Gene Expression I

What are the 4 nucleotides of DNA?

Adenine, Cytosine, Guanine, and Thymine

What is the basic structure of DNA?

double-stranded helix, with strands running antiparallel, end is 5’ phosphate and 3’ deoxyribose sugar

How do DNA bases pair?

A with T, C with G

What is the definition of a histone?

proteins that act as spools for DNA

What is the definition of a nucleosome?

histone with DNA wrapped around

What is the definition of chromatin?

loose, uncoiled form of DNA comprised of repeating nucleosome units (present in interphase)

What is the definition of chromosome?

tightly condensed chromatin, present during mitosis and meiosis

What is the definition of heterochromatin?

condensed DNA (hard to get to)

What is the definition of euchromatin?

loose and active chromatin (unwound)

What is the definition of a gene?

region of DNA that controls a discrete hereditary characteristic, usually corresponding to a single protein/RNA

What is an allele?

different versions of a gene

What is the central dogma?

DNA→ transcription → RNA → RNA processing → translation→ Protein → protein folding

What is transcription?

The process where DNA is transcribed into RNA

How is RNA different from DNA?

RNA nucleotides are ribonucleotides with a ribose sugar and contain uracil instead of thymine that pairs with adenine. RNA is usually single-stranded, short, short-lived, and can fold into many 3-D structures

What is mRNA?

messenger RNA, template for protein production from a gene

What are the steps of transcription?

initiation, elongation, and termination

What are the 2 most important proteins for transcription?

RNA polymerase II and general transcription factors

What are the steps of transcriptional initiation?

general transcription factors and RNA polymerase II bind to the promoter, DNA is unwound to make the single-stranded template

What are the steps of transcriptional elongation?

nucleotides are added to the mRNA strand by phosphorylation of Pol II by TFII to build RNA 5’→3’

What is the process of transcriptional termination?

polyadenylation signal (AAUAAA) appears in RNA transcript, RNA is cleaved and a polyA tail is added, RNA, RNA polymerase and DNA separate

What is unprocessed mRNA called?

pre-mRNA

What are the key steps of RNA processing?

addition of a 5’ cap, removal of introns by splicing, and addition of a 3’ polyA tail

Where does transcription occur in the cell?

in the nucleus

Where does RNA processing occur?

in the nucleus, required for mRNA to go into the cytoplasm

Where does translation occur in the cell?

in the cytoplasm, associated with ribosomes

When is the 5’ cap added to pre-mRNA?

when RNA emerges from polymerase during elongation

What is the 5’ cap that is added to pre-mRNA?

modified guanosine, it aids in mRNA stability and translation

When is the 3’ tail added to pre-mRNA?

during termination of transcription

What are exons?

protein-coding sections of genes

What are introns?

non-protein-coding regions of genes

What is the goal of splicing?

to remove introns from pre-mRNA

What facilitates splicing?

spliceosome which is made up of several small snRNA and protein factors

What does the spliceosome do?

cleaves and removes introns, joins exons to create final mRNA

What is the goal of translation?

mature mRNA to protein

What are amino acids?

building blocks of proteins made of backbone and side chain (R group). There are 20 that are classified on the side chain properties, negative, positive, uncharged polar, and nonpolar

How are amino acids linked together?

covalent peptide bond

What is the amino/N terminus of a protein?

the end of the protein carrying the amino group (NH3+)

What is the carboxy/C terminus?

the end of the protein carrying the free carboxyl group (COO-)

What are the forms of protein structure?

primary, secondary, tertiary, and quaternary

What is primary structure of proteins?

amino acid residues linked together, beads on a string

What is secondary structure of proteins?

alpha helices or beta sheets, relationships of amino acids together. stabilized by hydrogen bonds

What is tertiary structure of proteins?

relationship of tertiary structures, mediated by attraction between secondary structures

What is quaternary structure of proteins?

multiple tertiary structures together, oligomers (2+ polypeptides), dimers, etc. each polypeptide is called a subunit

What is a protein domain?

discrete folded units within a protein, usually have distinct properties

What is a transmembrane domain?

sequential stretch of 20-25 hydrophobic amino acid side chains in a protein that are placed within a hydrophobic cell membrane

What is the difference between a protein domain and protein subunit?

A protein subunit is 1 polypeptide that is part of a quaternary structure (oligomer) while a protein domain is a region of a protein that has a specific function

What is a codon?

set of three nucleotides in mRNA that encodes for an amino acid

What is the start codon?

AUG- methionine

What are the stop codons?

UAA (U Are Annoying), UGA (U Go Away), UAG (U Are Gone)

What is a reading frame?

RNA sequence can be read in one of three reading frames depending on where you start in a codon

What are the basic steps of translation?

initiation, elongation, termination

What is the initiation complex of translation?

tRNA, large ribosomal subunit, small ribosomal subunit, and mRNA

What is a ribosome?

larger complex of proteins and RNA’s that exist as two subunits (small and large)

What is a transfer RNA (tRNA)?

RNA molecule that recognizes and binds both the mRNA and amino acid

What occurs during initiation of translation?

ribosome, mRNA, and initiator tRNA form the initiation complex, codon for methionine is recognized by the initiator tRNA

What occurs during translational elongation?

tRNA that matches the next exposed codon within the ribosome brings the right amino acid, peptide bonds are formed between the amino acids building the polypeptide chain and cycle repeats a lot

What occurs during termination of translation?

a stop codon is reached, a release factor recognizes the stop codon, machinery dissociates, and polypeptide is released

What is alternative splicing and what is the goal?

different mRNA’s are generated from the same primary transcript of RNA, the goal is to be able to make all the necessary proteins from a limited amount of genetic information

What is the process of alternative splicing?

specific exons are cut-out along with the introns to make specific combinations of exons

What is the goal of post-translational modifications (PTM’s)?

regulating protein activity, levels, location, and/or interactions

What is phosphorylation as a PTM?

addition of a phosphate group to serine, threonine, or tyrosine. Added by kinases and can be removed by phosphatases to activate, deactivate, or change protein’s behavior

What is ubiquitination (ubiquitylation)?

addition of small protein (ubiquitin) to lysine residues, added by E3 ligases and reversed by DUB’s.

What does ubiquitination do?

mark a protein for degradation by a proteosome, modulates receptor endocytosis, DNA repair and alter transcription by adding to histones

What is proteolytic processing?

protein cleavage to convert enzymes from an inactive to active form, ensure activity or function at a particular time/location

What is the major goal of cancer therapeutics?

inhibiting transcription or splicing in tumors because they are dependent on transcription

What are some kinds of cancer therapeutics?

inhibition of transcription, spliceosome inhibition, combination therapy (target RNA splicing strategies)