Module 1

Nucleotide

sugar, nitrogenous base, and phosphate

make up DNA

Nucleoside

sugar and nitrogenous base

Deoxyribose

the DNA sugar

has a hydrogen on the 2’ carbon

Purines

nitrogenous bases with two rings

includes adenine (A) and guanine (G)

Pyrimidines

nitrogenous bases with one ring

includes cytosine (C), thymine (T), and uracil (U)

5’ End of DNA and RNA

phosphate group

3’ End of DNA and RNA

hydroxyl group

DNA Polymerase

enzyme that synthesizes DNA 5’ to 3’

Phosphodiester Bond

covalent bond linking nucleotides

Hydrogen Bonds

bond type between nitrogenous bases/base pairs formed through partial charges

two between adenine and thymine and three between cytosine and guanine

Ribose

the RNA sugar

has a hydroxyl on the 2’ carbon

Transcription

synthesis of RNA from DNA template

occurs in the nucleus and mitochondria

occurs 5’ to 3’

Genes

units of DNA that are transcribed by RNA polymerase to RNA

Template/Antisense Strand

strand of DNA read from 3’ to 5’ when RNA polymerase synthesizes RNA

Coding/Sense Strand

matches the new RNA strand with thymine instead of uracil

Messenger RNA (mRNA)

RNA that will be translated into protein

Regulatory Sequences

control when and where a gene is expressed

Enhancers & Silencers

cis-regulatory elements that fine tune the spatiotemporal pattern of gene expression

may be distant from the gene they control

Exons

expressed sequences

Introns

intragenic or intervening sequences

pre-mRNA

contains exons and introns

before splicing

Open Reading Frame (ORF)/Coding Sequence (CDS)

within the exons from start codon to stop codon

translated into protein

Promoter

immediately 5’ to transcriptional start site

docking site for RNA polymerase II and other transcriptional proteins

Start Codon

ATG which codes from methionine (met)

Stop Codons

TAA, TAG, and TGA

Untranslated Regions (UTRs)

contained in the first and last exon

5’ Untranslated Region

between transcriptional start site and translational start site

has roles in translation initiation and ribosome binding

3’ Untranslated Region

between stop codon and end of transcript

roles in poly(A) addition, mRNA export, stability, and localization, and translation efficiency

5’ Cap

co-transcriptional pre-mRNA processing in which a 7-methylguanosine is linked with 5’-5’ triphosphate linkage

confers stability and has roles in mRNA splicing, transport, and interaction with ribosomes

Splicing

co-translational processing that generates mature mRNA by getting rid of introns

Splice Donor & Acceptor Sites

sequences recognized by splicing machinery

Branch Site

sequence about 20 nucleotides from splice acceptor site that is recognized by splicing machinery

Spliceosome

consists of small nuclear ribonucleoproteins

Alternative Splicing

mRNA transcripts may not always be spliced the same way

SR Activator Proteins

serine and arginine rich proteins that bind to splicing enhancers to favor exon inclusion

hnRNP Repressor Complexes

bind to splicing silencers to favor exon skipping/exclusion

Poly(A) Signal Sequence

sequence in 3’ UTR required for transcription termination

AAUAAA

single mRNA may have multiple/alternative ones

Poly(A) Tail

posttranslational processing in which poly(A) polymerase adds non-templated adenosines to 3’ end of cleaved mRNA

length varies

aids in nuclear export and translation and stabilized mRNA

Peptide Bonds

hold amino acids together

N-Terminus

amino portion of an amino acid chain

C-Terminus

carboxyl portion of an amino acid chain

Ribosome

made of rRNAs and proteins in two subunits

critical for translation

Transfer RNAs (tRNAs)

bring amino acids to the ribosome

covalently carry amino acids with ester bonds

Anti-Codon

found on tRNAs and base pair with mRNA

Initiator tRNA

binds to 5’ cap and recognizes start codon

needed to begin eukaryotic translation

carries Met

Kozak Consensus Sequence

sequence that surrounds the start codon (AUG) and indicated which AUG is the start codon

Primary Protein Structure

amino acid sequence

Amino Acids with Nonpolar Side Chains

Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, and Pro

Amino Acids with Polar Uncharged Side Chains

Ser, Thr, Tyr, Asn, Gln, and Cys

Amino Acids with Polar Charged Side Chains

Acidic (-): Asp and Glu

Basic (+): Lys, Arg, and His

Secondary Protein Structure

hydrogen bonds within the backbone allow formation of alpha helices and beta sheets

Protein Tertiary Structure

covalent (disulfide) and noncovalent bonds between side chains in a single polypeptide

folding is crucial for function

Protein Quaternary Structure

covalent and noncovalent interactions between polypeptides