cell bio exam 1 - cells, unity and diversity, central dogma

molecules come together in cells with the help of four types of interactions

• non-covalent bonds

• electrostatic attraction

• van der waals forces

• hydrophobic forces

• hydrogen bonds

non-covalent bonds

interactions between neighboring molecules that are relatively weak and don’t involve sharing electrons

electrostatic attractions

permanent bonding between positive or negative charges between molecules

van der waals attraction

interactions due to movement of electrons in atoms, which create temporary dipoles; causes transient attraction when atom cores and electrons align by chance

hydrophobic force

hydrophobic molecules are driven together by water’s tendency to form hydrogen bonds with itself

hydrogen bonds

• special kinds of noncovalent bond

• occurs due to an unequal pull of electrons between H and an electronegative atom (F, N, O)

• strongest among intermolecular forces

[?] is a core principle shared by all cells and describes the flow of genetic information as [?]

the central dogma; DNA → RNA → protein

confocal microscopy

combines high intensity laser light with pinholes (blocks out-of-focus light that is reflected off the sample) to create an image with significantly higher resolution

in addition to membrane-less mechanisms, eukaryotic cells are also compartmentalized into membrane-bound organelles including

• nucleus - stores genetic info/DNA “information center”

• mitochondria - generates energy from food, own division and DNA distinct from cell “powerhouse”

• chloroplast - plants/algae, photosynthesis to create energy-rich molecules from light

• endoplasmic reticulum - synthesis of complex molecules

• golgi apparatus - continues synthesis of complex molecules, packages them for export/insertion into membrane

• cytoskeleton - contains three kinds of protein filaments (actin, microtubules, intermediate filaments), controls cell’s mechanical strength/shape/movement

theory of emergence of eukaryotic cells

believed that archael cell engulfed an early bacterial cell → beneficial symbiotic relationship b/c higher efficiency, energy sequestered in one region → evolution into early eukaryotic cell

in DNA, [?] bonds connect each nucleotide “step of the ladder” and [?] bonds connect the strands of complementary bases

phosphodiester & covalent; hydrogen bonds

what acts like engineers of transcription and interprets the information from DNA?

RNA polymerase, transcription factors (eukaryotes) or sigma factors (prokaryotes)

transcription proceeds in which direction?

5’ → 3’

RNA is different from DNA in three ways:

• RNA uses ribose sugars

• RNA uses uracil instead of thymine - more reactive, less stable

• RNA is single stranded and folds into specific structures

in eukaryotes, mRNA undergoes post-transcription processing in the nucleus which includes:

• addition of a 5’ cap

• addition of a poly-A tail to the 3’ end

• removal of introns via RNA splicing

how does RNA splicing work?

• spliceosomes: ribonucleoproteins made up of small nuclear RNAs to form a complex

• splicing factors (small proteins) attach to the ends of the introns

• spliceosome parts are guided by position of splicing factors and form the spliceosome complex

• spliceosome brings together ends of the exons together, cuts one end of intron and folds it on itself → loop, cuts off loop from remaining exon ends

• exon ends attached, intron and splice some disassemble

after mRNA is properly processed, it will be transported out of the nucleus, a process mediated by the

nuclear pore complex (holes in the nuclear membrane with proteins)

protein polymers are called

polypeptides, held together with covalent peptide bonds

amino acids are distinguished by

their side chains - gives proteins distinct chemistry, structure, function

tRNA structure

• made up of a single strand of RNA

• folded up into clover-like structure

• one end binds to amino acid; other end binds to codon of mRNA (anticodon)

how is an amino acid linked to a tRNA with a specific anticodon?

• enzyme aminoacyl-tRNA synthase able to recognize the specific tRNA and amino acid pair

• tRNA and amino acid bind to enzyme as substrates, enzyme catalyzes binding between the parts

ribosomes contain these three sites

• A - tRNA enters ribosome and amino acid is linked to elongating protein chain w/ peptide bond

• P - tRNA shifts over to this site with amino acid still attached; previous tRNA unbonds from its amino acid and shifts to E

• E - where the tRNA is ejected

• after tRNA is ejected from E, a new tRNA enters the A site

translation is initiated by [?] and ended by a [?]

start (AUG) codon; stop codon

regulation of protein abundance - increasing protein production

• polyribosomes

• several ribosomes bind at once to one mRNA in different locations

• creates spiral structures

• able to make many proteins at once

regulation of protein abundance - decreasing protein abundance

• protein breakdown by ubiquitin and proteasomes

• ubiquitin is a sequence chain that attaches to a site, which will “tag” it for degradation

• tagged protein enters proteasome and proteasome cleaves peptide bonds