Biology Khanacademy Unit 6: Gene expression and regulation

Prokaryotes

Single celled organisms belonging to either Bacteria or Archaea. (2/3 major domains of life). These don’t have a nucleus and other membrane-bound organelles eukaryotes usually have. Additionally they are usually 2% the size of eukaryotic cells.

Capsule

In the context of prokaryotes, the sticky outermost layer made up of polysaccharides that surrounds them. These protect against immune systems (if a virus), help keep the cell from drying out (sugars are generally charged), and help prokaryotes stick to each other and to surfaces.

Cell Wall

Structure located under the capsule of a prokaryote. Maintains cell shape and prevents cell from bursting due to external water molecules.

Peptidoglycon

A polymer of linked sugars and polypeptides. Is usually present in the cell wall of bacteria.

Plasma Membrane

In the context of prokaryotes, lies underneath the cell wall. A structure made up of amphipathic phospholipid molecules and proteins. In archaea this phospholipid bilayer becomes a monolayer as the hydrophobic ends of phospholipid connect to make one structure. This allows them to live happily in hot environments.

Appendages

Structures that allow bacteria to stick to surfaces, move around, or transfer DNA to other cells.

Picture outlines an example of a type of ______ (an flagellum)

Fimbriae

Type of appendages which are short and used for adhesion to help cells stick to objects and surfaces in their environment.

Typically shorter and more in numbers than Pili.

Pili

Long appendages which have different roles. Can be used by bacteria for DNA transfer, moving around environment, etc…

Typically are longer and fewer in number than fimbriae

Flagellum

The most common long appendage used by bacteria to move around. Used like propellers in watery environments.

Nucleoid

A structure in a prokaryote where the single circular chromosome they usually hold is present. Basically a substitute for the nucleus of a eukaryote.

Plasmids

Small rings of double stranded extra-chromosomal DNA. Carry a small number of non-essential genes and are copied independently of the chromosome inside the cell.

Helicase

A molecule that breaks hydrogen bonds between nitrogenous bases thus splitting up DNA.

It does this by moving replication forks, which make up a replication bubble, in opposite directions.

Topoisomerase

A molecule that unwinds DNA before it is to be broken down by helicase.

DNA Polymerase

A molecule that adds nucleotides to DNA that is split. Adds nucleotids at 3’ end. Can add around 700+ base pairs per second.

This molecule also creates nucleotides.

These basically both synthesize, and add nucleotides to a growing DNA chain. They only add to the 3’ end of a growing strand, they need a primer and a template. They also proofread their work by removing wrong nucleotides.

Nucleotide addition requires energy, this energy is gained by the dehydration synthesis of nucleotide triphosphate in which it loses 2 phosphate groups.

Different types of _____ _____ have different functions. For instance ______ ______ 1 serves to remove RNA primers after DNA replication is nearly done so that the replicated DNA has no RNA parts.

RNA Primer

Added by DNA Primase. Helps Polymerase add nitrogenous bases to lagging strand.

These are short stretches of nucleic acid that provide a 3’ carbon end for DNA polymerase to attach to and begin to produce, and add nucleotides in order to replicate a template strand. These basically add the first nucleotide and allow dna polymerase to continue the chain.

DNA Primase

Moves along a lagging strand and adds in RNA primers which allows DNA polymerase to add nucleotides. This basically adds molecules that then allow DNA polymerase to do its job.

DNA Ligase

Puts strands together during DNA replication. Basically seals any little holes after DNA replication is finished.

Lagging strand

Built in fragments

Leading strand

Built continuously

Semiconservative Replication

The way in which DNA replicates, a double helix strand is split into two and each strand is replicated.

Single Strand Binding Proteins

Proteins that coat seperated strands of DNA in order to keep them from coming back together during DNA replication.

Okazaki Fragments

Fragments on the lagging strand. (Strand that is replicated 5’ to 3’ away from the forks.) That require new primers for DNA polymerase to replicate starting from their point. This is needed because the DNA polymerase runs also from 5’ to 3’ and as new DNA is exposed it must go back, hence the ______ ______.

Sliding Clamp

Ring shaped protein which holds DNA polymerase of the lagging strand from floating off as it restarts a new Okazaki fragment.

Transcription

Process of encoding info that is in DNA into mRNA.

pre-mRNA

The type of mRNA produced during transcription that is then developed into mRNA. This mRNA type is only present in eukaryotes i.e. only they must process it. These also contain introns.

RNA Polymerase

Creates sequence that will become mRNA. Seperates a DNA strand after binding to it. Encodes from 5’ to 3’. Attaches to DNA, splits it, and transcripts it.

Promoter

A sequence of DNA RNA polymerase can attach to in order to begin creating sequences. All genes have these.

Template Strand

Strand that acts as a template for mRNA to form a complementary base.

Coding Strand

Strand on the opposite side of template strand. This strand will have the same genetic code as the mRNA except for thymine being exchanged with uracil.

Terminator

A part of a DNA strand that terminates the transcription of mRNA to signify the end of a gene. mRNA undergoes conformation change so it lets go.

5’ Cap

Modified version of guanine added to pre-mRNA in order to help in the translation process. It is added on the 5’ end. This alongside with the Poly A tail helps stabilize mRNA.

Picture attached outlines the _ ____.

Poly-A tail

Molecule with a chain of adenine molecules that help in the translation process and in making sure information is more robust. It is added to the 3’ end of pre-mRNA. This alongside with the 5’ cap helps stabilize mRNA.

Picture attached outlines a _____ molecule.

Introns

“Nonsense sequences” that don’t code for proteins the initial gene copied codes for. These are spliced out during eukaryotic processing.

Exons

Sequences in a gene and pre-mRNA that code for proteins the initial gene copied codes for i.e. are not introns.

Spliceosome

A molecule that splices introns off from Pre-mRNA during transcription processing.