Bio 13 Exam 2

Helicase

Separates the two strands of template DNA, energy from ATP hydrolysis “pays” to break the hydrogen bonds between base pairs

SSBPs (single strand binding proteins)

Bind to single strand DNA, prevents degradation or re-annealing (strands snapping back together)

Topoisomerase

Relieves supercoiling of DNA behind the replication fork by cutting the DNA backbone, unwinding the DNA, and resealing the backbone

Primase

Synthesizes RNA primer necessary to give DNA pol a starting 3’OH (synthesizes 5’ to 3’)

DNA Polymerase III

Adds appropriate nucleotide to 3’ end of RNA primer or new DNA strand

DNA Polymerase I

Removes ribonucleotides (RNA) from 5’ end of primer, adds deoxyribonucleotides to 3’ end of adjacent Okazaki fragments (gaps left between nucleotides not connected by phosphodiester bonds)

DNA Ligase

Catalyzes formation of phosphodiester bond between adjacent DNA segments (from Oka frags)

Telomeres

Ends of chromosomes, repeats of noncoding DNA so that when shortening occurs from replication the genes are not affected

Telomerase

Ribonucleoprotein (protein with RNA component). Enzyme that lengthens telomeres by synthesizing DNA to match and lengthen the unreplicated end. Usually only present in cells that will replicate many times

Promoter region

Only in prokaryotes, where RNA pol binds for transcription

UTR (prokaryotes)

5’ end, only 5-10 nucleotides long

Polycistronic

Prokaryotes are, meaning more than one gene is under the control of the same promoter. Either the long mRNA is cleaved or the final giant polypeptide is cleaved

Transcription Termination Signal (Prokaryotes)

encodes for mRNA to create a hairpin structure, intrastrand H-bonding creates secondary structure. Causes RNA pol to fall off (changes RNA pol conformation)

Transcription Termination Signal (Eukaryotes)

“Termination” is a PolyA signal

Transcription factors

General for all genes (recruit RNA pol) and specific for individual genes based on cell type, environment etc

Sigma Factor

General transcription factor for Bacterial transcription, recognizes specific sequences in promoter to orient RNA pol to determine which is the template strand (uses -35 box and -10 box).

RNA pol then opens helix by breaking h bonds, once synthesis of mRNA begins the sigma factor dissociates

Shine-Dalgarno Sequence

a ribosomal binding site (RBS) located in the 5' untranslated region (5' UTR) of mRNA

Formal Methionine

First met in prokaryotes, can only be the first AA

Translation Initiation for Eukaryotes

Ribosome binds to 5’ cap instead of the 5’ UTR, scans for start codons - UTR can be 100s to 1000s of nucleotides long, normal methionine instead of f-met

Active Site

part of ribosome where the codon matches with the tRNA anticodon

Peptidyl Site

part of ribosome where peptide bond forms between two amino acids

Exit Site

part of ribosome where amin acid detaches (tRNA stays stationary, ribosome moves along the mRNA)

Translation Termination

Stop codon - release factors mimic tRNA and bind into the A site, match up with stop codon and hydrolyze the covalent bond between tRNA and polypeptide chain and releases it into the cytoplasm. The complex of the ribosome, tRNA and polypeptide dissociates

Enhancers

a short region of DNA that binds proteins (called transcription factors) to increase the likelihood that a particular gene will be transcribed into messenger RNA

DNA Template Strand

What the mRNA will be complementary to

DNA Coding Strand/Non-Template

What the mRNA will mostly look like (T’s —> U’s)

Prokaryotic Transcription

Bacteria have no nucleus —> no spatial or temporal separation b/t transcription and translation, polysomes (multiple ribosomes translating mRNA at once)

RNA Polymerase II

Specific to mRNA synthesis

Eukaryotic Transcription Termination

no hairpin, RNA pol transcribes the polyA sequence —> RNA is cleaved and polyadenylated (by multiple enzymes). RNA pol keeps transcribing along after the cut, nucleases begin hydrolyzing the leftover RNA from the 5’ end behind the RNA pol and eventually knocks it off the DNA

5’ Cap

5’ Cap added (methyl guanosine) with a 5’ to 5’ triphosphate bond soon after transcription begins and prevents mRNA from being degraded by nucleases.

Splicing

Splicing performed next by spliceosome (complex of protein and small nuclear RNAs) and the snRNAs help by basepairing within the RNA so the spliceosome “knows” where to cut. Removed intron is called a “lariat” and is quickly degraded.

