Genes Flashcards
Genome
The entire DNA sequence of an organism is called the genome. There are between 20K and 25K genes in the human genome. Only a little over 1% of the human genome actually codes for protein.
There is little variation of the nucleotide sequence among humans. Human DNA differs between individuals at approximately one nucleotide out of every 1200 or about 0.08%. A small variation in the genome can make a big difference.
Gene
A gene is a sequence of DNA nucleotides that codes for rRNA, tRNA, or a single polypeptide via a mRNA intermediate. It is the gene, or DNA sequence, and not the trait, that is inherited.
Eukaryotes have more than one copy of some genes. Prokaryotes have only one copy of each gene.
Genes are often referred to as unique sequence DNA. Regions of non-coding DNA, which is found only in eukaryotes, are called repetitive sequence DNA. Eukaryotes have more unique sequence DNA.
Eukaryotic genes being actively transcribed by a cell are associated with regions of DNA called euchromatin. Genes not being actively transcribed are associated with tightly packed regions of DNA called heterochromatin.
In general: one gene, one polypeptide.
Central dogma
The central dogma of gene expression is that DNA is transcribed to RNA, which is translated to amino acids, which are the building blocks of proteins. All living organisms use this method to express their genes.
DNA
Deoxyribonucleic acid is a polymer of nucleotides.
Each nucleotide is made up of three parts- the phosphate group, the five carbon sugar, and the nitrogenous bases. DNA nucleotides differ from each other only in their nitrogenous base. The four nitrogenous bases in DNA are adenine, guanine, cytosine, & thymine.
Each nucleotide is bound to the next by a phosphodiester bond between the third carbon of one deoxyribose and the fifth carbon of the other, creating the sugar-phosphate backbone of a single strand of DNA, with 5’ -> 3’ directionality.
In a living organism, two DNA strands are anti-parallel, and held together by hydrogen bonds between nitrogenous bases, forming a double-stranded structure. In order for two strands to bind together, their bases must match up in the correct order. When complementary strands bind together, they curl into a double helix.
DNA is confined to the nucleus and mitochondrial matrix.
Purines
Adenine and guanine are two ring structures called purines
Pyrimidines
Cytosine and thymine are single ring structures called pyrimidines. Uracil is also a pyrimidine.
Phosphodiester Bond
Each nucleotide is bound to the next with a phosphodiester bond between the third carbon of one deoxyribose and the fifth carbon of the other. This creates the sugar phosphate backbone of a single strand of DNA, and has 5’ to 3’ directionality.
5’ to 3’ directionality
The 5’ and 3’ indicate the carbon numbers on the sugar. The end 3’ carbon is attached to an -OH group, and the end 5’ carbon is attached to a phosphate group. In a living organism, two DNA strands life side-by-side in opposite 3’ to 5’ directions.
Anti-parallel orientation
In a living organism, two DNA strands of my side-by-side in opposite 3’ to 5’ directions. This is called anti-parallel orientation. These two DNA strands are bound together with hydrogen bonds, forming a double-stranded structure.
Double-stranded structure
Hydrogen bonding between nitrogenous bases forms a double-stranded structure. This hydrogen bonding is commonly referred to as base pairing.
Base pairing
The hydrogen bonding between nitrogenous bases, which forms a double-stranded structure, is called base pairing. The length of a DNA strand is measured in base pairs (bp).
Complementary strands
Under normal circumstances, the hydrogen bonds form only between specific purine-pyrimidine pairs. Adenine forms 2 hydrogen bonds with thymine. Guanine forms three hydrogen bonds with cytosine. (This means that GC bonds require more energy to separate.)
In order for two strands to bind together, their bases must match up in the correct order. Two strands that match like this are called complementary strands.
Double helix
When complementary strands bind together, they curl into a double helix. The double helix contains two distinct groups called the major groove and the minor groove. Each groove spirals once around the double helix for every 10 base pairs. The diameter of the double helix is about 13 times the diameter of a carbon atom, or 2 nm.
DNA replication
One time in each life cycle, a cell replicates it’s DNA.
The process of DNA replication is governed by the replisome. Replication begins at the middle of a chromosome at a site called the origin of replication. A single eukaryotic chromosome contains multiple origins on each chromosome, while replication in prokaryotes usually takes place from a single origin on the circular chromosome.
