Exam 2 (CH 5,6,7,8,9)

active site

The region on an enzyme where substrate molecules bind and undergo a chemical reaction.

amino acid

Organic molecules that are the building blocks of proteins, containing an amino group, carboxyl group, and side chain.

aminoacyl tRNA-binding site (A site)

The site on the ribosome where an aminoacyl-tRNA enters during translation.

aminoacyl-tRNA synthetase

An enzyme that attaches the correct amino acid to its corresponding tRNA.

amino group

A functional group (-NH2) found in amino acids and proteins.

anticodon

A sequence of three nucleotides in tRNA that pairs with the complementary codon in mRNA.

carboxyl group

A functional group (-COOH) found in amino acids and proteins.

chaperone

Proteins that assist in the proper folding of other proteins.

charged tRNA

A tRNA molecule that is bound to its specific amino acid.

codon

A sequence of three nucleotides in mRNA that codes for a specific amino acid or stop signal.

decoding center

The region of the ribosome responsible for ensuring proper base-pairing between codon and anticodon.

degenerate code

Refers to the fact that multiple codons can specify the same amino acid.

domain

A specific functional or structural region of a protein.

elongation factor (EF)

Proteins that assist in the elongation phase of translation by facilitating ribosome movement and accuracy.

exit site (E site)

The site on the ribosome where uncharged tRNA exits after delivering its amino acid.

fibrous protein

A type of protein with long, extended fiber-like shapes, often structural (e.g., collagen).

frameshift mutation

A mutation involving the insertion or deletion of nucleotides that alters the reading frame of a gene.

genetic code

The set of rules defining how sequences of three nucleotides (codons) specify amino acids.

globular protein

A type of protein with a compact, spherical shape, typically functional (e.g., enzymes).

initiation codon

The codon (usually AUG) that signals the start of translation.

initiation factor (IF)

Proteins that help assemble the ribosome and initiate translation.

initiator tRNA

The special tRNA that carries the first amino acid (methionine) in translation initiation.

kinase

An enzyme that adds phosphate groups to other proteins.

Kozak sequence

A sequence in eukaryotic mRNA that helps identify the start codon for translation.

large ribosomal subunit

The larger part of the ribosome where peptide bond formation occurs.

nonsense codon

A codon that signals the end of translation (UAA, UAG, or UGA).

nuclear localization sequence (NLS)

A sequence that directs proteins into the nucleus.

peptide bond

The covalent bond formed between amino acids during protein synthesis.

peptidyl site (P site)

The site on the ribosome where the growing polypeptide chain is held.

peptidyltransferase center

The ribosomal region where peptide bond formation between amino acids occurs.

phosphatase

An enzyme that removes phosphate groups from proteins.

phosphorylation

The addition of a phosphate group to a molecule, often regulating protein function.

polypeptide

A chain of amino acids linked by peptide bonds.

primary structure (of a protein)

The linear sequence of amino acids in a protein.

proteasome

A protein complex that degrades unneeded or damaged proteins by proteolysis.

quaternary structure (of a protein)

The arrangement of multiple polypeptide subunits in a protein complex.

reactive group (R group), side chain

The variable group attached to the central carbon of an amino acid, determining its properties.

reading frame

A way of dividing the sequence of nucleotides in mRNA into consecutive, non-overlapping triplets (codons).

release factor (RF)

Proteins that help terminate translation by recognizing stop codons.

ribosomal RNA (rRNA)

RNA molecules that are structural and catalytic components of the ribosome.

ribosome

A molecular machine that synthesizes proteins by translating mRNA.

ribosome-binding site (RBS)

A sequence on mRNA where the ribosome binds to initiate translation (especially in prokaryotes).

secondary structure (of a protein)

The local folding of a protein into alpha-helices and beta-sheets.

Shine–Dalgarno sequence

A ribosomal binding sequence in bacterial mRNA that aligns the ribosome with the start codon.

signal sequence

A short amino acid sequence that directs the transport of a protein to specific cellular locations.

small ribosomal subunit

The smaller part of the ribosome involved in decoding mRNA.

stop codon (termination codon)

A codon that signals the end of protein synthesis (UAA, UAG, UGA).

subunit

A distinct component of a larger protein complex, like a ribosome subunit.

synonymous codon

A codon that specifies the same amino acid as another codon due to redundancy in the genetic code.

termination factor

Proteins that aid in the termination of translation.

tertiary structure (of a protein)

The three-dimensional folding of a single polypeptide chain in a protein.

transfer RNA (tRNA)

An RNA molecule that brings amino acids to the ribosome during translation.

triplet

A sequence of three nucleotides that codes for an amino acid or stop signal.

ubiquitin

A small protein that tags other proteins for degradation by the proteasome.

ubiquitination

The process of attaching ubiquitin to a protein, marking it for degradation.

wobble

Flexibility in base-pairing at the third position of a codon, allowing some tRNAs to recognize multiple codons.

3' splice site

3' untranslated region ( 3' UTR)

5' splice site

5' untranslated region ( 5' UTR)

7-methylguanosine (m^7G)

allosteric termination model alternative splicing

branch point

cap

carboxy-terminal domain (CTD) consensus sequence

co-suppression

deadenylase

decapping enzyme

decay

deoxyribose

double-stranded RNA (dsRNA) downstream

elongation

endonuclease

exon

exonuclease

factor-independent termination general transcription factor (GTF) half-life

helicase

intron

isoform

long noncoding RNA (lncRNA) messenger RNA (mRNA)

microRNA (miRNA)

noncoding RNA (ncRNA)

non-template strand (coding strand) nucleolus

phosphodiester bond

poly(A) polymerase (PAP)

poly(A) tail

polyadenylation

precursor RNA (pre-RNA)

preinitiation complex (PIC)

promoter

proteome

Rho-dependent termination

ribose

ribosomal RNA (rRNA)

ribozyme

RNA editing

RNA interference (RNAi)

RNA polymerase

RNA polymerase I

RNA polymerase II