Exam 2

proteogenic amino acids

the molecular building blocks used by ribosomes to synthesize proteins

all standard amino acids contain

• a central alpha carbon

• one amino group

• one carboxyl group

• one hydrogen

• one variable side chain

the amino group of the amino acid is usually

protonated

the carboxyl group of an amino acid is usually

deprotonated

the side chain of an amino acid determines

• size

• polarity

• charge

• hydrophobicity

• chemical reactivity

Ribosomes usually incorporate amino acids in the _ configuration

L-configuration

__ amino acids exist but are usually not used during ribosomal protein syntheis

D-amino acids

how many canonical amino acids are there

20

Selenocysteine

the 21st genetically encoded amino acid where a selenium atom replaces the sulfur of cysteine

selenocysteine is incorporated at specific __ under specialized conditions

UGA stop codons

What domains of life is Selenocyteine present in?

all domains of life

Pyrrolysine

the 22nd genetically encoded amino acid, incorporated at UAG stop codons in certain archaea and bacteria

insertion of Pyrrolysine requires

• specialized RNA structures in the mRNA

• dedicated tRNAs

• specialized elongation factors

peptide bond

covalent bond linking adjacent amino acids in proteins

what type of reaction does peptide bonds form through

condensation reaction

a peptide bond is formed between what groups of two amino acids

the carboxyl group of one amino acid and the amino group of another amino acid

proteins are synthesized from ___ to __

N-terminus to C- terminus

peptide bonds possess partial double bond character because of

electron delocalization

Electron delocalization makes peptide bonds

relatively rigid, planar, and less rotationally flexible than most single covalent bonds

rigidity strongly influences

protein folding

Primary protein structure

linear amino acid sequence

primary structure of proteins is stabilized by

peptide bonds

primary structure of proteins encodes all

folding information requires for higher-order structure

secondary structure of proteins

local folding patterns including alpha helices, beta sheets, and loops/turns

the secondary structure of proteins is stabilized by

hydrogen bonds involving backbone atoms

tertiary structure of proteins

overall 3D folding of a single polypeptide chain

tertiary structure of proteins is stabilized by

• hydrogen bonds

• ionic interactions

• van der Waals interactions

• disulfide bonds

• hydrophobic interactions

the tertiary structure of proteins largely determines

protein structure

quaternary structure of proteins

assembly of multiple polypeptide subunits into a larger complex

what is the most dominant driving forces for folding of most soluble proteins?

the hydrophobic effect

in an aqueous environment, hydrophobic side chains tend to become

buried inside proteins

in an aqueous environment, polar and charged side chains tend to

remain solvent exposed

does protein folding occur nonspontaneous or spontaneously

spontaneously

why does protein folding occur spontaneously

folded conformations minimize energetically unfavorable interactions between water and hydrophobic residues

many proteins begin folding co-translationally as they

emerge from the ribosome

when proteins unfold, hydrophobic residues normally buried in the core become

exposed

exposing the hydrophobic residues causes

abnormal intermolecular interactions

exposed hydrophobic patches on proteins promote

aggregation and formation of insoluble protein complexes

protein misfolding and aggregation are associated with many

diseases

amino acid side chains are often broadly classified according to

charge, polarity, and hydrogen-bonding potential

polar/charged amino acids typically contain

oxygen, nitrogen, sulfur, or ionizable groups

nonpolar amino acids contain mostly

hydrocarbons and hydrophobic groups

hydrocarbons and hydrophobic residues typically __ within protein cores or membranes

localize

chiral molecule

a molecule whose mirror image cannot be superimposed on itself (non-superimposable)

enantiomers

pair of chiral molecules

mirror image biomolecules are __ versions of natural biological molecules

synthetic enantiomeric

because natural enzymes evolved to recognize natural stereochemistry, mirror-image biomolecules are often

resistant to enzyme degradation

What makes mirror image biomolecules attractive for therapeutic applications?

their resistance to enzyme degradation

many therapeutic nucleic acids are chemically modified to

resist nuclease degradation

common backbone modifications of nucleic acids

• phosphorothioates

• peptide nucleic acids (PNA)

