BIOL 3010 Exam 2 Vocab

tRNAs

a transfer RNA molecule that acts as an adaptor between mRNA and amino acid

• charged by aminoacyl tRNA synthetases

• contains anticodons complementary to the mRNA

  • attaches specific amino acids to the growing peptide chain

Wobble position

the anticodon of tRNAs participate in promiscuous base pairing at this position

• can pair with standard or modified bases - accommodates degeneracy

less tRNAs than there are codons

RNA pol 1 & 3

transcribes rRNA to form ribosomes

(As opposed to pol2 that transcribes mRNA)

60S subunit

aka the large subunit of the ribosome

• contains A and P sites, attaches last

• Joins the small subunit during initiation of translation to form 80S

40S subunit

aka the small subunit of the ribosome

• binds initiation factors that facilitate scanning of mRNAs and initiation of protein synthesis.

80S subunit

the assembly of small and large subunits together

• responsible for protein synthesis

Initiation of translation

the small subunit of ribosome starts scanning down the length of mRNA to locate a start codon

• when found, a charged tRNA interacts with a small subunit and allows assembly of the complete ribosome

• methionine tRNA starts in the P site, and second one comes in through the A site

Elongation of translation

ribosome moves toward 3’ end of mRNA, tRNAs go from a→ p → e sites and are split out as the polypeptide grows

Termination of translation

stop codon contains a release factor that enters the A site and makes the ribosome dissociate/ fall off the mRNA

Kozak sequence

a preferred sequence surrounding the start codon that makes it more likely that the small subunit will recognize it and attach there

eukaryotic initiation factors (eIFs)

involved in the initiation of translation

-Associates with the 40S ribosome subunit, mRNA, and the 60S subunit to help stabilize and assemble the ribosome around the start codon

PABC

• associated with poly (A) tail - this is why this aspect is involved in translational initiation

associates with mRNA, and eIFs to create looping where the 3’ end is close to the 5’ end

• helps ribosome attach

Diamond-Blackfan Anemia

mutations in the small or large subunit create a stoichiometric imbalance between the units

• results in depletion of mature ribosome → less efficient translation

especially crucial for stem blood cells to be efficient, but they are unable to replenish themselves

Treacher-Colin Syndrome

mandibulofacial dystosis that creates problems with swallowing, breathing, etc.

• heterozygotes are the ones impacted

mostly due to mutation in TCOF1

• normally recruits RNA pol1 to nucleolus

  • detrimental because it can’t create ribosomal RNA

TCOF1

treacle ribosome biogenesis factor 1

• responsible for ~93% of cases of treacher-colin syndrome

in the nucleolus, responsible for recruiting RNA pol1 and localizing it in the nucleus where ribosomes can be made

amino-acyl tRNA synthetases

“charge” tRNAs by attaching an amino acid group on the amino end

uORFs

upstream open reading frames that regulate translation

• start codons that lack a Kozak sequence in 5’ UTR

  • regulates genes that code very potent proteins or important in development

• slows down the ribosome and ultimately translation because the small subunit is scanning down the mRNA, but signaling is poor

Sonic Hedgehog Signaling Pathway

important in body patterns during development

• have PTCH receptors for Shh protein

  • The amount of signaling is important for the identity of cell (more dorsal or more ventral fates)

• have uORFs that reduce amount of protein made to tightly regulate how much signaling in pathway

PTCH Receptor

protein that is regulated in the Sonic Hedgehog signaling pathway

• amount of receptors determines body patterning

why are uORFs important?

reduction of protein

• very normal and important for regulation / differentiation

• especially in genes encoding potent proteins or ones involved in development

fluorescent reporter in uORF experiments

to learn the role of uORF

• placed varying numbers of uORF from PTCH in front of coding sequence of FOXA2 gene

• less uORF → more translational efficiency (more fluorescence)

Nuclease degradation of mRNA

mRNA degraded by ribonucleases, especially poly(A) nuclease

• if you have a shorter tail, you have less PABC (important for translation initiation!)

microRNAs

aka miRNA- non-coding guides that bind to mRNAs

• regulate mRNA abundance

  • by either targeting for degradation or preventing translation

• must be processed by factors like Drosha, dicer

the single-strand associated with miRNA-induced silencing complex (includes RISC and argonaute proteins)

• if perfectly complementary → target for degradation

• if not, loop forms → prevents translation

Drosha

important in cropping miRNA during processing

- removes hairpin structure and the stem

in the nucleus!

Dicer

removes hairpin structure from stem in miRNA processing

• in the cytoplasm!