From the origin, two replisomes proceed in opposite directions along the chromosome making replication a bidirectional process. The place where the replisome attaches to the chromosome is called the replication fork. Each chromosome of eukaryotic DNA is replicated in many discrete segments.
DNA replication has five steps:
- Helicase unzips the double helix
- RNA polymerase builds a primer
- DNA polymerase assembles the leading and lagging strands
- The primers are removed
- Okazaki fragments are joined with ligase
DNA replication is fast and accurate. replication in a human cell requires about eight hours.
Although there are some differences, replication in eukaryotes and prokaryotes is very similar.
DNA polymerase
The enzyme that builds the new DNA strand. It can only add nucleotides to existing strands, and thus adds deoxynucleotides to the primer and moves along each DNA strand creating a new complementary strand. DNA polymerase reads the parental strand in the 3’ to 5’ direction, and creates the new complementary strand in the 5’ to 3’ direction. By convention, the nucleotide sequence in DNA is written 5’ to 3’ as well.
One of the subunits in DNA polymerase is also an exonuclease. It removes nucleotides from the strand. This enzyme automatically proofreads each new strand, and makes repairs when it discovers any mismatch nucleotides. DNA replication in eukaryotes is extremely accurate.
RNA primer
Because DNA polymerase can only add nucleotides to existing strands, primase, an RNA polymerase, creates an RNA primer approximately 10 ribonucleotides long to initiate the strand.
Lagging strand
The polymerization of the new strand is continuously interrupted and restarted with the new RNA primer. This interrupted strand is called the lagging strand. It is made from a series of disconnected strands called Okazaki fragments. Okazaki fragments are about 100 to 200 nucleotides long and eukaryotes and about 1000 to 2000 nucleotides long in prokaryotes.
Leading strand
The continuous new strand created by DNA polymerase is called the leading strand.
DNA ligase
Moves along the lagging strand and ties the Okazaki fragments together to complete the polymer.
Semidiscontinuous
Since the formation of one strand in DNA replication is continuous and the other fragmented. The process of replication is said to be semi-discontinuous.
Telomeres
The ends of eukaryotic chromosomes on DNA possess telomeres. Telomeres are repeated six nucleotide units from 100 to 1000 units long that protect the chromosomes from being eroded through repeated rounds of replication. Telomerase catalyzes the lengthening of telomeres.
RNA
Ribonucleic acid is identical to DNA in structure except that:
- Carbon number two on the pentose is not deoxygenated, it has a hydroxyl group attached
- RNA is single-stranded
- RNA contains the pyrimidine uracil instead of thymine
Unlike DNA, RNA can move through the nuclear pores and is not confined to the nucleus.
mRNA
Messenger RNA. Delivers the DNA code for amino acids to the cytosol where the proteins are manufactured. Almost all mRNA is directly translated to protein. mRNA is the template which carries the genetic code from the nucleus to the cytosol in the form of codons.
rRNA
Ribosomal RNA. Combines with proteins to form ribosomes, the intracellular complexes that directs the synthesis of proteins. rRNA is synthesized in the nucleolus.
tRNA
Transfer RNA. Collect amino acids in the cytosol, and transfers them to the ribosomes for incorporation into a protein.
Transcription
All RNA is manufactured from a DNA template in a process called transcription. Eukaryotic transcription takes place in the nucleus and mitochondrial matrix, since DNA cannot leave those two spots. Transcription starts with initiation.
Only the template strand of the DNA double helix is transcribed. The sequence of the coding strand resembles the sequence of the newly synthesized mRNA.
Initiation
The beginning of transcription is called initiation. A group of proteins find a promoter on the DNA strand and assemble a transcription initiation complex, which includes RNA polymerase. Prokaryotes have one type of RNA polymerase. Eukaryotes, except plants, have three: one each for mRNA and snRNA, tRNA, and rRNA.
Promoter
A promoter is a sequence of DNA nucleotides that designates a beginning point for transcription. The promoter and prokaryotes is located at the beginning of the gene, “upstream”. The transcription start point is part of the promoter. The first base pair at the transcription start point is designated +1, base pairs located before the +1 transcription site are designated by negative numbers.
