BSCI 330 Exam 2

central dogma

how information flows & determines when/how much translation/transcription occurs

prokaryote & eukaryote central dogma

DNA → RNA → Protein

how information content flows

DNA → mRNA → Protein

exceptions to central dogma

• retroviruses= converts RNA to DNA then protein

• transposons= DNA extracts themselves them reinsert later

• telomerase= synthesizes DNA from RNS to build telomeres

rna transcription

generates a single-stranded RNA molecule complementary to the DNA template strand

RNA is synthesize ___ and DNA is read ___

5’-3’ , 3’-5’

promoters

DNA sequences that initiate transcription

• prokaryotes= RNA polymerase binds strongly

• eukaryotes= requires general transcription factors

elongation factors

extends RNA chain

ATP hydrolysis

helps RNA polymerase move along chromatim

when does RNA transcription stop?

after RNA polymerase encounters special DNA sequence

• prokaryote= terminator

• eukaryote polyadenylation signal

mRNA processing

addition of methlguanosine cap to 5’ end of RNA

5’ cap

bonefied unbroken end that marks as RNA-to-be

exons

expressed sequences

introns

intervening sequences that interrupt coding sequences

RNA splicing

process of removing introns directed by RNA sequences found at intron-exon boundaries

• extremely flexible process that has many patterns

splicesome (snRNP)

small nuclear RNAs + multiple proteins

• assembles on pre-mRNA while being transcribed

poly-A tail

200-A’s added to the 3’ end by poly-A polymerase

• important for export from the nucleus & protein synthesis

where does RNA synthesis & processing occurs?

nucleus

where does protein synthesis occur?

cytosol

protein synthesis

peptide chain is added to the last tRNA and a new aminoacyl tRNA replaces it

non-coding RNAs

• snRNA

• snoRNA

• tRNA

• siRNA

• miRNA

once exported to the cytosol ___ is translate into ___ by ___

mRNA, protein, ribosome

triple nucleotide code

4 × 4 × 4 = 64 combinations

• to be able to form 20 different amino acids

codon

3 nucleotides combined to form amino acids

degenerate nature of genetic code

for a given protein sequence there may be more than one RNA sequence

tRNA

short RNA with a distinctive 3D structure that matches amino acids with codons

• contains anticodon loop that complements the amino acid codon

aminoacyl-tRNA synthetase

couples amino acid to tRNA where each amino acid has a different synthetase

conjunction to AMP

amino acid is activated and transferred from AMP to tRNA and synthetase proofreads for accuracy once complete

ribosome

where protein translation occurs

• can only synthesize 1 peptide chain at a time

polyribosome

a single mRNA that has several ribosomes translating simultaneously

ribozyme

catalytic core made up of rRNA that reads mRNA from 5’-3’ 3 bases as a time

AUG

starts translation

• uses initiator tRNA

elongation factors

facilitates translation elongation by GTPase activity which proofreads & speeds up ribosome translocation

UAA, UAG, UGA

terminates translation

• ribosome dissociates into subunits, releases mRNA, tRNA, & release factor

release factor

binds to ribosome & causes peptidyl tRNA hydrolysis to release protein

antibiotics

protein synthesis inhibitors the only affect prokaryotes due to differences between ribosomes

• cycloheximide= blocks eukaryotic translations reaction

• puromycin= cause premature termination to block eukaryotic ribosomes

why is protein & RNA synthesis energetically costly?

• conversion of NTP to NMP

• elongation

• mRNA splicing

• protein proofreading

information content of protein

• 3D structure

• cellular location

• protein function

information content of mRNA

• all content for proteins

• initiating translation

• terminating translation

information content of DNA

• all content of proteins & mRNA

• initiating transcription

• terminating transcription

• splicing

protein structure is determined by the ___ and divided into ___ or ___ domains

sequence of amino acids, functional, structural

polypeptide chains

highly ordered 3D structures that determines protein function

primary structure

linear sequence of amino acid residues determined by mRNA code

secondary structure

folding & twisting peptide backbone held together by weak H bonds

alpha helices

rigid cylindrical structure that forms when 4 amino acids are apart on the polypeptide backbone

• coils in a clockwise direction

beta sheets

flat sheet-like structures that forms when polypeptide chains are adjacent that are parallel or anti-parallel

rigid proline

inserts kink into protein backbone that disrupts secondary structures

tertiary structure

3D arrangement of secondary structures held together by non-covalent interactions between R-groups & surrounding environment

R-groups interactions

leads into folding secondary structure into 3D structures

covalent disulfide bonds

forms between cysteine residues to cross-link parts of the backbone to stabilize structure

3D folding

protein takes on the lowest energy state

• hydrophilic head= pointed out

• hydrophobic tail= pointed in

chaperonins

provides isolated chemical environment so proteins can fold

1. protein binds to chaperonin cage & enters it

2. lid seals the cage

3. protein folds into its appropriate shape & is released

quaternary structure

arrangement of multiple tertiary structures held together by weak & disulfide bonds

homomers

identical subunit polypeptides

heteromers

different subunit polypeptides

covalent modifications

rapid reversible phosphorylation that is coded by short amino acid sequence which causes changes in chemical properties of amino acid side chains

proteolytic cleavage modifications

removes amino acids from original sequence

phosphorylation

adding negatively charges phosphate group to serine, threonine, or tyrosine which is catalyzed by protein kinases

protein phosphatases

reverse phosphorylation by removing phosphate

phosphorylation drives what changes?

