Genetics - Exam 3 Study Set

gene expression 

transcription and translation 

hairpins 

when short, complimentary regions within a nucleotide strand pair and form secondary structures 

rRNA 

a type of RNA molecule that makes up the ribosome; RNA molecule that is a structural component of the ribosome 

mRNA 

a type of RNA that carries the coding instructions for a polypeptide chain and provides a template for the joining of amino acids; carries genetic information for the amino acid sequence of a protein 

Pre-mRNA(pre-messenger RNAs) 

eukaryotic RNA molecule that is modified after transcription to become mRNA 

tRNA 

a type of RNA molecule that carries an amino acid to the ribosome and transfers it to a growing polypeptide chain in translation 

3 Requirements of Transcription 

1. DNA template 

2. Substrates in triphosphate form (ribonucleoside triphosphates: ATP, CTP, GTP, UTP) 

3. RNA polymerase (+ other proteins) 

Christmas Tree Transcription 

where each tree represents a gene undergoing transcription; the “trunks” are DNA molecules, “branches” are mRNA and where the branches are the longest is the 5’ end whilst the shorter end is the 3’ end; the promoter is located on the shorter side and transcription begins here 

template strand 

the strand being used for transcription; RNA is synthesized from this strand and that RNA is complementary and antiparallel to this strand 

non-template strand(coding strand) 

the strand that is complementary to the template strand but is not transcribed 

transcription unit 

a stretch of DNA that encodes an RNA molecule and the sequences necessary for transcription 

Requirements of a transcription unit 

1. Promoter 

2. RNA-coding region 

3. Terminator  

promoter 

a DNA sequence that the transcription apparatus recognizes and binds to; it also indicates which of the two DNA strands is the template and the direction of transcription; is NOT transcribed 

RNA-coding region 

sequence of DNA nucleotides that encodes an RNA molecule 

terminator 

sequence of DNA nucleotides that causes the termination of transcription; is part of the RNA-coding sequence 

upstream 

located towards the promoter region 

downstream 

located towards the terminator region 

ribonucleoside triphosphates (rNTPs) 

an RNA molecule that is composed of a ribose sugar, base (nucleoside), and three phosphate groups 

RNA polymerase 

enzyme that synthesizes RNA from a DNA template during transcription; each one has a consensus sequence that recognizes it 

RNA polymerase I 

eukaryotic RNA polymerase that transcribes rRNA 

RNA polymerase II 

eukaryotic RNA polymerase that transcribes pre-mRNAs, mRNAs, snoRNAs, some miRNAs, and snRNAs 

RNA polymerase III 

eukaryotic RNA polymerase that transcribes tRNAs, small rRNAs, some miRNAs, and some snRNAs 

RNA polymerase IV & V 

plant RNA polymerases 

Bacterial RNA polymerase 

the only type of RNA polymerase within a prokaryote that catalyzes the synthesis of all RNA (mRNA, tRNA, rRNA) 

core enzyme 

set of five subunits at the heart of most bacterial RNA polymerases that, during transcription, catalyzes the elongation of the RNA molecule by the addition of RNA nucleotides 

sigma (σ) factor 

submit of bacterial RNA polymerase that allows the RNA polymerase to recognize a promoter and initiate transcription; usually detaches from core enzyme after a few RNA nucleotides have been joined together 

holoenzyme 

large multimeric enzyme that consists of a core RNA polymerase and a Sigma factor bound together 

Initiation of Transcription

when the transcription apparatus assembles on the promoter and begins the synthesis of RNA; triggered by binding of RNA polymerase to promoter w/ help of sigma 

1. Holoenzyme recognizes promoter 

2. First several RNA nucleotides are added 

3. RNA polymerase “escapes” the promoter 

Elongation of Transcription

when DNA is threaded through RNA polymerase and the polymerase unwinds the DNA and adds new nucleotides, one at a time, to the 3’ end of the growing RNA strand 

1. Begins when sigma factor leaves the holoenzyme 

2. RNA nucleotides are added to the 3’ end of the growing RNA molecule 

3. DNA winds back up as the transcription bubble moves down the gene 

Termination of Transcription

the recognition of the end of the transcription unit and the separation of the RNA molecule from the DNA template 

rho-independent terminators 

sequences in bacterial DNA that do not require the presence of the rho factor to terminate transcription 

inverted repeats 

sequences of nucleotides on the same strand that are inverted and complementary; when transcribed in RNA and bound to each other, hairpin structure forms which destabilizes DNA-RNA pairing and causes the RNA to separate from the DNA 

poly A tails 

follows the inverted repeat; all of the adenines produces a string of uracil nucleotides after the hairpin is transcribed which pauses RNA polymerase activity and allows the hairpin structure to form 

Differences in eukaryotic transcription 

1. Chromatin must be modified before transcription 

2. RNA polymerase II needs to be recognized by a promoter that consists of a core promoter and a regulatory promoter 

core promoter 

one of the parts of a promoter that is recognized by RNA polymerase II; is located immediately upstream of the gene and typically includes 1 or more consensus sequences 

