Gene Expression and Regulation

DNA monomer

nucleotides

Nucleotide structure

5 carbon sugar, phosphate group, nitrogenous base

Sugar in DNA

deoxyribose

Nitrogenous bases in DNA

Adenine, Thymine, Cytosine, Guanine

nucleotide bonds (bond between sugar and phosphate)

phosphodiester bond

DNA structure

DNA consists of two long chains of nucleotides twisted into a double helix and joined by hydrogen bonds between the complementary bases adenine and thymine or cytosine and guanine

Founders of the Structure of DNA

Watson, Crick, and Franklin

Base pairing in DNA

A-T

G-C

3' end of DNA

refers to the end that has a hydroxyl group attached to the number 3 carbon of deoxyribose AND attaches to the 5' phosphate group of the incoming nucleotide.

Antiparallel

referring to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5' -3' directions).

DNA strands are held together by

hydrogen bonds between AT (2 bonds) and CG (3 bonds)

Gene

sequence of DNA that codes for a protein and thus determines a trait

Genome

the complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes

DNA in prokaryotes

DNA is contained in the cytoplasm and consists of a ring of DNA

Chromosome

a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

Histones

protein molecules around which DNA is tightly coiled in chromatin

Nucleosome

repeating subunit of chromatin fibers, consisting of DNA coiled around histones

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

Heterochromatin

DNA that is densely packed around histones. The genes in this chromatin are generally inaccessible to enzymes and inactive.

DNA replication

the process of making a copy of DNA

Helicase

The beginning of DNA replication. An enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands.

origins of replication

Sites where the replication of a DNA molecule begins.

DNA topoisomerase

An enzyme that unwinds and winds coils of DNA that form during replication and transcription.

SSBP

single stranded binding proteins that help keep the DNA uncoiled

DNA polymerase I

removes RNA primers and replaces them with DNA

DNA polymerase III

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule. Can only add nucleotides to the 3' end of a strand. (5' to 3' direction)

RNA primase

An enzyme that creates an RNA primer for initiation of DNA replication.

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication. After replication, the primer is replaced by DNA so that the final strand contains only DNA.

leading strand

the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' to 3' direction

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

DNA ligase

an enzyme that eventually joins the sugar-phosphate backbones of the Okazaki fragments

semiconservative

method of replication that implies that each new strand of DNA is half original and half new

Telomeres

DNA at the tips of chromosomes

Hershey-Chase Experiment

Used radioactive material to label DNA and protein; viruses with radioactive DNA infected bacteria; helped prove that DNA is genetic material not proteins

Types of RNA

messenger RNA, transfer RNA, ribosomal RNA

Central Dogma of Biology

DNA-\>transcription-\>RNA-\>translation-\>protein

Protein Synthesis

the formation of proteins by using information contained in DNA and carried by mRNA

Transcription

the organic process whereby the DNA sequence in a gene is copied into mRNA. Occurs in the nucleus.

Promoters

specific region of a gene where RNA polymerase can bind and begin transcription

Antisense strand/Non-coding strand/Minus-strand/Template Strand

the strand of DNA that runs 3' to 5' and is complementary to the sense strand. It acts as a template strand during transcription.

Sense strand/Coding Strand

The strand is always the one running from the 5' to the 3'. mRNA is identical to the strand except Thymine is replaced with Uracil.

RNA polymerase

Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription. Builds RNA molecule from 5' to 3', so it binds to the 3' end of the template strand. Does not need RNA primers.

RNA processing

Modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends.

Exons

Coding segments of eukaryotic DNA.

Introns

sequence of DNA that is not involved in coding for a protein

Splicing

the process of removing introns and reconnecting exons in a pre-mRNA

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

polyA tail

After an mRNA is transcribed from a gene, the cell adds a stretch of A residues (typically 50-200) to its 3' end.

5' GTP cap

substance that is added to newly synthesized mRNA in RNA processing to the 5' end

Messenger RNA (mRNA)

A type of RNA, synthesized from DNA and attached to ribosomes in the cytoplasm; it specifies the primary structure of a protein.

Translation

Process by which mRNA is decoded and a protein is produced. Occurs in a ribosome.

Codon

three-nucleotide sequence on messenger RNA that codes for a single amino acid

Transfer RNA (tRNA)

form of RNA that brings amino acids to ribosomes during protein synthesis

Anticodon on tRNA

The region of a tRNA that is complementary to a codon on mRNA.

