?

A

methionine (Met)
AUG/ATG

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5
Q

protein primary structure

A
  • bonded by peptide bonds (covalent), H2O = byproduct
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6
Q

protein secondary structure

A

H-donor, O-acceptor
held by H bonds only

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7
Q

protein tertiary structure

A

(need in order to be functional)
- hydrophobic parts tend to clump inside

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8
Q

quaternary structure

A

multi-subunit protein
- tertiary structures are its subunits

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9
Q

diff protein functions

A
  • defense
  • transport
  • communication
  • storage
  • enzymes
  • structure
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10
Q

protein activity control

A

first step: post-translational modification (covalent) and transport
- not dictated by DNA or genome (unlike primary->quaternary structures)
- epigenetic
- N-terminal like 5’ end of gene
(N-terminal TO C-terminal)

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11
Q

polypeptide means

A

unfolded proteins

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12
Q

primary (structure) means?

A

nascent
native = functional; nascent = unfunctional

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13
Q

protein modifications for transport

A

(modifications necessary for transport from cytoplasm, where translation takes place)
- proteins that are membrane bound or destined for secretion (e.g., receptors and protein hormones) are synthesized by ribosomes associated with ER membranes
– the ER associated with ribosomes is rough ER (RER)
- this class of proteins all contain a N-terminus signal seq or signal peptide; transport is co-translational (N-terminus starts entering ER WHILE rest of peptide still being made by ribosomes)
- proteins destined for organelles: diff signal seq at N-terminus

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14
Q

protein modifications (11)

A
  • proteolytic cleavage
  • phosphorylation
  • sulfation
  • acylation or acetylation
  • glycosylation
  • methylation
  • prenylation
  • vitamin C-dependent modifications
  • vitamin K-dependent modifications
  • ubiquitin (ubiquitination)
  • control of protein stability
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15
Q

proteolytic cleavage

A

proteolytic cleavage: most proteins undergo this following translation
- simplest form - removal of first methionine

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16
Q

phosphorylation

A

phosphorylation
- post-translational phosphorylation one of most common modifications
- occurs as a mechanism to regulate protein activity
– transient (non permanent): phosphate (1 or more) is added and later removed (or transferred to other protein); gives 2 -ve charges per phosphate

  • enzymes involved:
    – kinases: transfer a phosphate group form donor (ATP) to acceptor (protein) (adds phosphate)
    – phosphorylases: transfer a phosphate group form an inorganic phosphate (adds phosphate)
    – phosphatases: remove phosphates

in animal cells, SERINE, THREONINE, and TYROSINE are AAs subject to phosphorylation (-OH group = phosphorylation site)

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17
Q

sulfation

A
  • sulfate modification of proteins occurs at tyrosine residues
  • since sulfate is necessary for biological activity, it is added permanently and NOT for regulatory modificaiton
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18
Q

acylation or acetylation

A
  • in most cases, acetyl group is added to N-terminal AA (after first Met is removed)
  • Acetyl-Coa is acetyl donor
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19
Q

Glycosylation

A
  • glycoproteins consist of proteins with covalently linked sugars
    – consensus AA for addition: Asn - X - Ser/Thr
    (X is any AA except Pro)
    Asn = asparagine
    – sugars are modified
    – major mechanisms for cell surface identification
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20
Q

Methylation

A
  • post-translational methylation occurs at lysine residues in some proteins
  • activated methyl donor is S-adenosylmethionine
  • ex. cytochrome c and calmodulin
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21
Q

Prenylation

A
  • addition of compounds derived from cholesterol biosynthetic pathway, hydrophobic fatty acid chains (membrane anchoring)
  • can make more non-polar
  • ex. Ras
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22
Q

Vitamin C-dependent modifications

A
  • modifications of proteins that depend on vit C as a cofactor
  • ex. collagens and peptide hormones like oxytocin and vasopressin
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23
Q

