Biology Nucleic Acids

Large macromolecules with a phosphate backbone and a base attached to the sugar.

ATP

DNA

RNA

Coenzymes

Monomers made up of

A phosphate group

One 5 carbon monosaccharide

Single nitrogenous base

A and G are Purin bases

They are slightly larger and have 2 rings

C and T

Have 1 ring

2 between A and T

3 between G and C

They are complementary which means they can be copied perfectly.

Antiparallel to each other

Electrical charges cause the double helix structure.

Eukaryotic chromosomes are composed of a double DNA strand combined with histone proteins,

8 histone proteins (4 kinds, 2 from each)  are wrapped twice by DNA, which is held by one more histone protein. The function of a nucleosome is to supercoil DNA and to regulate transcription. (transcription enzymes can’t reach tightly wrapped DNA)

The DNA on the DNA linkers can be used during transcription.

DNA is negatively charged and histones are positively charged.

Has 4 steps:

Initiation:

The small ribosomal subunit attaches to the mRNA and moves in a 5 to 3 prime end direction.

When the start codon is reached, the tRNA with the complementary anticodon binds to the codon.

The large ribosomal subunit forms the translation inititation complex with the small ribosomal subunit.

Elongation:

tRNA binds to the exposed A site. The intiatiator tRNA moves to the Psite. The polypeptide chain is moved to the tRNA on the A site and the chain grows in length. Ribosomes catalyze the formation of peptide bonds between two adjacent aa.

Translocation:

tRNa attaches to the A site, gets the chain, moves to P site, gives the chain, moves to e site and is dishcarged.

Termination: release factor

Start codon is close to the 5 prime end.

Because ribosome moves from 5 to 3.

Polypeptides fold into proteins.

RNA Polymerase unzips the DNA

RNA Polymerase synthesizes a complementary RNA strand to the antisense (template strand), starting from the promoter region and ending at the terminator region, which are nucleotide sequences signalling the start and the end of transcription. (in a 5 to 3 direction)

In eukaeyotes, splicing is done by snurps or snRNAs to get rid of introns and to be left with exons.

Helicase unzips the DNA strands.

DNA Gyrase unwinds the DNA in advance to prevent supercoiling.

RNA Primer adds short RNa sequences as attachments sites for DNA Polymerase III

DNA Polymerase attaches dNTP to the 3 prime ends of the RNA primer and synthesizes a complementary strand in a 5 to 3 direction.

In the lagging strand, this is away from the replication fork. In the leading, it is towards.

DNA Polymerase I replaces the RNA primers with DNA

DNA Ligase binds the Okazaki fragments on the lagging strand together.

Interactions between multiple polypeptides and prosthetics (conjugated proteins)

Three dimensional arrangement of the protein, stabilized by interactions between the R groups and the backbone. (enzymes)

Alpha helix or beta pleated sheets

Hydrogen bonds between non-adjacent amino acids

Is the sequence of aminoacids in a polypeptide chain

Determines all other levels of the structure

Covalent bonds between aminoacids

Binds to the A site

Releases the polypeptide

Releases the mRNA

Splits the ribosome into 2

They determine the active site of enzymes.

Because all properties of a protein are derived from the primary structure.

Hydrogen bonds between NH and CO groups?

Covalent bonds: between sulfur containing aa disulfide bridges

Hydrogen bonds: between polar amino acids

Ionic bonds: between ionic amino acids

Van der waals forces: interactions between non-polar amino acids

Translation of a single mRNA happens at multiple sites simultaneously by multiple ribosomes which are called polysomes.

Ensures that the store is stable and secure.

When a cell divides and the DNA is replicated, each replication (2) is made of one original strand and one newly synthesized strand. Because only specific bases stabilize each other and form hydrogen bonds, the strands are identical to each other.

Prokaryotes replicate their DNA continuously, while it is controlled by cyclins etc in eukaryotes.

Prokaryotes have naked DNA, eukaryotes have histones

Prokaryotes have a single circular chromosome, eukaryotes have several linear chromosomes.