TRAMP

targets the degradation of defective mRNAs in the nucleus

non-stop decay

transcript lacks a stop codon

• ribosome tries to translate into 3’ UTR

no-go decay

RNA has structure (Ex. hair pin) that prevents ribosome from progressing

non-sense mediated decay

introduction of premature termination codons

• results in truncated proteins - lack critical domain on carboxy end

EJC protein complex

exon junctional protein complexes

• found right before every exon-exon junction

• required for quality control

  • normally, ribosome removes proteins as it translates

  • but with PTC→ EJC is left and that acts as a signal to target the protein for degradation

B^0 thalassemia

non-sense mediated decay found→ PTC cause transcript loss and reduced hemoglobin

PTC

premature termination codon associated with non-sense mediated decay

• results in truncated protein

What causes Zika virus?

Zika infects the neural stem cells

• nucleus is oddly-shaped- has tri-spindle like apparatus

• chromosomes unable to segregate properly

  • makes daughter cells triploid and they die

this example proves how important normal replication is to development

G1

first part of the interphase

• the gap before duplication

S phase

when DNA synthesis and chromosome duplication occurs

-part of interphase

G2

interphase, gap before mitosis but after replication

G0

when a cell leaves the cell cycle

Role of growth factor in RTK pathway

ligands that activate the receptor tyrosine pathway (important for cell-cycle re-entry)

Overview of receptor tyrosine kinase pathway

• receptors dimerize

  • ligands are phosphorylated and bring receptors together where they transphosphorylate each other

• enables phosphorylation cascade of downstream targets such as GEF, RAS, RAF, MEK

• ultimately activates kinases that phosphorylate a transcription factor

  • this promotes transcription of downstream genes (ex. cyclin)

Cyclins/CDKs

important for initiation of S phase

• CDKs are cyclin-dependent kinases which need cyclin to function

• bounded together → phosphorylate 100s of target proteins at serine - threonine residues

  • enables specific steps of the cell cycle

Cyclin D

transcription is driven by RTK pathway

• binds to CDK-4

• phosphorylate retinoblastoma protein to make it detatch from E2F protein → initiates S phase

Cyclin E

transcription is driven by RTK pathway

• binds to CDK-2 → phosphorylates Rb so it dissociates from E2F→ activation of DNA synthesis

Rb protein

first identified as a tumor suppressor, but its main job is within cell cycle

• bind to E2F to inhibit its activity

  • once phosphorylated, allows E2F to separate and initiate DNA synthesis

E2F protein

protein necessary for activating DNA synthesis

• must be released from Rb to initiate DNA synthesis (activates genes)

p53 transcription factor

prevents G1 → S phase transition by

1)inducing expression of CDK inhibitor, p21

2) initiating apoptosis if severe

3)inducing expression of DNA repair enzymes

• mutations in p53 promotes cancer susceptibility

main point in the elephant example?

“Peto’s Paradox”

• large-bodied organisms typically live longer, but they have more cells and more time to accumulate cancer

  • how are cancer levels the same as small-bodied organisms?

• additional copies of tumor suppressor genes like p53 allow for more mutations without risk of cancer

Cyclin A

pairs with CDK2 during S phase

-promotes DNA synthesis

Semiconservative DNA replication

-proposed by watson and crick

one strand of the original DNA acts as a template for a new strand

• with further replications, original DNA will be present but less % of all DNA

Conservative DNA replication

2 original strands stay together and the whole thing acts as a template for a whole new strand

Dispersive DNA replication

different segments are replicated and daughter DNA is a mix of new and old

what adds nucleotides in replication?

DNA polymerase

-primer must be present

Origins of replication

recognized by CpG islands and promoters

-places where DNA replication may begin

Pre-replication complex (Pre-RC)

assemble at potential origins of replication

• include ORC, CDC 6, MCM proteins

• “license” origins of replication for use

  • only some become active

MCM complex

act as helicase to open/unwind the double strand

CDC6

loading the helicase and primase to prepare for replication

RPA (Replication Protein A)

keeps the single-strand from annealing before it can be replicated

Pol alpha

adds primer needed for replication

PCNA

acts as a sliding clamp to make sure new strand anneals to the template in DNA replication

Pol delta and epsilon

carries out replication off of DNA template

ligase 1

required for lagging strand- joins together Okazaki fragments

leading strand

continuous synthesis of DNA as the MCM complex and primer are moving the same direction

(polymerase chases replication fork)

lagging strand

discontinuous synthesis of DNA as MCM complex and polymerase are moving in opposite directions

• replicated in portions - Okazaki fragments

• polymerase must go back and replicate empty segments - requires ligase 1

“read-write” methylation

with chromatin remodeling - some parental histones remain in H3/H4 and some are newer- must adopt modifications

• enzymes recognize particular histone modification in nearby nucleosomes and adopt the same methylation

  • persistence of heterochromatin marks

telomeres

occur at the chromosomes to prevent degradation of chromosomes after replication

• repeats of TTAGGG

functions:

1) protect chromosome end from degradation

2) allows for own rejuvenation

3) pairing of homologous chromosomes during meiosis

G-overhang

150-300 bases of telomere that is single-stranded- must be protected with t/d loops!