Vitamin K-dependent modifications

A
  • vit K is a cofactor in carboxylation of glutamine residues
    – carboxylation adds a carboxyl group
  • protein can chelate calcium ions (chelate - arresting)
  • ex. some anticoagulants
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24
Q

control of protein stability

A
  • some proteins are rapidly degraded, whereas others are highly stable
  • specific AA seq in some proteins have been shown to promote rapid degradation (recognized by peptidases/proteases)
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25
Q

ubiquitin (ubiquitination)

A
  • covalent post-translational addition
  • addition of ubiquitin protein via Lys residues (7 Lys)
  • Mono-: can be a location signal for membrane transport
  • Poly-: signal for proteolysis
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26
Q

DNA, RNA, protein structure summary

A
  • nucleic acids use nitrogenous bases (DNA -> RNA = transcription)
  • proteins use amino acids (mRNA -> protein = translation)
  • DNA is highly regulated, rarely modified, relatively permanent - very few intentional modifications after replication
  • RNA is highly regulated, modifiable, transient
  • protein is highly regulated, modifiable, transient
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27
Q

chromatin = ?

A

protein + DNA

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28
Q

chromatin structure (E. coli example)

A

diameter of bacterial cell is around 1nm; DNA is around 4 mil bp (1.36 mm long DNA thread which is 2nm wide)

29
Q

bacterial “chromosome”

A
  • genome forms a compact structure = nucleoid (mixture of supercoiled and relaxed regions)
  • DNA organized in 50-100 loops (domains)
  • circular molecule is compacted by association with:
    – polyamines
    – HU (heat unstable) proteins
    – supercoiling
30
Q

polyamines

A

(spermine and spermidine, +ve charge) - NOT proteins, molecules

31
Q

HU (heat unstable) proteins

A

(small, basic, +ve, dimeric) and H-NS (histone-like nucleoid structuring) (monomeric, neutral) DNA binding proteins

32
Q

supercoiling

A

can occur in space or around proteins
- unrestrained - path is supercoiled in space and creates tension
- restrained - path is supercoiled around protein but creates no tension

33
Q

avg of euk chromosome?

A

150 Mbp = 150 million bp

34
Q

there are ___ chromosomes in human somatic cell

A

46

35
Q

approx ____m of DNA/human cell

A

2.5

36
Q

avg size of eukaryotic cell =

A

10-100 micrometers

37
Q

eukaryotic chromatin (chromosome, nucleoprotein, pulsed-field gel electrophoresis. dark field electron microscopy)

A
  • eukaryotic genomes organized to form linear chromosomes
  • each chromosome has single, linear DNA molecule
  • nucleoprotein material of eukaryotic chromosome is chromatin
  • individual chromosomes can be separated by pulsed-field gel electrophoresis (one band = one chromosome)
    – electric field repeatedly alternated
    – AND by dark field electron microscopy, fiber structure of a chromosome resembles “beads on a string”
38
Q

chromatin organization

A

“beads on a string”
- fundamental unit of organization of chromatin = nucleosome
- each nucleosome has a CORE PARTICLE of histone proteins, that are wrapped by DNA
- also: non-histone proteins = important for chromatin organization

39
Q

what is nucleosome?

A

nucleosome core + core DNA

40
Q

chromatin organization: histones

A
  • in all eukaryotic nuclei
  • small proteins rich in lysine and arginine (at normal pH their “extra” amino groups become NH3+) - basic, +ve proteins
    – electrostatic interactions
    – N terminals wrap around DNA
41
Q

histone’s 5 major subunits

A
  • H1 (linker), H2A, H2B, H3, H4
    – H2A, H2B, H3, H4 form a octet complex (8 proteins)
42
Q

H1 (linker) is in nucleosome core (T/F)

A

False

43
Q

how does histone octet in nucleosome core form? what does linker (H1) do?

