Term
Levels of Complexity of Life
Lecture: Flow of Biological Information |
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Definition
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Atoms->Molecules->Cells->Tissues->Organisms->Populations->Ecosystems
[LUCA is the Last Universal Common Ancestor]
Whether single celled or multi-cellular, core features of all organisms are conserved, and living organisms must be:
1: Separate in some way from their environment (membranes in euk and simple compartmentalization in prok->allows euk to be more complex and regulated with specific environments in same cell and organelles with their own DNA i.e. mitochondria and chloroplasts)
2: Able to store information in a stable way
3: Able to reliably replicate and pass information to the next generation
4: Able to extract energy from their surroundings
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Term
4 Basic Classes of Molecules
Lecture: Flow of Biological Information |
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Definition
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All are polymers:
§ Nucleic acids are made up of nucleotides. The nucleic acids DNA and RNA store and carry information
§ Proteins are made of amino acids, and carry out most cellular functions
§ Lipids are comprised of fatty acids and form membranes around cells and organelles
§ Carbohydrates include small sugars and larger polysaccharides and have a wide range of roles such as energy storage, cell adhesion, cell structure, signaling, etc
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Term
DNA Molecule Overview
Lecture: Flow of Biological Information |
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Definition
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§ DNA (deoxyribonucleic acid) is the means of storing information in a stable, heritable form
§ In humans, there are 3 billion bp and 10^4 genes
§ DNA is a type of nucleic acid made up of 4 nucleotides (all planar):
§ guanosine (G)
§ adenosine (A)
§ thymidine (T)
§ cytidine (C)
§ The order of nucleotides in DNA is the information in the genetic “code”
§ DNA forms a double helix with nucleotides paired, A with T and C with G
§ 2 strands make up the DNA (although there can be ssDNA, almost all living things with 2 strands), 1 template and 1 backup
§ The double helix is directional – strands lie in “head to toe” antiparallel polarity, DNA is always read 5'-3', copied in both directions 3'-5' and 5'-3' but DNA polymerase only works in 3'-5' direction in replication [original will 3'-5' and copy made will be 5'-3']
[image]
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Term
DNA/RNA Replication Overview
Lecture: Flow of Biological Information |
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Definition
§ The two stranded structure of DNA allows separation and copying of information in either orientation
1: Original strands separate
2: Nucleotides are added to the separated strands to form new strands. Nucleotides are added in a COMPLEMENTARY fashion – A/T and C/G
3: Two new double-stranded DNA molecules are produced from one original molecule
§ All the DNA sequences in an organism form its GENOME, the blueprint for that particular organism
§ Genetic information needs to be passed to the next generation, or to new cells of the same organism: this is transmission of the genome (w/o checkpoints and regulation only 1/2^23 replication processes would yield an exact replica of original strand)
§ Another nucleic acid, RNA (ribonucleic acid), is most often single-stranded and mainly used for information transfer and regulation of gene expression
§ The extra oxygen in RNA allows for it to act enzymatic and have several fxns
§ RNA is made by copying the sequence of a region of the genome into an RNA molecule (transcription)
§ The RNA is either used directly by the cell or used as information to direct manufacture of a particular protein
§ Transcription is the copying of DNA into RNA (ribonucleic acid) molecules
§ RNA polymerase synthesizes RNA
§ Regions of DNA signal RNA polymerase when to start making RNA and when to stop
§ RNA does not have thymidine, so it is replaced by uracil. Uracil (U) pairs with adenosine (A)
§ The RNA produced is the primary transcript – this is further refined into the final product: Both exons and introns are copied into RNA. The introns are spliced out to create mRNA for translation
[image]
(Copying DNA into mRNA, and only fragment of DNA unlooped) |
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Term
Gene Overview
Lecture: Flow of Biological Information |
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Definition
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§ The genome largely consists of genes and “junk” DNA
§ A gene is a region that controls a discrete hereditary characteristic, usually a specific product like a protein
§ A gene has the information for a product, but also instructions for when and where the product is made. A single gene can code for many different products
§ Much “Junk” DNA is non-genic, but is proving to be functional in not fully understood ways
§ DNA is packaged into linear or circular units called chromosomes
§ In eukaryotes, DNA is wrapped around packing proteins (histones) and compacted in a space-efficient way
§ Some cells have small extra pieces of DNA (plasmids)
§ Chromosome - chromo = light, can pass light through w/ microscope
§ Gene expression is carefully regulated – at the transcriptional, post-transcriptional, translational and post-translational levels
[image]
[Transformation to higher degree protein as chromosome condenses]
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Term
Genome Diversity
Lecture: Flow of Biological Information |
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Definition
