Cell Bio Exam 2

two lipid bilayers (inner and out nuclear envelope)

lumen of nuclear envelope; continguous with the lumen of the endoplasmic reticulum

• fluid phase interior of nucleus
• contiguous with cytoplasm but there is no free flow

conferred by a system of proteins in and out of the nucleus

integral membrane protein that spans the outer envelope of the nucleus

integral membrane protein that spans the inner envelope of the nucleus

cytoskeletal molecules that are not A/GTPases

• intermediate filament proteins that live just inside the surface of the inner nuclear envelope
• phosphorylation induces disassembly

• family of proteins: H1 [H2A,H2B,H3,H4]
• positive charge
• basic pH

• DNA looped around histone complex (10nm)
• connected by linker sequences

• coil wound into a tightly packed helix
• histone H1 holds it together

combination of DNA and the proteins associated with it (eg histones)

• very dark, dense, and very protein rich; tighly packed
• generally not unraveled
• found at telomeres and centromeres

• lighter/less dense than heterochromatin both in the amount of DNA present and the amount of protein present
• partially unwrapped chromosomes
• makes the genes for proteins to transcribe them (transcriptionally active)

adding an acetyl group to a histone to neutralize some of its positive charge to allow thte histones to release the DNA partially so it can unravel

 conserve half of the genetic material

• occurs during G1
• building up components around the origin for replication
• limites replication to a single cycle by building up the martials that will be used for replication

• origin
• a DNA sequence that is A-T rich (easier to separate than C-G)
• 1000s in eukaryotes are scattered throughout chromosomes

• origin recognition complex
• pre-replication complex; structural molecule
• six proteins (ORC1-ORC6)
• binds origin; serves as a landmark

• pre-replication complex; structural molecule
• protein that binds to the ORC complex and Cdt1

• Cyclin dependent transcript #1
• pre-replication complex; structural molecule
• binds Cdc6p and MCM

• mini-chromosome-maintenance
• heterohexomer (MCM 2-7)
• provide helicase activity to separate DNA strands
• activated by Cdc45p

binds MCM complex and activates it

• Replication Protein A
• binds single stranded DNA (ssDNA) and stabilizes it in its single stranded form

phosphodrestal bond: bond with 3' hydroxyl of one base and the 5' phosphate of another base

• contains primase activity
• first few bases are RNA primary followed by DNA primer bases
• error prone

• Replication Factor C
• recognizes primer and binds to it
• binds to PCNA

• Proliferating Cell Nuclear Antigen
• binds RFC; wraps around DNA
• binds DNA polymerase d(elta)

• longer runs
• requires a primer
• proofreading activity
• low error rate (1/10,000,000)

seals the gaps in DNA

cuts a nick in one strand of DNA to unwind strands (relieve stress)

cuts two strands and ties them back together (requires ATP)

• ORC is bound to the origin
• Cdc6 and Cdt1 bind
• recruit MCM (but don't turn it on)

• cdc45p binds MCM complex and activates its helicase activity
• replication bubble is opened p
• ORC, cdc6 and cdt1 leave the complex
• ORC returns at the end of S-phase; cdc6 and cdt1 do not return until G1

• replication forks start to extend
• RPA is recruited (keeps strands separate)
• DNA polymerase a(lpha) is recruited
• primase synthesizes primer (RNA - DNA) reading 5'-3'

• RFC is recurited by primer and is bound to it
• RFC recruits PCNA
• PCNA recruits DNA polymerase d(elta)

RNAase H

shortening of telomeres

the presence/absence of hydroyl on C2 ribo/deoxynucelic acid

• shorter sequences
• base pairs w/ it self creating hairpin loops (short) and stem looks (large)
• tertiary structure in some RNAs
• can be catalytic

splicing of mRNA catalyzed by RNA

• Read: 3'-5'
• Write 5'-3'

• 1. entire genome is not transcribed
• 2. Takes place throughout most of the cell cycle
• 3. primers are not required
• 4. RNA polymerases are much less accurate than DNA polymerases (b/c molecules are disposable)

makes rRNAs

mkaes mRNAs

makes tRNA and snRNA (small nuclear RNA)

• just upstream from coding sequence
• transcriptional machinery binds here

• 7-9bps long
• specific binding site and recognition site for transcription factors

