A report on Protein and Base pair

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).
Depiction of the adenine–thymine Watson–Crick base pair
John Kendrew with model of myoglobin in progress
Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.
Resonance structures of the peptide bond that links individual amino acids to form a protein polymer
A ribosome produces a protein using mRNA as template
The DNA sequence of a gene encodes the amino acid sequence of a protein
The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: All-atom representation colored by atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).
Molecular surface of several proteins showing their comparative sizes. From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme).
The enzyme hexokinase is shown as a conventional ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.
Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen
Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white)
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units

In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code.

- Base pair

The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes.

- Protein
A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).

12 related topics with Alpha

Overall

The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.

DNA

9 links

Polymer composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses.

Polymer composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses.

The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.
Chemical structure of DNA; hydrogen bonds shown as dotted lines. Each end of the double helix has an exposed 5' phosphate on one strand and an exposed 3' hydroxyl group (—OH) on the other.
A section of DNA. The bases lie horizontally between the two spiraling strands ([[:File:DNA orbit animated.gif|animated version]]).
DNA major and minor grooves. The latter is a binding site for the Hoechst stain dye 33258.
From left to right, the structures of A, B and Z DNA
DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone is very different from the typical DNA helix. The green spheres in the center represent potassium ions.
A covalent adduct between a metabolically activated form of benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA
Location of eukaryote nuclear DNA within the chromosomes
T7 RNA polymerase (blue) producing an mRNA (green) from a DNA template (orange)
DNA replication: The double helix is unwound by a helicase and topo­iso­merase. Next, one DNA polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand. This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together.
Interaction of DNA (in orange) with histones (in blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA.
The lambda repressor helix-turn-helix transcription factor bound to its DNA target
The restriction enzyme EcoRV (green) in a complex with its substrate DNA
Recombination involves the breaking and rejoining of two chromosomes (M and F) to produce two rearranged chromosomes (C1 and C2).
The DNA structure at left (schematic shown) will self-assemble into the structure visualized by atomic force microscopy at right. DNA nanotechnology is the field that seeks to design nanoscale structures using the molecular recognition properties of DNA molecules.
Maclyn McCarty (left) shakes hands with Francis Crick and James Watson, co-originators of the double-helix model.
Pencil sketch of the DNA double helix by Francis Crick in 1953
A blue plaque outside The Eagle pub commemorating Crick and Watson
Impure DNA extracted from an orange

Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double-stranded DNA.

Gregor Mendel

Gene

5 links

Gregor Mendel
Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes. The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.
Schematic of a single-stranded RNA molecule illustrating a series of three-base codons. Each three-nucleotide codon corresponds to an amino acid when translated to protein
Protein coding genes are transcribed to an mRNA intermediate, then translated to a functional protein. RNA-coding genes are transcribed to a functional non-coding RNA.
Inheritance of a gene that has two different alleles (blue and white). The gene is located on an autosomal chromosome. The white allele is recessive to the blue allele. The probability of each outcome in the children's generation is one quarter, or 25 percent.
A sequence alignment, produced by ClustalO, of mammalian histone proteins
Evolutionary fate of duplicate genes.
Depiction of numbers of genes for representative plants (green), vertebrates (blue), invertebrates (orange), fungi (yellow), bacteria (purple), and viruses (grey). An inset on the right shows the smaller genomes expanded 100-fold area-wise.
Gene functions in the minimal genome of the synthetic organism, Syn 3.
Comparison of conventional plant breeding with transgenic and cisgenic genetic modification.

In biology, a gene (from γένος, ; meaning generation or birth or gender) is a basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

Two chains of DNA twist around each other to form a DNA double helix with the phosphate-sugar backbone spiraling around the outside, and the bases pointing inwards with adenine base pairing to thymine and guanine to cytosine.

DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.

DNA replication

4 links

Biological process of producing two identical replicas of DNA from one original DNA molecule.

