BIO111 - Molecular genetics - Keywords

snoRNA (small nucleolar ribonucleic acid) don't code for proteins, but work as so called guide RNA, helping enzymes to get to place in the cell/body, where they are needed. 

There are twenty standart amino acids, each of which has the same overall structure: 

An amide between the carboxyl group of one aa and the amino group of the next aa. It has a rigid planar structure. 

Linear polymers of amino acids. They have several levels of organisation: 

Primary structure: sequence of aa

Secondary structure: local 3D structure

- Alpha helix

- Beta pleated sheet

- Turns, other

Tertiary structure: overall 3D structure

Quaternary structure: Association of several polypeptides in multi-polypeptide proteins

Polypeptide = Sequence of amino acids bound together by peptide bonds (=Protein). 

Group of 3 nucleotides

A codon (= 3 nucleotides = triplet) is the unit of genetic information that codes for one amino acid. 

The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. 

The genetic code is called degenerate, because most amino acids are specified by more than one codon. 

An anticodon is a short tRNA-sequence, which consists of a triplet. With this anticodon, which is complementary to a codon of the mRNA, the tRNA can bind to the mRNA during protein synthesis. 

Base pairing between the last base of the codon and the first base of the anticodon ist not as strict as the other two base pairs. The last base pair is known as the wobble position. Wobbling allows the 61 sense codons to be covered by fewer than 61 different tRNAs (usually 30-50 different tRNAs). 

The stop signals for the tRNA are called stop codons. There are three of those: 

- UAA

- UAG

- UGA

Thus, of the 64 codons known, only 61 actually code for amino acids (sense codons). 

The initiation (or start codon) is the AUG. It is used both to specify the start of translation and to direct the incorportation of Methionine.

Synonymous codons encode for the same amino acid. 

tRNAs that carry the same amino acid but recognize different sets of codons. This is necessary, because, desipte wobbling, many amino acids will require more than one tRNA to cover all possible codons. 

All tRNAs end at their 3' end with CCA. tRNAs are charged at this 3' end with amino acids, trough an ester bond between the carboxyl group of the amino acid and either the 2' -OH or the 3' -OH of the 3' terminal A. 

This process charges the tRNA (activates it). It is done by the aminoacyl-tRNA synthetases. 

There are 20 different (for each amino acid) aminoacyl-tRNA synthetases. Each aminoacyl-tRNA synthetase can recognize one amino acid, and all tRNAs that need to carry that specific amino acid. 

The aminoacyl-tRNA synthetases dicriminate between the various tRNAs by recognizing some specific variable positions:

The 5' UTR is the region of the mRNA that is directly upstream from the initiation codon. It begins at the transcription start site and ends one nucleotide before the initiation sequence of the coding region. In prokaryotes, it is usually 3-10 nts long, in eukaryotes it tends to be anywhere from 100 to several 1000 nts long. 

The 3' UTR is the section of mRNA that immediatly follows the translation termination codon. It often contains regulatory regions that post-transcriptionally influence gene expression. 

The A (aminoacyl-tRNA) of a ribosome is a binding site for charged (aminoacyl-tRNA) tRNA molecules during protein synthesis. It is the first location (point of entry) the tRNA binds during the protein synthesis process. 

The P site (peptidyl-tRNA) is the second binding site for tRNA in the ribosome. During translation, the P site holds the tRNA which is linked to the growing polypeptide chain. When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P site is cleaved releasing the newly synthesized protein. 

The E site (exit) is the third and final binding site for tRNA in the ribosome. 

The peptidyl transferase is the primary enzymatic function of the ribosome, forming peptide bonds between adjacent amino acids using tRNAs during the translation. Its activity is carried out by the ribosome. 

In prokaryotes, the 50S (23S component) ribosome subunit contains the peptidyl transferase component and acts as a ribozyme. 

in eukaryotes, the 60S (28S component) ribosome subunit contains the peptidyl transferase component and acts as a ribozyme. 

In bacteria, the initiating AUG is preceded by a conserved consensus sequence known as the Shine-Dalgarno sequece or RBS (ribosome binding site). Base pair interactions between the Shine-Dalgarno sequence and the 3' end of the 16S rRNA on a free 30 S small subunit position the initiating AUG into the P site of the ribosome. 

The Kozak sequence ((eukaryotic start site) 5' -ACCAUGG- 3') is a consensus sequence found in eukaryotic mRNA. It is the eukaryotic start site.The initiating AUG will usually be the first AUG that shows a reasonable similarity to the Kozak consnesus sequence.

The process of scanning occurs, when the 43S preinitiation complex is bound a the 5' cap. It then moves along the mRNA in a 5' to 3' direction, scanning for an initiating AUG. This process is mediated by helicases and requires ATP hydrolysis. 

The eukaryotic initiation factor 4 (elF4) binds to the 5' cap of mRNAs. elF1A and elF3 bind to free 40 S subunit. Charged initiator tRNA complexed with elF2 GTP binds to 40 subunit, to generate the 43 S preinitiation complex. This complex then binds to the elF4 mRNA complex at the cap. 

As the genetic code is a non-overlapping triplet code, there are 3 ways to read a particular sequence. Which reading frame is used depends only on which frame the start codon is in: 

An open reading frame (ORF) is a region in an mRNA (or DNA) that starts with an AUG and ends with a stop codon. Only one of the three possible reading frames in an mRNA has a long open reading frame. This ORF will correspond to the protein-coding region of the mRNA. The other two frames are continuously interrupted by stop codons. 

Gene that encode proteins or mRNAs that are used in metabolism or biosynthesis or that play a structural role in the cell. Examples are actin, hexokinase

Regulatory genes encode proteins or mRNAs that physically interact with nucleic acid sequences (DNA or RNA) and thereby regulate gene activity. Examples are the TATA binding protein (TBP), lacl, miRNAs

Regulatory elements are parts of genes that control their expression. Examples are the promoter, the operator, the enhancer. 

A segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an orgnamism. 

Parts of proteins that have a specific function and a specific tertiary structure. Each domain is responsible for a particular function of a protein. Possible domains include: 

- A sequence- specific DNA binding domain

- A domain that interacts with the transcription machinery (e. g. with DNA pol)

- A domain that can bind other regulatroy proteins

- A domain that can control the condensation status of the local chromatin

- A domain that can bind to a small molecule, and can act as a sensor to tell the protein whether the molecule in question is present or absent