Biology - Central Dogma: DNA to RNA (Week 6)

Deoxyribonucleic acid (DNA)

The principal molecule of biological heredity; a linear polymer of nucleotides

Nucleotide

A constituent of nucleic acids, consisting of a 5-carbon sugar, a nitrogen-containing base, and one or more phosphate groups

Sugar

The simplest carbohydrate molecule

Base

A nitrogen-containing compound that makes up part of the nucleotide; provides each nucleotide with its chemical identity.

Phosphate group

A chemical group consisting of a phosphorus atom bonded to four oxygen atoms; give the backbone of a nucleic acid polymer a negative charge

Deoxyribose

A 5-carbon sugar that lacks an oxygen atom on its 2’ carbon; sugar in DNA nucleotides

Purines

Either of the bases adenine (A) and guanine (G), which has a double-ring structure.

Pyrimidines

Any of the bases thymine (T), cytosine (C), and uracil, which have a single-ring structure.

Nucleoside

A molecule consisting of a 5-carbon sugar and a nitrogen-containing base.

Nucleoside monophosphate

A nucleoside with one phosphate group.

Nucleoside diphosphate

A nucleoside with two phosphate groups.

Nucleoside triphosphate

A nucleoside with three phosphate groups.

Phosphodiester bond

A bond that forms when a phosphate group in one nucleotide is covalently bonded to the sugar unit in another nucleotide; stabilizing and gives a DNA strand its polarity and directionality.

Polarity

An asymmetry such that one end of a structure differs from the other.

Complementary

Describes the relationship of purine and pyrimidine bases (A and T pair, G and C pair)

Base stacking

Stabilizing hydrophobic interactions between bases in the same strand of DNA

Major groove

The larger of the two grooves on the outside of a DNA duplex.

Minor groove

The smaller of the two grooves on the outside of a DNA duplex.

Antiparallel

Oriented in opposite directions.

Replication

The process of copying DNA so genetic information can be passed from cell to cell or from an organism to its progeny.

DNA polymerase

An enzyme that carries out the synthesis of new DNA strands.

Mutation

Any heritable change in genetic material; results from an error in replication or a mutagen.

Central dogma of molecular biology

The usual flow of information in a cell from DNA to RNA to protein.

Transcription

The synthesis of RNA from a DNA template; information is transcribed in the same language of nucleic acids.

Translation

The synthesis of protein from an RNA template; information is transcribed in a different language of amino acids.

Gene expression

The production of a functional gene product; this process is regulated (“turned on” or “turned off”)

Denaturation

The separation of paired complementary strands of nucleic acid.

H-bonding and base stacking

Stabilizing mechanisms in DNA that are not resistant to changes in pH and temperature

3 H-bonds

Number of H-bonds between G and C

2 H-bonds

Number of H-bonds between A and T

Uracil

RNA base that replaces the thymine (T) base from DNA

Sugars and phosphate groups

DNA elements that form the backbone of the molecule.

Ribosome

A complex structure of RNA and protein that synthesizes proteins from amino acids as directed by the sequence of mRNA; located in the cytoplasm

RNA

A polymer of nucleotides in which the 5-carbon sugar is ribose; polar and linked by phosphodiester bonds.

Ribose

The 5-carbon sugar component of RNA; carries a hydroxyl group on the 2’ carbon

Uracil

The base in RNA that replaces thymine in DNA; has a hydrogen attached to its 5’ carbon

RNA world hypothesis

The hypothesis that the earliest organisms relied on RNA for both catalysis and information storage

RNA transcript

The RNA sequence synthesized from a DNA template; complementary, with the exception of uracil replacing thymine

RNA polymerase

The enzyme that carries out polymerization of ribonucleoside triphosphates from a DNA template to produce an RNA transcript; adds nucleotides to the 3’ ends of the transcript

Nontemplate strand

The strand of DNA that is not used as a template for RNA synthesis during transcription; also called the coding, sense, and plus strand because it matches the RNA sequence

Initiation

Process by which RNA polymerase and other proteins are recruited to double-stranded DNA, the strands are separated, and transcription of the template strand begins; first stage of transcription

Elongation

The process by which successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand; second stage of transcription

Termination

The process by which the RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released; third stage of transcription

Promoter

A regulatory region where RNA polymerase and associated proteins bind to the DNA duplex in the process of transcription

TATA box

A DNA sequence present in many promoters in eukaryotes and archaea that serves as a protein-binding site for a key general transcription factor

Terminator

A DNA sequence at which transcription stops and the transcript is released

Sigma factor

A protein that associates with RNA polymerase that facilitates its binding to specific promoters; used by bacteria cells

General transcription factors

Six different proteins that combine to the promoter of a gene and whose combined action is necessary for transcription

Transcriptional activator protein

A protein that binds to enhancer DNA sequences to enable transcription to begin; determines the “when” and “where”

Enhancer

A specific DNA sequence located upstream, downstream ,or within a gene that is necessary for transcription

Mediator complex

A complex of proteins that interacts with the Pol II complex and allows transcription to begin

Pol II

The RNA polymerase responsible for transcription of protein-coding genes

Primary transcript

The initial RNA transcript that is synthesized as a complement to the template DNA strand.