A
  • H3-H4 tetramer
  • H2A-H2B dimer (NOT tetramer on its own, need H3-H4 tetramer)
  • linker histone -> on side, packs DNA closer to nucleosome core
44
Q

chromatin organization: nucleosome

A
  • nucleosome = octet of histones and wrapped DNA
  • DNA (147 bp) wraps around octet approx 1.65x
  • H1 associates with DNA and octet in linker region -> binds two distinct regions of DNA duplex
45
Q

nucleosomes are uniformly distributed (experiment)

A
  • low conc micrococcal nuclease (don’t want full digestion)
  • only linkers (DNA) were cleaved (nucleosome is too packed to cleave)
  • realized nucleosomes are uniformly distributed
46
Q

chromatin organization (fiber length)

A
  • 10-11 nm fiber
    – likely a consequence of unfolding during extraction in vitro
    – H1 NOT required
  • 30 nm fiber
    – basic constituent of interphase chromatin, mitotic chromosomes
    – H1 required
47
Q

chromatin organization: fibers

A
  • core histones alone: ~4-fold compression
  • core histones + H1: 25- to 100-fold compression
  • nucleosome is 10-11 nm in diameter
  • 10 nm fiber re-packed into a 30 nm diameter fiber
  • higher salt conc during isolation (stabilizes DNA) - diff forms (10 nm nucleosomes - beads
    -> more condensed 30 nm fibers)
  • recent electron microscopic studies - dynamic structure
48
Q

chromosome organization: morphology

A
  • 30 nm chromatin fiber condenses to metaphase chromosome = 1400 nm
  • attachment of chromatin fibers to non-histone protein complexes = scaffold (genes in scaffold loops)
  • nucleosome fibers condense more into 30 nm chromatin fiber. different theories about its form (solenoid or zig-zig). pre-dominant form in interphase nucleus
  • duplex DNA winds around histone octamers to form nucleosomes = 10-11 nm histone fiber
  • primary structure of DNA = duplex helix = 2 nm duplex
49
Q

chromatin is organized in distinct CTs, meaning?

A

chromosome territories

50
Q

chromatin has ___ and ___

A

loops and domains

51
Q

chromosome structure (euchromatin/heterochromatin)

A

euchromatin
- less tightly packed, consists of transcriptionally active DNA, susceptible to DNase digestion

heterochromatin
- tightly packed, less susceptible to DNase digestion and transcriptionally inactive
– constitutive heterochromatin - highly condensed inactive chromatin; consists of repetitive DNA, very few genes (constitutive = always)
— e.g., centromere (specific seq, attachment point for sister chromatids and spindle fibers
—- e.g., telomere (end of chromosome)

– facultative heterochromatin - not active in any particular tissue. forms under specific circumstances and/or certain tissues to silence gene expression (facultative = optional; sometimes euchromatin becomes heterochromatin)
— X-chromosome inactivation (Barr body formation)
— imprinting

52
Q

chromatin elements and centromeres

A

chromatin elements (elements = particular nucleotide seq, DNA regions)
- locus control regions - shared control regions (usu upstream form gene clusters) - control chromatin condensation
- matrix and scaffold associated regions - mostly AT-rich DNA which anchors to nuclear matrix (AT easier to unwind than GC)
- insulators - regulatory domains in DNA - define domains of gene expression (can block enhancers from approaching gene)

centromere = chromosome region which contains site of attachment for spindle fibers
- kinetochore = centromere + protein (connect to fibers)
- in situ hybridization of metaphase chromosomes shows satellite DNA at centromeres (highly repetitive seq)

telomeres
- specialized DNA regions at chromosome ends
- repetitive seq
- protect chromosomes from shortening during replication and from degradation (by “looping” of 3’ overhang)

53
Q

chromatin organization: non-histone proteins

A
  • matrix attachment regions (MARs) or scaffold attachment regions (SARs)
  • DNA elements bound by scaffolding riboproteinaceous structures
    – suggested: this binding is required for replication and transcription
    – MARs A:T rich but no universal (consensus) seq
    – may incl cis-acting sites that regulate transcription
    – usu recognition site for topo II (role in packing)
  • SMC proteins (responsible for scaffolding)
  • DNA replication proteins
  • transcriptional factors, chaperone proteins, etc
54
Q

chromatin organization: histone proteins

A
  • highly conserved proteins esp H4 (important for living)
  • H1 least conserved, most variations
  • H5 = extreme variant of H1
  • specialized: H3 variant specific for centromeres - CenH3
55
Q