Elongation
After binding to the promoter, RNA polymerase unzips the DNA double helix creating a transcription bubble. Next the complex switches to to elongation mode. In elongation, RNA polymerase transcribes only one strand of DNA nucleotide sequence into a complementary RNA nucleotide sequence.
Only one strand in a molecule of double-stranded DNA is transcribed, the template strand. The other strand, coding strand, protects its partner against degradation.
RNA polymerase
RNA polymerase is included in the transcription initiation complex. After binding to the promoter, it unzips the DNA double helix, creating a transcription bubble. Like DNA polymerase, RNA polymerase moves along the DNA strand in the 3’ to 5’ direction, building the new RNA strand in the 5’ to 3’ direction.
Note that RNA polymerase does not have a proofreading mechanism, so the rate of errors for transcription is higher than for replication.
Termination
The end of transcription is called termination. This requires a special termination sequence and special proteins to dissociate RNA polymerase from DNA.
Activators and repressors
Replication makes no distinction between genes. Instead, genes are activated or deactivated at the level of transcription. Most regulation occurs via proteins called activators and repressors. These bind to DNA close to the promoter, and activate or repress the activity of RNA polymerase. They are allosterically regulated by small molecules like cAMP.
The amount of a given type of protein within a cell is likely to be related to how much of it’s mRNA is transcribed.
Operon
An operon is a sequence of bacterial DNA containing an operator, a promoter, and related genes. The genes of an operon are transcribed on one mRNA. Genes outside the operon may code for activators and repressors.
The lac operon codes for enzymes that allow E. coli to import and metabolize lactose when glucose is not present in sufficient quantities. Low glucose levels lead to high cAMP levels. cAMP binds to and activates CAP. Activated CAP to a CAP site, activating the promoter, allowing the formation of an initiation complex and the subsequent transcription and translation of three proteins. The operator, located adjacent and downstream of the promoter, provides a binding site for a repressor protein. The repressor protein is inactivated by the presence of lactose in the cell. It will bind to the operator unless lactose binds to the repressor protein.
The binding of the lac repressor to the operator in the absence of lactose prevents the transcription of the lac genes. Lactose can induce the transcription of the operon only when glucose is not present.
Post transcriptional processing
The addition of the 5’ cap to eukaryotic mRNA, which serves as an attachment site in protein synthesis and as a protection against degradation by exonucleases.
The polyadenylation of the 3’ end of mRNA with a poly-A tail, also protecting it from exonucleases.
The splicing of introns from the primary transcript.
Primary transcript
The initial mRNA nucleotide sequence arrived at through transcription is called the primary transcript. The primary transcript is processed in three ways: by the addition of nucleotides, deletion of nucleotides, and modification of nitrogenous bases.
Introns and exons
The primary transcript is much longer than the mRNA that will be translated into a protein. Before leaving the nucleus, the primary transcript is cleaved into introns and exons. Enzyme-RNA complexes called small nuclear ribonucleoproteins (snRNPs) recognize nucleotide sequences at the end of the introns. Several snRNPs associate with proteins to form the spliceosome. Inside the spliceosome, the introns are looped bringing the exons together. The introns are then excised by the splicesome and the exons are spliced together to form the single mRNA strand that ultimately codes for a polypeptide. Intron’s do not code for protein and integrated within the nucleus. Although there are only an estimated 20 to 25,000 protein coding genes in the human genome, there are about 120,000 proteins made possible by differential splicing of exons. Introns represent about 24% of the genome. Exons represent about 1.1%.
Denaturing
When heated or immersed in high concentrations salt solution or high pH solution, the hydrogen bonds connecting the two strands in a double-stranded DNA molecule are disrupted and the strands separate. The temperature needed to separate the DNA strands is called the melting temperature. DNA with more GC base pairs has a greater melting temperature, since guanine and cytosine make three hydrogen bonds. Heating two 95°C is generally sufficient to denature any DNA sequence.
Denatured DNA is less viscous, denser, and more able to absorb UV light. Separated strands will spontaneously associate with their original partner or any other complementary nucleotide sequence.
Nucleic acid hybridization
Separated strands will spontaneously associate with their original partner or any other complementary nucleotide sequence. Thus different double-stranded combinations can be formed through hybridization- DNA and DNA, DNA and RNA, and RNA and RNA. Hybridization techniques allows scientists to identify nucleotide sequences by binding unknown sequence with an unknown sequence.