Messenger RNA (mRNA)

The RNA molecule that combines with a ribosome to direct protein synthesis; carries the genetic message from DNA to the ribosome

Prokaryote primary transcription

Primary transcripts are translated immediately because transcription and translation are coupled; the primary transcript is mRNA and contains genetic information for synthesis of two or more proteins

Polycistronic mRNA

A single molecule of mRNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA; code for multiple proteins

Eukaryote primary transcription

Primary transcripts undergo three types of chemical modification

RNA processing

A series of chemical modifications that convert the primary transcript into finished mRNA, which can then be translated by the ribosome

5’ cap

The modification of the 5’ end of the primary transcript by the addition of the nucleotide 7-methylguanosine, attaching to mRNA by unusual linkage; allows ribosomes to recognize mRNA and helps stabilize the RNA transcript

Polyadenylation

The addition of a long strand of consecutive A-bearing ribonucleotides to the 3’ end of the primary transcript; helps export mRNA to the cytoplasm and stabilizes the RNA transcript

Poly (A) tail

The nucleotides added to the 3’ end of the primary transcript of polyadenylation; prevent the rapid breakdown of mRNA and allow for the transportation of mature mRNA to the cytoplasm

Exon

A sequence that is left intact in mRNA after RNA splicing and therefore expressed in the protein

Intron

An intervening sequence that is removed from the primary transcript during RNA splicing

RNA splicing

The process in which exons are joined and introns are removed from the primary transcript

Spliceosome

An RNA-protein complex that catalyzes RNA splicing

Alternative splicing

A process in which primary transcripts from the same gene are spliced in different ways to yield different mRNAs and protein products

Ribosomal RNA (rRNA)

Noncoding RNA found in all ribosomes that aid in translation

Nucleolus

A distinct, dense, non-membrane bound structure within the nucleus that contains the genes and transcripts for ribosomal RNA

Transfer RNA (tRNA)

Noncoding RNA that carries individual amino acids for use in translation

Small nuclear RNA (snRNA)

Noncoding RNA found in eukaryotes and involved in splicing, polyadenylation, and other processes in the nucleus; component of the spliceosome

MicroRNA (miRNA)

Small, regulatory RNA molecules that can cleave or destabilize RNA or inhibit its translation

Small interfering RNA (siRNA)

Small, double-stranded regulatory RNA that can cleave or destroy single-stranded RNA with a complementary sequence.

5’ to 3’

Sequence at which RNA is transcribed

3’ to 5’

Sequence at which the DNA template is read

RNA nucleotides

Adenine, cytosine, guanine, and uracil

DNA nucleotides

Adenine, cytosine, guanine, and thymine

Nucleus

Location of transcription in eukaryotes

Cytosol

Location of translation in eukaryotes

Negative

Charge of DNA

10 base pairs

Number of base pairs wound in one turn of DNA

Hydrolysis of a pyrophosphate group

A polymerization reaction is made irreversible by:

1 prime

In nucleic acids, where the carbon on the sugar attaches to the nitrogenous base

5 prime

In nucleic acids, where the sugar attaches to the phosphate group

2 prime

The distinguishing feature on the carbon of RNA and DNA sugars

3

Number of phosphate groups attached to a singular nucleotide

1

Number of phosphate groups when added to a nucleic acid polymer (DNA or RNA strand)

Single-stranded

Typical structure of RNA strands

Double-stranded

Typical structure of DNA strands

Nonpolar and hydrophobic

Characteristics of bases

Charged and hydrophilic

Characteristics of backbones (sugars and phosphate groups)

Facing outward

Orientation of backbones in DNA

Facing inward

Orientation of nitrogenous bases in DNA

Chargaff’s rule

The amount of guanine should be equal to the amount of cytosine and the amount of adenine should be equal to the amount of thymine

Adenine and guanine

Purines

Cytosine, thymine, and uracil

Pyrimidines

Hydrogen bonding

Bonding between nitrogenous bases of different strands

G-C base pair

Base pair with a higher annealing temperature (more stable)

Annealing

The process of combining two single nucleotides into a double-stranded complex

tRNA and rRNA

Examples of noncoding RNA (undergo transcription but not translation)