nucleosome disassembly and reformation

A
  • replication of DNA requires particle disassembly of nucleosome
  • newly replicated DNA immediately packed: first bind H3-H4 tetramer and THEN two H2A-H2B dimers, H1 is last
  • H1 -> tighter DNA wrapping
  • more DNA (from replication) - newly synthesized histones are needed
  • old and new histones present on both daughter chromosomes
  • chaperone proteins - -ve charged proteins, assist assembly of histones (escort dimers to replicating target DNA); negative bc they repel DNA and bind to histones
  • replicating DNA is ABSOLUTELY NECESSARY for nucleosome assembly
56
Q

chromatin organization: histone tails

A
  • histones have N-terminal tails extending out from nucleosome - several +ve lysines (basic AAs)
  • protruding tails integrate into “grooves of screw” - directly wrapping around DNA
  • tails are required for formation and stabilization of 30 nm fiber through interaction with adjacent nucleosomes
57
Q

transcriptionally active genes and chromatin condensation

A
  • eukaryotic transcription and replication occur in context of chromatin:
    chromatin modification necessary for replication to start and change gene expression:
  • transient modification of AAs in HISTONE TAILS
58
Q

modifications of histone tails

A
  • acetylation of histone tail (lysine) generally associated with active gene expression (repels DNA when added, leads to local unwinding)
  • ubiquitinylation of histone tails (lysine) - mono = non-destructive modifications (same as ubiquitination)
  • methylation of histone tail (arginine and lysine); may be associated with active or inactive genes
  • phosphorylation (Serine) - generally assocaited with active gene (not very clear b/c histones are phosphorylated during mitosis)
  • methylation and acetylation of lysine and phosphorylation of serine REDUCES overall +ve charge of protein
59
Q

histone code hypothesis

A
  • serial modifications of histones’ tails are “landmarks” for proteins which read chromatin (domains recognize modified tails)
  • creates “open” chromatin necessary for transcription, replication, repair, and recombination
60
Q

___ binds to methylated lysine of histones

A

chromodomain

61
Q

____ binds to acetylated lysine of histones

A

bromodomain

62
Q

chromodomain and bromodomain are not proteins. they are ____

A

parts of proteins

63
Q

what do methylation and acetylation of lysine AND phosphorylation of serine do?

A

reduce overall +ve charge of protein
-> keep DNA loose (from -ve repel)

64
Q

acetylation and deacetylation of histones’ tails (details, enzymes)

A
  • enzymes: histone acetyltransferase (HAT) - catalyzes forward equation, promote gene exp)
  • histone deacetylase (HDAC) - catalyzes reverse equation, suppress gene exp)

Histone + Acetyl-Coa <-> Acetyl-Histone + coenzyme A

  • acetylated form is negative (H+ atom replaced by -acetyl group)
    – affects chromatin’s condensation
    – necessary for activation of transcription
  • nucleosome free regions - contain actively transcribed DNA (gene exp in progress) - DNase-sensitive regions
65
Q

DNase I test

A
  • isolate nuclei, treat with diff conc DNase
  • separate protein, DNA
  • digestion, gel electrophoresis, southern blots

2 possibilities:
1. no signal - gene expression was in progress; DNA was free of histones, available for digestion by DNase
2. signal - no gene expression (too tight, couldn’t cleave)

66
Q

transcription assay

A
  • usually involved “naked” nucleosome-free DNA, since usu in vitro
    (naked DNA = DNA w/o proteins
67
Q

prok vs euk

A

prok:
- no membrane-bound nucleus
- single, circular chromosome
- no membrane-bound organelles
- single cell organisms

euk:
- membrane-bound nucleus
- linear chromosomes (23 pairs in humans)
- have membrane-bound organelles
- single or multicellular

68
Q

extrachromosomal means

A

not in chromosome
ex. plasmid, mitochondrial DNA

69
Q

human chromosomes:

A

7 groups of autosome (classified by size), 2 groups of sex chromosomes

BIOL 308 Molecular Biology (14 decks)

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