AP Biology Unit 6 - Gene Expression and Regulation

Central Dogma of Molecular Biology

The process of DNA to RNA to Protein

Transcription

The synthesis of RNA from DNA

Translation

The synthesis of a polypeptide (protein) from RNA

Codon

A triplet of nucleotides (or letters of nitrogenous bases) on mRNA which codes for an amino acid

64, 20

There are __ codons but __ amino acids

Start

The AUG codon codes for...

Stop

The UAA, UAG, UGA codons code for...

RNA Polymerase

The enzyme which connects to a promoter and unzips DNA during transcription

5' to 3'

Translation can only go in this orientation

Promoter

The area where RNA Polymerase attaches to DNA

Transcription Unit

The portion of DNA being transcribed

TATA Box

The region of the promoter which RNA Polymerase binds to

Ribonucleic Acid

RNA's full name is...

Uracil

In RNA, Thyamine (T) is replaced with...

Messenger RNA

This RNA is made from transcription. It serves as a message for the section of transcribed DNA which codes for the protein needed to be made. Its prefix is "m"

Transfer RNA

This RNA floats around in the cytoplasm. At one end it contains anitcodons which align with the corresponding codons in mRNA. At the other end it contains a corresponding amino acid. Its prefix is "t"

Cap, Tail

mRNA cannot survive outside of the nucleus by itself. Because of this, before it exits the nucleus, a ___ must be put on the 5' end and a ___ must be put on the 3' end

Guanine

On the 5' end, a cap of a special ___ molecule is put on before exiting the nucleus.

Adenine

On the 3' end, a tail of around 50-250 ___ molecules are put on before exiting the nucleus. This chain is called a Poly-A-Tail

RNA Splicing

The process in which the uneeded parts of the mRNA are cut out before it exits the nucleus.

Introns

The non-coding regions of mRNA which are cut out during RNA Splicing

Exons

The coding regions of mRNA which are needed and not cut out during RNA Splicing

Small Nuclear Ribonucleoproteins

snRNA (Small Nuclear Riboneucleic Acid) and proteins combine to create this. This molecule later combines with a spliceosome during RNA Splicing. It is abbreviated as "snRNP."

Spliceosome

A molecule which combines with snRNPs to slice RNA during RNA Splicing.

mRNA

Amino Acids are coded for by the ___'s codon sequences

Polypeptide

A chain of amino acids. Is also another name for a protein

Anticodon

A sequence of 3 nucleotides on tRNA which matches up with another 3-nucleotide sequence on mRNA

Ribosome

An organelle that is made up of 2 subunits called "large" and "small." It is composed of proteins and a special type of RNA. It is where mRNA binds during translation translation and where protein synthesis occurs.

Ribosomal RNA

A special type of RNA which, combined with proteins, is what ribosomes are made up of. Its prefix is "r"

3

Each ribosome has ___ binding sites for tRNA

A Site

The ribosomal binding site that holds the next tRNA in line. Also known as the "entrance" or "accepting" site.

P Site

The ribosomal binding site that holds the tRNA with the polypeptide attached (tRNA with the most recently attached amino acid).

E Site

The ribosomal binding site where tRNA detaches after dropping off its amino acid. Also known as the "exit" site.

Mutation

A change in DNA

Point Mutation

A mutation which causes a change in a single nucleotide base

Frame-Shift Mutation

A mutation which inserts or deletes a base, changing the entire codon sequence after it

Nonsense Mutation

A type of point mutation which causes a stop in the amino acid sequence

Silent Mutation

A type of point mutation which causes no change in the amino acid sequence

Missense Mutation

A type of point mutation which codes for a different amino acid in the sequence

Operons

Genes that can be turned off or on as needed. They are made up of an operator, a promoter, some enzymes, and a gene. Are only present in prokaryotes and very few eukaryotes.

Operator

A segment of DNA which acts as an on and off "switch" for the Operon. Are only present in prokaryotes and very few eukaryotes.

Promoter

A segment of DNA where RNA Polymerase attaches to the operon. It is a nearby control sequence on DNA which allows the binding of RNA Polymerase and Transcription Factors. Are present in both prokaryotes and eukaryotes.

Repressors

Molecules that turn off an operon.

Inducers

Molecules that turn on an operon.

Repressible Operon

An operon that can be turned off (e.g. Trp Operon)

Inducible Operon

An operon that can be induced/stimulated (e.g. Lac Operon)

DNA Packing

A type of gene regulation which coils and folds DNA to allow it to fit into the nucleus. Forms/Levels of DNA packing are nucleosomes, chromatin fiber, looped domains, and chromosomes

Nucleosomes

The first level of DNA packing where negatively charged DNA wraps around positively charged histone proteins. Looks like beads on a string

Histone Proteins

Positively charged amino acids which, with 8 of them, bind to DNA during the first level of DNA packing.

Off

DNA that is tightly packed around a histone causes a gene to be turned...

On

DNA that is loosely packed around a histone causes a gene to be turned...

Heterochromatin

Tightly packed DNA which appears darker

Euchromatin

Loosely packed DNA which appears lighter

Methylation

A process which blocks DNA transciption factors by attaching methyl groups (-CH3) to cytosine. It blocks transcription and causes genes to be turned off. Causes a near permanant inactivation of genes (e.g. Barr Bodies)

Acetylation

A process which unwinds DNA from aroudn the histones by attaching acetyl groups (-COCH3) to histones. It enables transcription and causes genes to be turned on. Causes a conformational change in histone proteins and allows transciption factors to have en easier access to genes

Transcription

A type of gene regulation which controls regions on DNA being transcribed via nearby (promoter) or distant (enhancer) control, DNA packing, or transcription factors. This controls the initiation of...