TATA box 

a consensus sequence that is common to the core promoter and is typically located –25 to –30 bp upstream of the start site; sequence is TATAAA and determines the start point for transcription 

regulatory promoter 

a DNA sequence located immediately upstream of the eukaryotic core promoter; contains consensus sequences to which transcriptional regulator proteins bind 

TATA-binding protein 

a polypeptide chain found in several different transcription factors that recognizes and binds to the TATA box; acts like a molecular saddle to DNA 

exons 

coding regions of genes 

introns 

noncoding regions of genes; are spliced out in a mature mRNA transcript 

codon 

a set of three nucleotides that encodes on amino acid in a protein 

5’ untranslated region (5’ UTR) 

a sequence of nucleotides at the 5’ end of the mRNA that does not encode any of the amino acids of a protein 

Shine-Dalgarno sequence 

a consensus sequence in prokaryotic mRNA found in the 5’ UTR that serves as the ribosome-binding site during translation; is found upstream of the start codon 

protein-coding region 

the part of mRNA consisting of the nucleotides that specify the amino acid sequence of a protein 

3’ untranslated region (3’ UTR) 

a sequence of nucleotides at the 3’ end of mRNA that does not encode the amino acids of a protein, but affects both the stability of the mRNA and its translation 

5’ cap 

a backwards guanine that is added to the 5’ end of the mRNA which increases stability 

3’ poly-A-tail 

an enzyme cuts towards the 3’ end and adds a string of adenine nucleotides to the mRNA which protects it from degradation and increases stability; consensus sequence tells enzyme where to cut 

RNA splicing 

the process by which introns are removed from RNA and exons are joined together in a spliceosome; introns are identified by their consensus sequences to be properly removed 

spliceosome 

a large structure (5 RNA molecules + 300 proteins) where splicing takes place 

cloverleaf 

secondary structure of tRNA 

anticodon arm 

bottommost arm of a tRNA that contains the anticodon 

anticodon 

a sequence of 3 nucleotides in tRNA that pairs with the corresponding codon in mRNA in translation 

aminoacyl tRNA synthetase 

enzyme that catalyzes the correct linkage of an amino acid to a tRNA; there is one of these for every tRNA 

ribosomal subunits 

rRNAs + proteins

amino acids 

the monomers of proteins which are linked by peptide bonds (type of covalent bond; strong bond); all have an amino group, carboxyl group, hydrogen, and a radical group (aka side chain or I know it as an R group) 

polypeptide/protein 

a chain of amino acids linked by peptide bonds 

codon 

a triplet of RNA nucleotides that code for an amino acid 

degeneracy 

the fact that the genetic code contains more codons than are needed to specify all 20 common amino acids 

synonymous codons 

codons that code for the same amino acid 

reading frame 

the particular way in which a nucleotide sequence is read in groups of three nucleotides (codons) in translation; 3 ways in which the amino acid sequence can be read in groups of 3

universality 

the fact that particular codons specify the same amino acids in almost all organisms 

4 stages of Translation(protein synthesis) 

1. tRNA charging 

2. Initiation 

3. Elongation 

4. Termination 

tRNA charging 

a chemical reaction catalyzed by aminoacyl-tRNA synthetase where tRNAs bind their corresponding amino acids; the first stage of protein synthesis 

aminoacyl-tRNA synthetase 

enzyme that catalyzes the correct linkage of an amino acid to a tRNA; there is one of these for every tRNA; each one recognizes a particular amino acid and the tRNA that accepts that amino acid

Initiation of Translation

when components necessary for translation are assembled at the ribosome; the second stage of protein synthesis 

Shine-Dalgarno sequence

a sequence of nucleotides where the 16S rRNA (small ribosomal subunit) binds to attach the mRNA and position the ribosome at the START codon in the p-site; is specific to prokaryotes 

Cap Binding Complex (CBC)

a group of proteins in eukaryotes that binds to the 5’ cap and initiates translation; also associates with the 3’ poly-A-tail 

Kozak sequence

the consensus sequence in eukaryotes that identifies the start codon by surrounding it; positions the start codon in the P-site

Elongation of Translation

when amino acids are joined to the growing polypeptide chain; the third stage of protein synthesis 

Aminoacyl(A) site 

the first site in a ribosome occupied by a tRNA during translation; charged tRNAs first enter via this site 

Peptidyl (P) site

the second site in a ribosome occupied by a tRNA during translation; during elongation tRNAs move from the aminoacyl(A) site to this site 

Exit (E) site

the third site in a ribosome occupied by a tRNA during translation; during elongation tRNAs move from the peptidyl (P) site to this site and can then exit the ribosome from this site 

peptidyl transferase

enzyme that catalyzes the dehydration synthesis reaction to create a peptide bond between amino acids during translation 

translocation 

movement of the ribosome down the mRNA

Termination of Translation

when protein synthesis halts at the stop codon and the translation components are released from the ribosome; the fourth stage of protein synthesis