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§ Genomes vary widely in the size of genome, number of genes and gene spacing
-E. coli is 98% genic
§ Generally, single celled organisms have fewer genes than multicellular organisms. However, larger genome size and increased genome complexity do not always correlate with organisms having greater complexity
-For example, the genome of the single-celled amoeba is more than 200x the size of the human genome (more introns)
§ § § Genomes often have transposable elements – pieces of DNA that copy themselves within a genome and increase genome size
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Term
Translation Overview
Lecture: Flow of Biological Information |
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Definition
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§ Coding RNAs that contain the information to produce a protein are called messenger RNAs (mRNAs)
§ Proteins are built from amino acids
§ Twenty amino acids are commonly used
§ Proteins can range from a few amino acids long (e.g. calmodulin), to many thousands (e.g. hemaglutinin)
§ Proteins may contain distinct separate proteins that come together to form a functional unit
§ The process of turning the information in an mRNA into a protein is called translation
§ Distinct sequences in the mRNA indicate where translation is to begin and finish
§ Each amino acid is represented (encoded) by three nucleotides in the mRNA molecule called a codon
§ Translation is performed by the ribosome, which has protein and RNA components
§ Transfer RNA (tRNA) interprets the information in mRNA into the protein sequence
[image] [image]
(tRNA binding to mRNA with anticodon and forming hairpin loop secondary structure due to H bonding)
[image]
(tRNA then brings amino acid and allows for polymer to form)
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Term
Ribozymes Overview
Lecture: Flow of Biological Information |
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Definition
- Protein synthesis via the ribosome is an example of a conserved fundamental process which heavily involves RNA.
- The ribosome is made of RNA and protein. The ribosomal RNA (rRNA) contributes to catalysis, making the ribosome a “ribozyme”
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Term
Codon Overview
Lecture: Flow of Biological Information |
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Definition
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§ Most amino acids can be encoded by more than one codon
§ Methionine (codon AUG) usually indicates the start of a protein
§ Stop codons indicate the end of a protein (UAA,UAG,UGA)
§ All codons have an outcome, so the code is referred to as “non-ambiguous”
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Term
Phenotype Overview
Lecture: Flow of Biological Information |
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Definition
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§ The activity and interplay of all the genes in a cell produce the phenotype for that cell or organism
§ The phenotype is the visual features of an organism, whereas the genotype is the collective DNA sequence
§ Organisms have a ploidy - the number of copies of its genome that the organism has
§ Yeast can thrive as a haploid – one copy of its genome – or as a diploid
§ More complex eukaryotes – like humans – have two copies and are diploid. Others are polyploid i.e. frogs
§ Having extra copies of chromosomes can provide a “back-up” if a gene is defective on one chromosome but fully functional on a homologous chromosome
§ “Forward” genetics is where a mutant phenotype is observed, and the gene then identified that causes the phenotype
§ “Reverse” genetics is where a gene of interest is disrupted, and the phenotype observed
§ Copies of a gene that are similar but non-identical (such as wild-type and mutant genes) are referred to as alleles
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Term
Mutations Overview
Lecture: Flow of Biological Information |
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Definition
Mutations lead to the diversity of life
[image]
§ Single nucleotide changes can alter the encoded amino acid – missense mutations
§ Single nucleotide changes can introduce a premature stop codon – nonsense mutations
§ Single nucleotide changes that do not alter the encoded amino acid -- silent mutations
§ Mutations in somatic cells only affect the organism itself, but mutations in germline cells affect subsequent generations
§ Mutations frequently lead to disease. If a mutation in a single gene causes a disease, this is monogenic
§ Example: phenylkenonuria
§ Polygenic disease are those that result from changes in several genes
§ Examples: Alzheimer’s disease and diabetes
§ Mutations do not always result in disease, but can increase likelihood of a disease. Penetrance is the percentage of people with the mutation that will develop the disease
§ Example: Mutations in the BRCA1 and BRCA2 genes in humans increases the risk of breast cancer
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Term
Nucleotide Overview
Nucleic Acid Structure |
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Definition
[image]
[deoxyadenosine 5′-monophosphate (dAMP)]
§Nucleotides comprise a base, a sugar, and phosphate
§ Nucleotides have additional biological functions, such as energy storage (ATP) and molecular transport
§ DNA and RNA are polymers of nucleotides
§ Nucleotides are joined by a phosphodiester bond between the 3′ hydroxyl of one sugar and the phosphate attached to the 5′ hydroxyl of the next sugar
§ NA strands are thus directional – one end has an exposed 3′hydroxl, the other end has an exposed 5′ phosphate