Alternative Splicing

Exon skipping/inclusion, intron retention, mutually exclusive exons (either one)

Addition of PolyA tail

~100-250 adenines after RNA cleavage at polyA signal sequence, added by Poly A polymerase,

Translation

polypeptide synthesized N to C terminus (template read 5’ to 3’)

Housekeeping Genes

Always expressed, used for extracting energy from nutrients

operon

multiple genes under same promoter (prokaryotes only)

LacY Gene

Creates permease, transports lactose into the cell

LacZ Gene

beta-galactosidase, breaks glycosidic linkages b/t glucose and galactose which lactose is made of

LacI Gene

encodes for repressor of lac operon if no lactose is present. if lactose IS present, then it allosterically regulates the repressor, causing it to detach from the operator region

CAP

catabolite activator protein (enhances transcription) binds to activator-binding region. w/o activator, some transcription still occurs

cAMP (cyclic AMP)

hunger signal, is high when glucose is low. binds to the activator and causing it to bind to the DNA and enhance txn.

nucleosome

DNA wound around histones

euchromatin

spread out,”free DNA” accessible for txn

heterochromatin

condensed, inaccessible for txn

DNA methylation

in mammals: cytosines can be methylated, methylcytosines are binding site for proteins that condense chromatin

Histone Modification

Histones have tails where func groups can be added/removed, can affect interactions with DNA or they create binding sites that compact chromatin or increase txn

Histone Acetylation

Histones have lots of positively charged lysines (an amino acid) which interacts strongly with negative DNA phosphate groups. An acetyl group neutralizes the positive charge, weakening the IMF between DNA and histones and allowing for greater gene expression

Enhancers

region of DNA for activators to bind, leading to increased txn

Silencers

DNA sequence where repressors can bind —> decreases txn

Mediator complex

necessary for distal components, loops DNA to bring enhancers/silencers physically closer to the promoter, impacts RNA pol II activity (txn levels)

RNA interference

(eukaryotes only): a biological response to the presence of double-stranded RNA that down-regulates expression of protein-coding genes

micro RNAs

encoded in the genome, decrease tln or mRNA stability of matching mRNAs. complementary intra-strand base pairing creates hairpin.precursor miRNA has ends trimmed, in cytoplasm the “loop” is trimmed

RISC

RNA induced silencing complex: unwinds the two strands of miRNA and matches them with mRNA (usually 3’ UTR)

Low Base Pair Match miRNA

RISC represses translation (recruits proteins to halt initiation)

High Base Pair Match miRNA

RISC cleaves mRNA —>rapidly degrades, no more tln

siRNA

short interfering RNAs, taken up by the cell from outside (ex added in a lab). Uses RISC to target coding region of mRNA of interest and decrease tln. Usually an exact match, mRNA is cleaved

Post-translational modification

most commonly is the addition of a fxnl group or larger molecule, can cause change in shape (conformational change) or affect binding partners (fxnl change)

Protein phosphorylation

kinases add phosphates, phosphatases remove them

proteolytic cleavage

splitting proteins like caspase, proteins made as inactive precursors and cut (peptide bonds hydrolyzed) to activate

targeted degradation

commonly, protein is ubiquitinated which tags it for destruction by proteasome complex (recycles protein into AA building blocks)

ERAD

Endoplasmic reticulum associated degradation —> misfolded proteins sent from ER to cytosol, tagged with ubiquitin, degraded by proteosome

centriole

2 inside each centrosome

prophase

DNA condenses

prometaphase

nuclear envelope breaks down, microtubules extend

mictrotubules

astral - attach to the plasma membrane

kinetochore - binds to chromosomes

polar - binds to microtubules on the opposite end of the cell

metaphase

chromosomes line up on the metaphase plate

anaphase

sister chromatids are separated, kinetochores degrade

telophase

nuclear envelope reforms, chromosomes decondense back into chromatin

cytokinesis

cytoplasm splits

plant cells: cell plate forms from vesicles

animals: ring of proteins pinch inwards

cyclins

levels oscillate over cell cycle, peak during start of M phase

Cyclin-Dependent Kinase (CDK)

when active, CDK phosphorylates target proteins that begin mitosis.

Regulation of CDK

cyclin binds and activates CDK so its active site is available for ATP to bind. Phosphorylation at the inhibition site inactivates CDK. Once the cell enters M phase, CDK is phosphorylated (inactivated) and the cyclin degrades

gamete

egg or sperm, cell with half the genetic info

zygote

product of fertilization between sperm and egg

bivalent

pair of homologous chromosomes held together by proteins

Independent assortment

genes on non-homologous chromosomes are sorted independently

Crossing over

exchange of DNA b/t non-sister chromatids of homologous chromosomes in prophase I