• structural

• activity

• solubility

• may create a new recognition site

ubiquitin

small cytosolic protein covalently attached to other proteins that serve as a tag for protein degradation & directs proteins to specific locations in the cell

ligands

molecule that all proteins bind through & determine biological properties

true or false: non-covalent bonds are reversible

true

enzyme catalysts

stabilize the reaction transition state by lowering the activation energy to speed up cellular reactions

• only required in small amounts

• must be left unchanged at the end of a reaction

• catalyzes forward & backward reactions equallt

cofactors

non-protein components for enzyme function

• enzyme prosthetic groups

coenzymes

organic molecules that act as cofactors

allosteric regulation

non-substrate ligands with a shape that is distinct from the enzyme’s own natural shape that regulates enzymes

• binds at a site away from the catalytic site

• may be part of the protein chain or a regulatory subunit

how enzyme catalysts function

1. bind to substrate at stereo-specific site

2. form enzyme-substrate complex

3. substrate is chemically converted to product

4. form enzyme-product complex

Vmax

rate when the enzyme is saturated with substrate

Km

dissociation constant for enzyme-substrate complex

• lower = enzyme has higher affinity for substrate

transition states

when substrates go through a state with a higher energy level before the reaction

prosthetic groups

non-protein molecules that aid protein function that are covalently or non-covalently bound by the protein

molecular tunnels

distinctive active sites where enzymes perform sub reactions & direct the intermediate products from one active site to the next

• prevents the diffusion of intermediates

• prevents decomposition of unstable molecules

• speeds reaction rates

multi-enzyme complexes

enzymes in metabolic pathways that require reactions to occur in a specific highly regulated order

• prevents the diffusion of the products & allows for coordination regulation of the pathway

why are enzymes tightly regulated?

so they can quickly respond to changing cellular & extracellular conditions

true or false: most enzymes constitutively active

false, they must be turned on or off

molecular integrators

regulation of key enzymes that involve multiple inputs

feedback control

a downstream product regulates an upstream enzyme in a given pathway

irreversible enzyme inhibitors

covalently bind to amino acid residue to inactivate & remove active enzyme molecules

• rare in nature

• lowers Vmax

reversible enzyme inhibitors

competitive or non-competitive

• common in nature

competitive inhibitors

reversibly bind to the active site & compete with substrate

• increases Km

non-competitive inhibitors

reversibly bind away from the active site which causes change in enzyme structure

• lowers Vmax

• lowers catalytic efficiency

molecular motors

shape changes in proteins generate movement

molecular pumps

have the ability to transport molecules across membranes

molecular pumps enable proteins to

• take in nutrients

• export waste

• receive & send signals

• pump specific substances into/out of the cell/organelles

• harness energy from

  • ATP/GTP hydrolysis

  • movement of ions

  • transfer of high energy electrons

ABC transporters

pumps that export hydrophobic molecules out of the cell in eukaryotes & import nutrients in bacteria

hydrolysis of ATP drive ___ changes that allows molecules to ___ the membrane

conformational, move across

steps of cell communication

• reception

• transduction

• response

signaling molecules reaching the target

extracellular signal molecules are secreted & act over short or long distances

paracrine signaling

local mediators that only affect cells in the immediate environment of the signaling cell

endocrine signaling

travel long distances through the bloodstream to act on distant targets

synaptic signaling

travel via axons

autocrine signaling

cells secrete signal molecules that bind back to its own receptor

contact dependent signaling

signal molecules that remain bound to the surface of the signaling cell & influence cells in contact

• embryonic development immune responses

overall action of signaling molecules

extracellular signals that act slowly or rapidly to alter target cell function

• each cell type is restricted to different environments in the body

• each cell is programmed to respond to specific combos signaling molecules

• different cells respond differently to the same signaling molecule

• the same signaling molecule can have different effects on a cell depending on the concentration

morphogens

molecules thar diffuse out from signaling centers in developing tissues

• creates morphogen concentration gradient

types of signals from signaling molecules

• mechanical

• light

• heat

• chemical

forms of chemical stimuli

• secreted from cell into extracellular space

• exposed to extracellular space while remain tightly bound to cell surface

• released by diffusion through plasma membrane

molecules secreted from cell as chemical stimuli

• amino acids, small peptides, proteins

• nucleotides

• steroids

• fatty acid derivatives

• dissolved gases

lipid soluble signals

• cortisol→ influences metabolism (adrenal glands)

• sex hormones→ determines secondary sex characteristics(ovaries & testes)

• vitamin D→ regulates Ca uptake & excretion (skin)

• thyroxin→ regulates metabolism (thyroid hormone)