§ By convention, NA sequences are written in the 5′ to 3′ direction
§ The sugars and phosphates form a repeating unit – the sugar-phosphate backbone, covalently bonded
§ The backbone is always the same, but the attached bases vary
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Term
Deoxyribose and Ribose Structures
Nucleic Acid Structure |
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Definition
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Term
Base Structures
Nucleic Acid Structure |
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Definition
[image]
[image]
§ Bases are planar rings that are typically uncharged under physiological conditions
§pKa values denote the pH at which half the molecules in a population are charged at a given atom (pKa = pH + log(protonated/unprotonated))
§ Each base is joined to a sugar by a glycosidic bond between the C1′ of the sugar and the N1 of a pyrimidine or N9 of a purine
[image]
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Term
Tautomers of Bases
Nucleic Acid Structure |
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Definition
[image]
§ Bases can exist in two tautomeric forms (isomeric structures in which a proton has migrated to a different place)
§ Usually, less than 0.01% of bases are in the less common tautomeric form
§Tautomers have implications for the accuracy of DNA replication, and can provide genetic variation
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Term
Base Stacking
Nucleic Acid Structure |
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Definition
[image]
§ The most energetically favorable formation of double-stranded DNA is for the two strands to wind around one another in a right-handed double helix
§ The hydrophobic bases cluster in the center, away from the aqueous cellular environment
§ The hydrophilic sugar phosphate backbone interacts favorably with water, and so is on the outside of the molecule since phosphate is negative
§ Base pairs form a stack on the interior of the helix. Van der Waals interactions between bases stabilize the interactions (main force)
§ This “base-stacking” arrangement is very energetically favorable, and is important for the stability of DNA
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Term
Different DNA Configurations
Nucleic Acid Structure |
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Definition
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In all forms, A-T and G-C base pairs have similar widths, so the helix diameter is ~20 Å
§ B-DNA is the predominant configuration in DNA. The helix repeats every 10.5 base pairs, and base pairs are 3.4 Å apart. The helix forms a major groove (~13 Å) and a minor groove (~9 Å)
§ A-DNA is a right-handed helix, but has 11 base pairs per turn, making the grooves move evenly sized. The A conformation can be induced by DNA binding proteins. The 2′ OH means that RNA favors an A-type helix rather that the B-type helix of DNA (Geometric interference,Sugar pucker)
§ Z-DNA, a left-handed helix, can result from methylation of cytosine, tortional stress, and high salt concentrations
[image]
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Term
History of DNA Structure Discovery
Nucleic Acid Structure |
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Definition
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§ TWatson and Crick published their deduction of the structure of DNA in 1953, using several pieces of then recently discovered evidence
- Bases were proposed to be perpendicular to the sugar backbone, and in the enol or imino form (Donohue)
- Adenine and thymine were always found in 1:1 ratios, as were cytosine and guanine (Chargaff)
T The key information came from X-ray diffraction studies of DNA fibers (Franklin)
- The cross pattern with short lines is characteristic of a helix
- The spacing of the lines suggested the dimensions of the helix
- Diffraction patterns suggested two intertwining helices
[image]
Few differences from present day:
- Base pairs are not precisely planar
- There are slightly more than 10 base pairs per turn
- The helix axis is not perfectly straight
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Term
Supercoiling Overview
Nucleic Acid Structure |
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Definition
§ To induce supercoiling, a circular molecule is cut and held at one end while the other end is twisted
§ This changes the number of bases per turn
§ When the two ends are stuck back together (ligated) the DNA twists to restore the preferred number of bases per turn
§ This causes the DNA to wrap around itself in a coiled structure
§ Supercoiling can be positive or negative, depending on the direction of the DNA twisting
§ Clockwise winding of the DNA, tending to separate the strands, leads to negative supercoiling
§ Twisting in the counterclockwise direction induces positive supercoiling
§ Linear pieces of DNA can also be supercoiled if one end is immobile
§ Supercoiling is released if one of the DNA strands is cut
§ Supercoiling can be toroidal or interwound
[image]
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Term
Sugar Pucker
Nucleic Acid Structure |
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Definition
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§ The sugar part of nucleic acid molecules have buckled conformations, known as sugar pucker
§ The 2′ OH of ribose causes it to have a different sugar pucker to deoxyribose
§ In ribose, the formation is called C3′endo, and is favored by the A-type helix
§ The C2′ endo form is found in deoxyribose and favors the B-type helix
§ The 2′ OH also allows RNA to form hydrogen bonds more prolifically than DNA, allowing more inter- and intra- molecular interactions
[image]
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