Initiation (Translation)

mRNA is attached to a subunit of the ribosome, the first codon is always AUG

start codon (AUG)

On mRNA, the specific three-nucleotide sequence (AUG) to which an initiator tRNA molecule binds, starting translation of genetic information.

A site, P site, E site

Locations on the large subunit of the ribosome. Each tRNA moves from A to P to E as they drop off their amino acid.

Elongation (Translation)

addition of amino acids to the polypeptide chain; continues until it reaches a stop codon. Peptide bonds form between the amino acids.

Termination (Translation)

occurs when a stop codon in the mRNA reaches the A site of the ribosome. Translation stops and the polypeptide or protein folds up and is released into the cell.

stop codon

codon that signals to ribosomes to stop translation (UAA, UAG, UGA)

Ribosomal RNA (rRNA)

Produced in nucleolus, type of RNA that makes up the major part of the ribosomes

Gene Regulation

ability of an organism to control which genes are transcribed in response to the environment

Pre-transcriptional gene regulation

turns transcription of genes on/off or up/down based on the needs of the cell before transcription. This is the largest point of gene regulation.

Transcription Factors

A regulatory protein that binds to DNA and affects transcription of specific genes. Can encourage or inhibit transcription, typically by making it easier or harder for RNA Polymerase to bind to the start site

Epigenetic changes

stable alterations of chromatin structure that may be passed on to cells or individual organisms (usually occur through the modification of a histone protein; changes the packaging of DNA so that it is harder for transcriptional machinery to access a gene)

Operons

In prokaryotic cells, a cluster of genes under control of a promoter.

parts of an operon

structural gene, promoter gene, operator, regulatory gene

Structural Gene

a gene that codes for a product, such as an enzyme, protein, or RNA, rather than serving as a regulator

Promoter gene

region where RNA polymerase binds to begin transcription

operator

short DNA region, adjacent to the promoter of a prokaryotic operon, that binds repressor proteins responsible for controlling the rate of transcription of the operon

regulatory gene

A gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.

Repressor

A protein that binds to an operator and physically blocks RNA polymerase from binding to a promoter site

Inducer

A specific small molecule that inactivates the repressor in an operon.

Post-transcriptional regulation

the control of gene expression at the RNA level, therefore between the transcription and the translation of the gene. RNAi molecules take part in this

Post-translational regulation

Regulation of gene expression by modification of proteins (e.g., addition of a phosphate group or sugar residues) after translation. Often done if a cell has made a protein that it does not need to use yet

Zygote

fertilized egg

Fertilization

Process in sexual reproduction in which male and female reproductive cells join to form a new cell

Cell Differentiation

the process by which a cell becomes specialized for a specific structure or function. Zygotes go through a series of cell divisions in during which the embryo becomes increasingly differentiated.

Mutation

An error in the genetic code

Base Substitution

Aka a point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides. There are 3 types: Nonsense, Missense, and Silent Mutations.

Nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

Missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

Silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

Gene rearrangement

Involve DNA sequences that have deletions, duplication's, inversions, and translocations which are often caused by chemical or radioactive agents

Frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

Insertion

A mutation involving the addition of one or more nucleotide pairs to a gene.

Deletion

A change to a chromosome in which a fragment of the chromosome is removed.

Duplication

change to a chromosome in which part of the chromosome is repeated

Inversion

A genetic mutation in which the order of a segment of genetic material is reversed. This type of mutation can involve a small number of nucleotides as well as larger sections of a chromosome containing more than one gene

Translocation

Change to a chromosome in which a fragment of one chromosome attaches to a nonhomologous chromosome.

Transposons

(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material

Bacteria

single-celled organisms that lack a nucleus; prokaryotes. Can infect many things which they sometimes help and other times harm

Conjugation

In bacteria, the direct transfer of DNA between two cells that are temporarily joined. Can lead to antibiotic resistance. They do this because bacterial fission does not increase their genetic diversity.

Viruses

tiny particles, smaller than bacteria and other pathogens, which must invade living cells in order to reproduce; when they invade, the cells are damaged or destroyed in the process releasing new particles to infect other cells

Host

The thing infected by a virus

Bacteriophage

A virus that infects bacteria

Lytic cycle

a viral reproductive cycle in which copies of a virus are made within a host cell, which then bursts open, releasing new viruses

Transduction in bacteria

the transfer of DNA between bacterial cells using a lysogenic virus

Retrovirus

An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses. HIV is an example of this. RNA viruses like this mutate quickly since they have no proofreading mechanisms in their replication of genomes.