Enhancer Sequence

A distant control sequence on DNA which makes enhancer proteins to turn a gene on. These sequences can be turned on or off by silencers or activators. Are present only in eukaryotes.

Activator Proteins

Proteins which are made by the enhancer sequence to stimulate transcription/turn on a gene. Are also called enhancer proteins

Silencer Sequence

A distant control sequence on DNA which makes silencer proteins to turn an enhancer sequence off. Are only present in eukaryotes

Silencer Proteins

Proteins which bind to the enhancer sequence to turn it off and block gene transcription

mRNA Degradation

A type of gene regulation which regulates mRNA's life span which in turn determines amount of protein synthesis. Is a type of post-transcriptional control.

Small Interfering RNA

Short segments of RNA (21-28 bases) which bind to RNA to create segments of double-stranded mRNA. This acts as a "death tag" for mRNa and causes degradation. Its prefix is "si." Is a type of RNA inteference.

Gene Silencing

A type of RNA inteference which turns off the gene after transcription has already occured. Is a type of post-transcriptional control.

Protein Processing

A type of gene regulation which includes the process of folding, cleaving, the adding sugar groups, and the targeting for transport of proteins. Is a type of post-translational control.

Protein Degradation

A type of gene regulation which recycles or degrades protein after translation has already occured. Is a type of post-translational control.

Ubiquitin

A molecule that serves as a "death tag" for the degradation of proteins after translation (post-translational control)

Proteasome

A molecule that degrades and recycles proteins after translation (post-translational control)

Post-Transcriptional Control

mRNA processing, RNA splicing, the placement of caps and tails on RNA, and degradation via siRNA are types of gene regulation called...

Translation

Regulatory proteins can block attachment of ribosomal subunits and initiator tRNA or can attach to the 5' end of mRNA to prevent attachment of ribosomal subunits and initiator tRNA. These are a type of gene regulation that control the initiation of...

Post-Translational Control

Protein processing and protein degradation are types of gene regulation called...

Virus

An infectious agent made of nucleic acid (DNA or RNA) in a protein coat. They can only reproduce inside another living organism's cells. By this standard, they are not considered to be alive. Are smaller than ribosomes

Bacteriophages

Viruses that infect bacteria. Are also called "phages" for short.

Lytic Cycle

A reproductive cycle of viruses which kills the host organism

Lysogenic Cycle

A reproductive cycle of viruses which allows replication of the nucleic acid without killing the host organism. Most virsus do this type of cycle.

Retrovirus

A type of virus composed of RNA instead of DNA. They also have a unique enzyme which allows them create DNA out of their RNA after entering a cell

Reverse Transcriptase

A retrovirus enzyme which reverts RNA back into DNA

Human Immunodeficiency Virus

A retrovirus which causes AIDS (Acquired Immunodeficiency Syndrome). As of now, it is unknown what triggers the AIDS to show up after obtaining this retrovirus. An infection caused by this virus cannot be stopped or removed from the host after its RNA is released. Its abbreviation is "HIV"

Vaccines

Harmless variants or derivatives of pathogenic microbes which cause the immune system to create defences against the actual pathegen

Bacteria

A microorganism that can reproduce and mutate rapidly. Can be good, bad, or neutral

Nucleoid

The genetic material of bacteria. It is a tight coiled, long strand of DNA.

True

T/F: Using antibacterial soap and antibiotics too often can be bad because it will only kill off the weaker bacteria and leave the stronger bacteria alive, causing super bugs to be created and people to develop antibiotic resistance.

Herd Immunity

When a high percentage of the population is vaccinated, lowering the chance of disease to spread

Innate Immunity

Immune system defences which are present at birth (skin, mucous membranes, antimicrobial proteins, etc.)

Acquired Immunity

Immune system defences which are acquired later in life through exposure

Lysozyme

An enzyme that digests the cell walls of bacteria. Is a type of innate immunity

Phagocytic Cells

Cells that attach to invaders and eat them. Some examples are white blood cells like Neutrophils (the most abundant white blood cell in the body) and Macrophages ("big eaters"). Is a type of innate immunity

Interferons

Proteins that protect against viruses. Is a type of innate immunity

Inflammatory Response

An immune responce that is triggered when tissue is damaged and causes inflammation. Is a type of innate immunity

Mast Cells

Cells which release chemicals to increase blood flow to a damaged site during an inflammatory response.

Histamines

Chemicals that are released by Mast Cells to increase blood flow to a damaged site during an inflammatory response

Natural Killer Cells

Cells which patrol the body and attack virus-infected cells. Is a type of innate immunity

Antigen

A foreign molecule that triggers an immune response

Antibodies

An immune response that will attach to antigens (foreign molecules) and attack them. They are speciliazed for a specific type of antigen. Is a type of acquired immunity.

B Cells

A type of lymphocyte (white blood cell) that will mature into plasma cells that produce antibodies

Memory B Cells

B Cells that store information about/remember a pathogen that has already triggered an immune response in the past to allow for faster antibody production if the pathogen is encountered again

Humoral Immune Response

A type of acquired immunity which produces antibodies to fight off antigens via B Cells

Primary Immune Response

A humoral immune response that occurs after the the first exposure to an anitgen

Secondary Immune Response

A humoral immune response that occurs after the the second exposure to an anitgen

Helper T Cells

T cells that help B Cells mature into plasma cells to release antibodies

Killer T Cells

T cells that target and kill cells infected with a virus by attaching to a targeted cell and releasing a toxic molecule which will poke holes in the targeted cell, causing it to self-destruct