ch 14 genetics

Section 14.1 Learning Objective

Discuss how the concept of a gene changed as geneticists learned more about the molecular nature of genetic information.

Gene concept evolution

A sequence of DNA nucleotides transcribed into a single RNA molecule, though complex transcription makes this definition problematic.

Introns vs Exons distribution

Introns are noncoding sequences that interrupt coding sequences (exons); common in eukaryotic cells, rare in bacterial cells.

Section 14.2 Learning Objective

Outline the different ways that mRNAs are modified in eukaryotic cells.

mRNA primary regions

A 5' untranslated region, a protein-coding region, and a 3' untranslated region.

Bacterial vs Eukaryotic mRNA processing

Bacterial mRNA is translated immediately with little processing; eukaryotic pre-mRNA undergoes 5' capping, 3' cleavage, polyadenylation, internal base modification, and splicing.

Spliceosome

A structure composed of several small nuclear RNAs (snRNAs) and proteins that removes introns from pre-mRNA.

Self-splicing introns

Some introns found in rRNA genes and mitochondrial genes can excise themselves without proteins.

Alternative processing of pre-mRNA

Different combinations of exons are spliced together or pre-mRNA is spliced at different 3' cleavage sites to produce multiple protein variants from one gene.

RNA editing

Alteration of mRNA sequence by addition, deletion, or modification of nucleotides in the coding sequence post-transcriptionally.

Section 14.3 Learning Objective

Describe the structure and processing of tRNAs.

tRNA structure and modification

Short molecules that form a cloverleaf secondary structure, attach to amino acids, and contain modified bases.

tRNA processing

Processed by cleavage, trimming, nucleotide addition, and base modification.

Section 14.4 Learning Objective

Compare the structures of prokaryotic and eukaryotic ribosomes and describe how rRNA is processed.

Ribosome structure

Sites of protein synthesis composed of several rRNA molecules and numerous proteins organized into small and large subunits.

Prokaryotic vs Eukaryotic ribosomes

Differ in size and number of rRNA molecules and proteins (70S in prokaryotes vs 80S in eukaryotes).

rRNA processing

Ribosomal RNA is extensively modified in both prokaryotes and eukaryotes.

Section 14.5 Learning Objective

Describe the types of small RNAs and their functions.

Small RNA functions

siRNAs, miRNAs, piRNAs, and crRNAs play important roles in gene silencing, defense, and regulation.

Section 14.6 Learning Objective

Describe lncRNAs and circRNAs and their functions.

Long noncoding RNAs (lncRNAs)

Non-protein-coding RNA molecules longer than 200 nucleotides that function in controlling gene expression.

Circular noncoding RNAs (circRNAs)

Common noncoding RNAs formed into closed loops that can serve as sponges or decoys for miRNAs.

colinearity

Direct linear correspondence between the nucleotide sequence of a gene and the amino acid sequence of the encoded protein.

exon

Coding region (and untranslated regions) of a gene that remains in the mature mRNA after splicing.

intron

Noncoding sequence within a gene that is transcribed into pre-mRNA but excised before translation.

group I intron

Self-splicing intron found in nuclear rRNA and organelle genes that requires an external guanosine nucleoside.

group II intron

Self-splicing intron found in organelle and bacterial genes that splices via a lariat-like intermediate.

nuclear pre-mRNA intron

Standard eukaryotic nuclear introns that require a spliceosome for removal.

transfer RNA intron

Introns in tRNA genes excised by protein-catalyzed cleavage and ligation reactions rather than splicing complexes.

codon

Sequence of three nucleotides in mRNA that specifies a single amino acid or translation stop signal.

5' untranslated region (5' UTR)

mRNA sequence upstream of the start codon that regulates ribosome binding and translation initiation.

Shine–Dalgarno sequence

Consensus sequence (5'-UAAGGAGG-3') in bacterial 5' UTRs serving as the ribosome-binding site.

protein-coding region

mRNA segment between the start and stop codons that codes for the polypeptide chain.

3' untranslated region (3' UTR)

mRNA sequence downstream of the stop codon that affects mRNA stability, localization, and translation.

5' cap

Modified 7-methylguanosine base attached to the 5' end of pre-mRNA via a 5'-to-5' triphosphate linkage.

poly(A) tail

Stretch of 50 to 250 adenine nucleotides added to the 3' end of pre-mRNA following cleavage.

RNA splicing

Process of excising introns and joining exons together to form a mature mRNA.

5' splice site

Conserved junction at the 5' end of an intron (usually GU) where the first cleavage reaction occurs during splicing.

3' splice site

Conserved junction at the 3' end of an intron (usually AG) where the second cleavage reaction occurs during splicing.

branch point

Adenine nucleotide within an intron (18–40 nucleotides upstream of 3' splice site) required for lariat formation.

spliceosome

Large ribonucleoprotein complex composed of snRNAs and proteins (snRNPs) that catalyzes pre-mRNA splicing.

lariat

Loop-and-tail structure formed when the 5' end of an excised intron forms a 2'-5' phosphodiester bond with the branch point adenine.

trans-splicing

Splicing reaction joining exons from two separate pre-mRNA transcripts into a single mRNA.

alternative processing pathway

Mechanisms like alternative splicing or multiple 3' cleavage sites that yield distinct mRNAs from one gene.

alternative splicing

Process by which specific exons or splice sites are selectively included or excluded to produce varied protein isoforms.

multiple 3' cleavage sites

Presence of two or more polyadenylation sites on a pre-mRNA, producing mRNAs of different lengths.

RNA editing

Post-transcriptional alteration of mRNA nucleotide sequences through base insertion, deletion, or chemical conversion.

guide RNA (gRNA)

Small RNA that hybridizes with pre-edited mRNA to provide a template for nucleotide insertion or deletion during RNA editing.

modified base

Standard base in tRNA or rRNA that is chemically altered post-transcriptionally (e.g., pseudouridine, inosine).

tRNA-modifying enzyme

Enzyme that chemically converts standard bases in tRNA precursors into modified bases.

cloverleaf

Characteristic two-dimensional secondary structure of tRNA consisting of four major stems and loops.

anticodon

Sequence of three nucleotides on the central loop of a tRNA that base-pairs with a complementary codon on mRNA.

large ribosomal subunit

Larger component of the ribosome (50S in prokaryotes, 60S in eukaryotes) containing peptidyl transferase activity.

small ribosomal subunit

Smaller component of the ribosome (30S in prokaryotes, 40S in eukaryotes) that binds mRNA and matches codons to tRNAs.

RNA interference (RNAi)

Gene-silencing mechanism driven by small noncoding RNAs that trigger target mRNA degradation or translation inhibition.

RNA-induced silencing complex (RISC)

Protein-RNA complex containing single-stranded siRNA or miRNA that targets complementary mRNA for silencing.

long noncoding RNA (lncRNA)

Non-protein-coding RNA longer than 200 nucleotides involved in gene regulation, chromatin remodeling, and scaffolding.

enhancer RNA (eRNA)

Noncoding RNA transcribed from enhancer regions that helps drive target gene expression by stabilizing chromatin loops.

circular RNA (circRNA)

Noncoding RNA formed into a closed continuous loop via back-splicing, often acting as miRNA sponges.