• inside promoter
• builds transcriptional machinery

upstream from the gene. Serves as a recruting element for transcription factors

proteins bonding DNA-> recruiting/activating polymerase

• required for transcription of all genes
• bind in promoter region (TATA box)

DNA sequences of transcriptional start site

• transcriptional factor
• TBP-TATA box binding protein

• transcriptional factor
• bind to each other, the TATA box, and PolII(makes mRNAs)

• transcriptional factor
• binds TFII-H and PolII(makes mRNAs)

• binds to TFII-E and Pol II
• binds helicase and kinase(phosphorylated PolII)
• opens strands + transcription bubble

• makes mRNA
• needs to be phosphorylated before it can be activated

• capping enzyme complex
• binds to the 5' base of mRNA

• stabilizes mRNA
• serves as a signal for nuclear export
• signals translation of gene

• occurs after transcription with a spliceosom (composed of RNA and proteins)
• cuts out introns and ligates exons back together

• 1. Polyadenylation signal (AATAAA) signals polymerase II to slow down and stop
• 2. Termination facts bind polymerase II and mRNA to cleave the mRNA

• Poly A polymerase binds 3' end of mRNA and adds 100-300 As (polyAtail)
• serves as a timer- when too many As have fallen off, the mRNA is enzmatically destroyed

1/1000 amino acids

cytoplasm in ribosomes (mRNA must be translocated through nuclear pores out to the cytoplasm)

• 5'-3'
• N-terminal to C-terminal

whenever

• AUG
• methionine

UAA UAG UGA

• A(dd): new tRNA enters ribsome here
• P(olypeptide): contains tRNA that is linked to a growing polypeptide chain
• E(xit): bound to tRNA that has lost its amino acid

cloverleaf

• CCA
• amino acid

• mRNA Initiation Factors
• bind 5' cap and recruit small ribosmal subunit

• Eukaryotic Initation Factor 2
• when turned on (bound to GTP) it prevents translation until the GTP is hydrolysized to GDP (when AUG is reached) (allows large ribosomal subunit to bind)

• small proteins that serve as switches
• bound to GTP (on) until hydrolysis is trigged externally (GDP-off)

• elongation factor 1
• it is an activated g-protein that prevents peptide bond formation unless the codon and anticodon match (GTP is hydrolyzed when there is a match)

• Elongation Factor 2
• an activated g-protein that ensures that peptide bond formation is physically coupled to ribosome translocation in the 3' (->) direction down mRNA

• large ribosomal subunit
• EF2 hydrolyzes GTP allowing ribosome to move forward 3 bases (1 step)

• stop codon is reached
• termination factor enters A site

primary piece of information received by the cell

• hormones (chemical)
• damage (physical)
• cell to cell contact (physical)

• the component that receives and responds to the signal
• can be a single cell, group of cells, tissue, organism

• 1. endocrine
• 2. paracrine
• 3. juxtacrine
• 4. autocrine

• longest range
• chemical (eg hormone)
• source: gland
• gets to target through blood

short ranges (less than a mm)

• very short rainge (direct cell to cell contact)
• signal produced on surface of cell

• cell signals to itself
• signal released is received by a receptor in its own plasma membrane

• 1. receptor-ligand bonding
• 2. phosphorylation
• 3. use of g-proteins
• 4. 2nd messengers
• 5. localization

addition of a phosphate group (rapid, catalytic)

• enzyme that phosphorylates proteins
• many; protein specific

• proteins that remove phosphates
• low in number, less protein specific than kinases
• always active unless turned off

• 1. serine-threonine kinases (S/T) (most common)
• 2. tyrosine kinsase (Y)

(a few kinases also have duality)

• Guanine nucleotide Exchange Factor
• knocks off GDP from g-protein and allows GTP to attach

• GTPase Activating Protein
• binds to GTP-bound g-protein and causes it to hydrolyze GTP to GDP

• ions (Ca2+)
• lipids (PIP2)
• carbohydrates (IP3)
• nucleotides (CAMP)

• tripartite
• n-terminal, middle, c-terminal

• transcriptionally active domain (TAD)
• recruiting factor for activators of transcription

DNA binding domain