• morpholinos

phosphorothioates

one non-bridging phosphate oxygen is replaced by sulfur

peptide nucleic acid

PNA; sugar-phosphate backbone is replaced by peptide-like backbone

advantages of the common backbone modifications of nucleic acids

• increases molecular stability

• prolong therapeutic activity

• improve pharmacological properties

limitations of synthetic mirror image nucleic acids

• synthesis becomes difficult for long molecules

• costs increase rapidly with length

• large-scale production remains challenging

a mirror image DNA polymerase could enzymatically amplify

mirror-DNA

Amplifying mirror DNA would enable

rapid large-scale synthesis of long mirror nucleic acifs

why must mirror proteins be synthesized chemically?

mirror ribosomes don’t exist

because mirror ribosomes don’t exist, ___ proteins are substantially easier to synthesize

smaller

how many nucleotides do typical cellular DNA polymerases synthesize per seconf?

hundreds to thousands

How many nucleotides does engineered mirror polymerase X synthesize per hour?

a few nucleotides

is it common for DNA polymerases to also transcribe RNA?

naur

dual DNA/RNA synthetic activity in engineered polymerases may reflect

altered substrate specificity under experimental conditions

amino group

functional group attached to the alpha carbon of every amino acid on the side opposite of the carboxyl group; NH₂

carboxyl group

the -COOH group at the side opposite of the amino group on every amino acid

left-handed animo acids

the L stereoisomers in which the amino group sits on the left when the molecule is drawn with the R group pointing towards you

right-handed amino acids

the D stereoisomer and the mirror image of the L forms

glycine

the smallest amino acid with hydrogen as its R-group

proline

an amino acid whose side chain loops back and covalently bonds to its own amino group, forming a rigid ring

cysteine

an amino acid with thiol (C-SH) as its R group

disulfide bond

a covalent S-S link formed when two cysteine oxidize

alpha helix

a right-handed coiled backbones conformation where each peptide bond’s NH hydrogen bonds to the carbonyl oxygen 4 residues ahead

beta sheet

a flat, pleated structure formed when extended peptide segments lie side by side and hydrogen-bond across strands

ribbon diagram

a schematic protein drawing where alpha helices appear as coiled ribbons, beta strands as flat arrows, and loops as thin tubes

post-translational modification

any covalent change made to a protein after it is synthesized

protein aggregation

the clumping of misfolded or partially unfolded proteins into insoluble assemblies, often via exposed hydrophobic patches or cross-beta structures

aptamer

a short-single stranded nucleic acid that folds into a specific 3D shape and binds a target molecule with high affinity and specificity

right-handed DNA

the standard B-form double helix, which twists clockwise when viewed down its axis

genetic code

defines how nucleotide triplets (codons) are translated into amino acids during protein synthesis

how many codons are in the genetic code

64

how many codons in the genetic code are sense codons

61

how many codons in the genetic code are stop codons

3

what are the three stop codons

UAA, UAG, AND UGA

what is the start codon that begins translations

AUG

what amino acid does AUG encode

methionine

the genetic code is largely __ across life

quasi-universal

what does the genetic code being quasi-universal across life suggest

ancient evolutionary origin

how many amino acids does each codon specify

one; the code is unambiguous

how is the genetic code redundant (degenerate)

multiple codons encode the same amino acid

exceptions to the genetic code

• mitochondria (uses variant genetic code)

• rare organisms (display limited codon reassignment)

translation machinery

• mRNA

• polycistronic mRNAs

• tRNAs

• aminoacyl-tRNA synthetases (aaRs)

• ribosomes

• initiation factors

• elongation factors

• release/recycling factor

mRNAs contain

one or more open reading frames (ORFs)

each mRNA open reading frame consists of

codons between the stop and start codons

polycistronic mRNAs are common in

prokaryotes

polycistronic mRNAs are rare in

eukaryotes

tRNA

an adapter molecule that recognizes codons through anticodons and delivers amino acids to the ribosome

how many nucleotides long is the translation machinery

70-90

which end is the amino acid attached to

3’

aminoacyl-tRNA synthetases (aaRs)

enzymes that attach the correct amino acid to its corresponding RNA

why is high fidelity essential with aminoacyl-tRNA synthetases (aaRs)

incorrect aminoacylation can cause mistranslation

how many aminoacyl-tRNA synthetases (aaRs) do most organisms possess

at least one for each amino acid