T-loop

prevents the attack of G-overhang by nucleases

• overhang folds over and invades other strand- pairing complementary bases

D-loop

result of G-overhang pairing with other strand

-aka displacement loop, smaller

Shelterin Complex

required for the formation of T-loop

• telomere decorated with complex in G-overhang

Telomerase

active in the rejuvenation of telomeres

• a ribonucleoprotein consisting of TERT enzyme and TERC

• complementary to telomere repeats

• uses RNA as a template for DNA

  • add sequences to G-overhang, then opposite strand filled in by DNA polymerase

telomerase reverse transcriptase (TERT)

enzyme that uses TERC RNA as template to synthesize complementary DNA

Diploid

describes cells carrying two matching sets of chromosomes; symbolized as 2x.

• somatic cells of human body

Haploid

describes cells, organisms, or nuclei that contain one set of chromosome

• gamete cells of humans

Sister-chromatids

identical copies of a chromosome joined together by centromere after replication

• eventually split in anaphase

Prophase

-chromosomes condense and become visible

-centrosomes move toward poles

-nuclei begin to disappear

Prometaphase

-nuclear envelope breaks down

-centromeres invade the nucleus

-sister chromatids attach to microtubules

Metaphase

chromosomes align on the metaphase plate

• sister chromatids face opposite poles

Anaphase

connections between centromeres severed, chromatids move to opposite poles

Telophase

nuclear membrane and nucleoli reform, spindle fibers disappear, chromosomes become tangled chromatin

Cytokinesis

actual division of cytoplasm and rest of cell

Cohesins

maintains contact between sister chromatids

• form -quasi-ring around DNA

loaded in G1 phase but needs to be acetylated by ESCO1/2 during S phase to be stabilized

• partially dissociates and only attached to centromere in prophase

ESCO1/ESCO2

acetylates cohesion during S phase to stabilize the complex

Separase

in anaphase, cohesion completely dissociates → done so by separas

Robert’s Syndrome

cohesion not stabilized by ESCO2

• causes severe abnormalities of limbs and face as a result of slowed mitosis and damaged DNA

• - sister chromatids not linked correctly

DNA packaging in mitosis

chromatin condensed into radial-loop scaffolds

condensin 1 and 2

make the loops that go out from center structure to condense the chromatin

topoisomerase lla

untangles and opens up the DNA molecule

-allow other molecule to pass through it

further condensing of chromatin

Centromeres

heterochromatin consisting of A-T-rich DNA

• replaces H3 with variant called CENP-A to assemble to kinetochore

• kinetochore joins chromatid to spindle microtubules

meiosis overview

one replication but two divisions → haploid gametes

• only in germ cells

• increased genetic diversity through independent assortment and crossing over

law of segregation

homologous chromosomes separate at meiosis 1

expect 3:1 ratio when crossing heterozygotes

law of independent assortment

pairs of homologous chromosomes separate independently of one another

• allows new combinations of alleles in gametes

crossing over

exchange of genetic material of 1 chromatid to non-sister chromatid

Zygotenes

during prophase 1, onset of pairing homologous chromosomes at synaptonemal junctions

synaptonemal junctions

joins homologous chromosomes during crossing over

pachytene

assemble of recombination nodules at sites where crossing over occurs

• stage of prophase 1

diplotene

recombination between chromosomes at chiasmata

back-crossing

crossing a heterozygote with one of the parental genotypes

• method used in fly example about recombinant phenotypes displaying crossing over

overview of crossing over

• Spo11 cleaves phosphodiester bonds

• exonucleases degrade ends to expose single-stranded tails

• strand invasion of non-sister chromatid → heteroduplex

• reciprocal 2nd strand invasion

• branch migration lengthens heteroduplex region

• resolutions of holliday junctions

Spo 11

cleaves phosphodiester bonds at the beginning of crossing over to induce a double-strand break of the chromatid

heteroduplex

regions between holliday junctions where two strands may differ

holliday junction

X between non-sister chromatids during crossing over