Translation- Genetics

Types of RNA that are involved in Translation

Transfer RNA (tRNA) Messenger RNA (mRNA) Ribosomal RNA (rRNA)

what is an amino acid?

An amino acid is a molecule that contains two functional groups , an amine and a carboxylic acid. There is an additional groups called the side chain, designated with an R. The variation seen in naturally occurring amino acids arises from differences in this side chain.

Anaphase: meiotic or mitotic cell division

Anaphase: stage of meiotic or mitotic cell division in which the chromosomes move away from one another to opposite poles of the spindle. (N6220 Ant/Phys Cellular Biology.ppt, sld 25, FC)

How many hydrogen bonds between the different base pairs (ie. G to C and A to T)

Between G & C: 3 hydrogen bonds Between A & T or A & U: 2 hydrogen bonds

Alternative splicing: good/bad

Can be good or it can be bad aka splicing errors Exon skipping: after splicing occurs one exon gets lost through an error (ex: muscular dystrophy) Cryptic splice site selection: it mistakenly splices the intron 1 out but with it, it takes some of exon 2 which can lead to protein dysfunction (ex: cancer)

Centromere

Centromere: the region of a chromosome that separates the 2 arms centromeres are the sites of attachment of spindle fibers during cell division.

Ribosomal RNA (rRNA)

Compose the ribosome. The rRNA are responsible for reading the order of amino acids and linking the amino acids together

Mitosis

Diploid- 2 of each chromosome (ex:somatic cell). In humans, the diploid number is 46

Endonuclease:

Endonuclease: Any of a group of enzymes that degrade DNA or RNA molecules by breaking linkages within the polynucleotide chains. Enzymes that cleave the phosphodiester bond in the middle of a polynucleotide chain.

Exon/Intron

Exon/Intron Found in the coding region to the right of the promoter region or UTR region Starts with exon 1 and then intron 1 and then exon 2 intron 2 etc... The introns are not protein coded they actually get spliced out later on after transcription has occurred in the final mRNA transcription After the last exon there's a termination code where it tells the cell to stop making both RNA and protein. Exons and introns can be any size that they want

Exonuclease:enzymes

Exonuclease:enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3' or the 5' end.

What are functional groups on amino acids? Why are they important?

Functional groups give each amino acid their different and unique function (both structurally/physically and biochemically)

G-Protein-linked receptors examples

G-Protein-linked receptors: epinephrine, glucagon, serotonin

G1 Phase

G1 phase (Gap 1 phase): is the first of four phases of the cell cycle that takes place in eukaryotic cell division. In this part of interphase, the cell synthesizes mRNA and proteins in preparation for subsequent steps leading to mitosis. G1 phase ends when the cell moves into the S phase of interphase.

G2 Phase

G2 phase: the third and final subphase of Interphase in the cell cycle directly preceding mitosis. It follows the successful completion of S phase, during which the cell's DNA is replicated.

Meiosis

Haploid- 4 cells; half the number of chromosomes. Haploid: cell that contains one copy of each chromosomes. Gametes are examples of haploid cells that reproduce by meiosis. In humans, the haploid number is 23

Holliday junction:

Holliday junction: cross-shaped (four-way DNA junction) structure that forms during the process of genetic recombination, when two double-stranded DNA molecules become separated into four strands in order to exchange segments of genetic information. Cross-like configuration of recombining DNA molecules that forms during generalized recombination

Know how DNA codons are associated with the essential amino acids?

In the genetic code each of the 20 amino acids is represented by at least one codon. Most of the amino acids are coded for by more than one codon.

Transfer RNA (tRNA)

Interprets the nucleotide sequence of mRNA to build the corresponding amino acid sequence. It reads codons of mRNA to build proteins. It does its job after the mRNA is made ready for translation

Metaphase:

Metaphase:second stage of cell division during which the chromosomes become attached to the spindle fibers. (N6220 Ant/Phys Cellular Biology.ppt, sld 25, FC)

What happens to mis-folded proteins?

Mis-folded Proteins: Protein folding Is determined by primary amino acid sequence of the polypeptide and non-covalent interactions between amino acids. Proteins must achieve and retain a specific 3-dimensional conformation in order to function properly. If protein folding is disrupted, proteins can display sticky surfaces and aggregate through several stages eventually assembling into fibers , and such nonfunctional protein aggregates can be toxic. Protein misfolding diseases are found in multiple organs, and can be defined histopathologically by the presence of specific misfolded protein(s) deposits.

Mitochondria:

Mitochondria: cytoplasmic organelles that are important in cellular respiration. The mitochondria have their own unique DNA. The mitochondria have their own extranuclear DNA molecules. Several codons of mitochondrial DNA encode different amino acids than do the same nuclear DNA codons.

Basics of cell signaling What is non-covalent interaction?

Non-covalent is essential to protein folding Reversible Allows for amino acids to come together and be attracted Examples: electrostatic attractions, hydrogen bonds, van der Waals attractions

Polar body:

Polar body: a cell produced during oogenesis (process that produces and ova) that has a nucleus but very little cytoplasm.