Prokaryotes have one origin of replication, while eukaryotes have more than one simultaneously

Both are bi-directional

Both require primers

DNA polymerase works from 5 to 3

Both have leading and lagging strands

Both are semiconservative

The complete DNA sequence of an organism

DNA RNA Protein

Regions of DNA coding for proteins.

One piece of DNA coding for one protein.

Location of specific gene on a chromosome.

Some highly repetitive sequences (jumping genes, transposable element)

Regulators of gene expression (introns)

Structural DNA (centromeres, telomeres)

Some genes that code for tRNA

Are short tandem repeats, repeating sequences of DNA, normally composed of 2-5 base pairs which are different for everyone and can be used in DNA profiling.

• In order to fit into the nucleus
• For cell differentiation
• For gene expression
• For cell division (chromosomes)

Unwinds and unzips DNA by breaking the hydrogen bonds between complementary base pairs using ATP.

Single stranded binding proteins or SSbs are used. These prevent DNA from coiling back onto itself and keep it from being digested by nuclease.

Moves in advance of helicase and relieves strain and prevents sypercoiling on the separated DNA strands.

Adds a short length of RNA, attached by complementary base pairing to the template of the DNa strand. (this acts as an attachment site for DNA Polymerase III)

Adds free building units called dNTP to the 3 end of the primer and then to the forming strand of DNA. In this way, the template is from 3 to 5 and it 5 to 3. The two extra phosphate groups are broken down and the energy is used to continue the synthesis.

A nucleotide with two extra phosphate groups.

Removes the RNA primers and replaces them with DNA.

Is present only on the lagging strand, joins the Okazaki fragments together to create a continuous strand.

DNA Polymerase III attaches to the 3 end of the RNA primer and adds dNTP in a 5 to 3 direction, moving away from the replication fork on this strand.

• RNA polymerase unzips the DNA
• Copies the DNA (antisense or template strand) in a 5 to 3 direction after it attaches to the promoter region. Transcription ends at the terminator region.
• Like replication, it only works in one direction.
• Afterwards, RNA polymerase binds together the two strands.

It is the strand that is not used as a template for mRNA during transcription. It has the same sequence as the mRNA except for D instead of R and T instead of U.

Their DNA doesn’t have introns.

• After pre mRNA is produced, it has introns and exons and the introns must be removed to move on to translation.
• A cap consisting of Guanine nucleotide with 3 phosphates and a poly-a tail with 50-250 adenine nucletotides are added to the 5 and 3 prime end in order to protect the mRNA in the cytoplasm and to enhance translation.
• Afterwards, introns are removed in cleavages using snRNAs (snurps)
• Exons may be shuffled, which increases the number of proteins that could be produced by a gene. Also, some genes may act like introns at times so this also gives rise to multiple proteins being produced by one gene.

They happen at the same time.

It is the process in which the instructions in our DNA are converted into a functional product such as protein. It can be influenced by external and internal elements.

• Methyl CH3 binds to DNA, causing them to wrap more tightly around histones and not allowing transcription enzymes to reach it.
• Orn: one x chromosome in females is heavily methylated.
• Hypermethylation and hypomethylation also cause cancer.

• Proteins that assist the binding of RNA polymerase of the promoter region of the gene.
• These can be
• Transcription activators
• Or silencers
• What are transcription activators?
• They are proteins that assist transcription by bringing the promoter and the activator region of the gene closer together.

Are repressor proteins that bind to segments of DNA and prevent the transcription of a specific gene.

Are 3 bases on mRNA that correspond to one aminoacid in a polypeptide.

• AUG
• Codes for methionine.

• Signal for translation to stop
• UAG UAA
• UGA

• Single stranded but folded due to hydrogen bonds
• Has attachment site for aminoacids on 3 prime end.
• Has anticodon (seuqnece of 3 nucleotides corresponding to the codon on mRNA)

• It is the step when
• 20 tRNA activating enzymes bind the tRNA to 20 specific amino acids using ATP and resulting in activated tRNA

Holds the tRNA carrying the next aa to be added to the polypeptide chain.

Holds the tRNA carrying the growing polypeptide chain.

Site where tRNA is discharged.

• If produced on free ribosomes, used within the cell
• If produced by ribosomes bound to the ER
• Lysosomes or secretion