Messenger RNA (mRNA)

Produced by transcripton from DNA; is decoded by a ribosome to produce a specific amino acid chain, or polypeptide which later folds into an active protein and performs its functions in the cell

Promoter region

Promoter region Found in the 5 prime Untranslated Region (UTR) Where a cell decides whether or not the gene to the right of the dotted line is going to make a messenger RNA which will become a protein Is the light switch or on/off switch Controls the "decision" to synthesize mRNA from adjacent genes

Prophase

Prophase: stage of mitosis in which the chromatin condenses into double rod-shaped structures called chromosomes in which the chromatin becomes visible. (N6220 Ant/Phys Cellular Biology.ppt, sld 25, FC)

Proteasome

Proteasome (trash compactor of the cell): are protein complexes inside all eukaryotes and archaea, and in some bacteria. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds.

S Phase

S phase: DNA replication phase of interphase. It is the part of the cell cycle in which DNA is replicated, occurring between G1 phase and G2 phase.

Ribosome

Ribosome- The Workhorse of Translation- site of translation of mature mRNA into amino acid sequence. Ribosomes are made up of many different proteins and nucleic acids

Ribosomes are comprised of?

Ribosomes are comprised of rRNA and several proteins

Examples of Second Messengers

Second Messengers ex: cAMP, cGMP, Phosphoinositides, Calcium (From Molecular Cell Biology pwrpt III)

What are second messengers?

Second messengers: molecule inside cells that acts to transmit signals from a receptor to a target. They are nonprotein, water-soluble molecules or ions components of signal transduction pathways.

Basics of cell signaling How is a signaling cascade activated?

Signaling cascade is activated by the release of a hormone, protein, drug, or chemical from a cell to bind at one of the receptors mentioned above, stimulating the activation of the receptor cell

Spliceosome:

Spliceosome: a large and complex molecular machine found primarily within the splicing speckles of the cell nucleus of eukaryotic cells. The spliceosome is assembled from snRNAs and protein complexes. The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript.

Steps to translation:

Steps to translation: On the ribosome there are three sites that we recognize - the A, P, and E sites (APE) Aminoacyl-tRNA binds to a vacant A-site Aminoacyl-tRNA moves to the P-site causing a peptide bond to form with the adjacent amino acid This then moves to the E-site (ejector site) and the ribosome resets. All amino acids are identical except for the "R" or functional group

Telophase:

Telophase: the cell is nearly done dividing, and it starts to re-establish its normal structures as cytokinesis (division of the cell contents) takes place. (N6220 Ant/Phys Cellular Biology.ppt, sld 25, FC)

What type of bond that connects two amino acids?

The bond that connects two amino acids is a peptide bond.

What is the transcriptional start site in a gene?

The coding region; TATA (the region upstream of the "start" site that helps to direct where transcription begins); The +1 position in the promoter region

Translation:

The mRNA formed in transcription is transported out of the nucleus, into the cytoplasm to the ribosome where it directs protein synthesis; mRNA is not directly involved but rather tRNA is the main RNA involved.

Alternative Splicing

There are 25,000 genes in a cell and we have a million proteins to produce therefore we have alternative splicing!

Alternative splicing

There are different versions produced of the same gene through this process The cell gets creative in the exons by the sides that stick together. Exon can be spliced out with the introns which give more flexibility to the use all of our 25,000 genes because you can come up with different versions of it Tend to be tissue specific Adds another layer of complexity to who we are

Where does translation occur?

Translation occurs in the cytoplasm on ribosomes

Basics of Cell Signaling What is Phosphorylation?

What is Phosphorylation? Phosphorylation is the addition of a phosphate group (PO43−) to a molecule. Phosphorylation and its counterpart, dephosphorylation, turn protein enzymes on and off, thereby altering their function and activity. Protein phosphorylation is one type of post-translational modification.

ex: Non covalent Hydrogen bonds

ex: Non covalent Hydrogen bonds are weaker and easier to break than covalent bonds but are strengthened d/t base facing each other. DNA bonds need to be able to break/be disrupted for DNA replication. Non-covalent interactions are essential for protein folding, allow amino acids to come together/ be attracted to each other. Examples of non-covalent interactions: electrostatic attractions, hydrogen bonds, van der Waals attractions. Non-covalent interactions are reversible.

What is the single letter abbreviation for each of the amino acids? For example, G goes with glycine)

https://quizlet.com/159688096/amino-acid-single-letter-code-with-3-letter-code-flash-cards/?new

G-Protein-linked receptors:

ligands bind to the receptor protein. once ligand binds to receptor, interacts with G protein. Once this interaction occurs, leads to downstream cascade of events. Effector proteins become activated by G proteins and lead to downstream release of second messengers (cAMP, acetyl triphosphate, diacylglycerol) **See Dr. O's lecture on Molecular cell biology III

Messenger RNA produced by transcription is decoded by the ribosome to produce an amino acid

mRNA---->decoded by ribosome---->amino acid