Biological process of producing two identical replicas of DNA from one original DNA molecule.

DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.
DNA polymerases adds nucleotides to the 3′ end of a strand of DNA. If a mismatch is accidentally incorporated, the polymerase is inhibited from further extension. Proofreading removes the mismatched nucleotide and extension continues.
Overview of the steps in DNA replication
Steps in DNA synthesis
Role of initiators for initiation of DNA replication.
Formation of pre-replication complex.
Scheme of the replication fork.
a: template, b: leading strand, c: lagging strand, d: replication fork, e: primer, f: Okazaki fragments
Many enzymes are involved in the DNA replication fork.
The assembled human DNA clamp, a trimer of the protein PCNA.
E. coli Replisome. Notably, the DNA on lagging strand forms a loop. The exact structure of replisome is not well understood.
The cell cycle of eukaryotic cells.
Dam methylates adenine of GATC sites after replication.
Replication fork restarts by homologous recombination following replication stress
Epigenetic consequences of nucleosome reassembly defects at stalled replication forks

A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis.

Nucleobases are matched between strands through hydrogen bonds to form base pairs.

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.

RNA

4 links

Polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

Polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.
Three-dimensional representation of the 50S ribosomal subunit. Ribosomal RNA is in ochre, proteins in blue. The active site is a small segment of rRNA, indicated in red.
Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)
Structure of a fragment of an RNA, showing a guanosyl subunit.
Secondary structure of a telomerase RNA.
Structure of a hammerhead ribozyme, a ribozyme that cuts RNA
Uridine to pseudouridine is a common RNA modification.
Double-stranded RNA
Robert W. Holley, left, poses with his research team.

Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of the four major macromolecules essential for all known forms of life.

This antisense-based process involves steps that first process the RNA so that it can base-pair with a region of its target mRNAs.

The interaction of tRNA and mRNA in protein synthesis.

Transfer RNA

3 links

Adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins.

Adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins.

The interaction of tRNA and mRNA in protein synthesis.
Secondary cloverleaf structure of tRNAPhe from yeast.
Tertiary structure of tRNA. CCA tail in yellow, Acceptor stem in purple, Variable loop in orange, D arm in red, Anticodon arm in blue with Anticodon in black, T arm in green.
3D animated GIF showing the structure of phenylalanine-tRNA from yeast (PDB ID 1ehz). White lines indicate base pairing by hydrogen bonds. In the orientation shown, the acceptor stem is on top and the anticodon on the bottom
Bulge-helix-bulge motif of a tRNA intron

As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code.

The anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis.

Simplified diagram of mRNA synthesis and processing. Enzymes not shown.

Transcription (biology)

3 links

Process of copying a segment of DNA into RNA.

Process of copying a segment of DNA into RNA.

Simplified diagram of mRNA synthesis and processing. Enzymes not shown.
Regulation of transcription in mammals. An active enhancer regulatory region of DNA is enabled to interact with the promoter DNA region of its target gene by formation of a chromosome loop. This can initiate messenger RNA (mRNA) synthesis by RNA polymerase II (RNAP II) bound to the promoter at the transcription start site of the gene.  The loop is stabilized by one architectural protein anchored to the enhancer and one anchored to the promoter and these proteins are joined to form a dimer (red zigzags).  Specific regulatory transcription factors bind to DNA sequence motifs on the enhancer.  General transcription factors bind to the promoter.  When a transcription factor is activated by a signal (here indicated as phosphorylation shown by a small red star on a transcription factor on the enhancer) the enhancer is activated and can now activate its target promoter.  The active enhancer is transcribed on each strand of DNA in opposite directions by bound RNAP IIs.  Mediator (a complex consisting of about 26 proteins in an interacting structure) communicates regulatory signals from the enhancer DNA-bound transcription factors to the promoter.
This shows where the methyl group is added when 5-methylcytosine is formed
Simple diagram of transcription elongation
Image showing RNA polymerase interacting with different factors and DNA during transcription, especially CTD (C Terminal Domain)
The Image shows how CTD is carrying protein for further changes in the RNA
Electron micrograph of transcription of ribosomal RNA. The forming ribosomal RNA strands are visible as branches from the main DNA strand.
Scheme of reverse transcription

The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA).

Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language.

This nucleotide contains the five-carbon sugar deoxyribose (at center), a nucleobase called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a <u title="Nucleotide">Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a <u title="Deoxyadenosine monophosphate" href="deoxyadenosine monophosphate">nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.

Nucleotide

4 links

Nucleotides are organic molecules consisting of a nucleoside and a phosphate.

Nucleotides are organic molecules consisting of a nucleoside and a phosphate.

This nucleotide contains the five-carbon sugar deoxyribose (at center), a nucleobase called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a <u title="Nucleotide">Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a <u title="Deoxyadenosine monophosphate" href="deoxyadenosine monophosphate">nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.
Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At the upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (a double helix) of nucleic acid, shown at upper left.
Structural elements of three nucleo tides —where one-, two- or three-phosphates are attached to the nucleo side (in yellow, blue, green) at center: 1st, the nucleotide termed as a nucleoside mono phosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms a nucleoside di phosphate; 3rd, adding a third phosphate results in a nucleoside tri phosphate. + The nitrogenous base (nucleobase) is indicated by "Base" and "glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).
The synthesis of UMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(128,0,0);">inorganic molecules
The synthesis of IMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(227,13,196);">metal ions , <span style="color: rgb(128,0,0);">inorganic molecules

They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular functions that demand energy, including: amino acid, protein and cell membrane synthesis, moving the cell and cell parts (both internally and intercellularly), cell division, etc. In addition, nucleotides participate in cell signaling (cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+).

In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA.

Chemical structure of RNA

Nucleic acid sequence

2 links

Succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA or RNA (GACU) molecule.

Succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA or RNA (GACU) molecule.

Chemical structure of RNA
A series of codons in part of a mRNA molecule. Each codon consists of three nucleotides, usually representing a single amino acid.
A depiction of the genetic code, by which the information contained in nucleic acids are translated into amino acid sequences in proteins.
Electropherogram printout from automated sequencer for determining part of a DNA sequence
Genetic sequence in digital format.

The nucleobases are important in base pairing of strands to form higher-level secondary and tertiary structure such as the famed double helix.

In biological systems, nucleic acids contain information which is used by a living cell to construct specific proteins.

Graphical representation of the idealized human diploid karyotype, showing the organization of the genome into chromosomes. This drawing shows both the male (XY) and female (XX) versions of the 23rd chromosome pair. Chromosomes are shown aligned at their centromeres. The mitochondrial DNA is not shown.

Human genome

3 links

Complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria.

Complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria.

Graphical representation of the idealized human diploid karyotype, showing the organization of the genome into chromosomes. This drawing shows both the male (XY) and female (XX) versions of the 23rd chromosome pair. Chromosomes are shown aligned at their centromeres. The mitochondrial DNA is not shown.
Number of genes (orange) and base pairs (green, in millions) on each chromosome.
Human genes categorized by function of the transcribed proteins, given both as number of encoding genes and percentage of all genes.
TSC SNP distribution along the long arm of chromosome 22 (from https://web.archive.org/web/20130903043223/http://snp.cshl.org/ ). Each column represents a 1 Mb interval; the approximate cytogenetic position is given on the x-axis. Clear peaks and troughs of SNP density can be seen, possibly reflecting different rates of mutation, recombination and selection.
Populations with a high level of parental-relatedness result in a larger number of homozygous gene knockouts as compared to outbred populations.
A pedigree displaying a first-cousin mating (carriers both carrying heterozygous knockouts mating as marked by double line) leading to offspring possessing a homozygous gene knockout.

Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization) consist of 3,054,815,472 DNA base pairs (if X chromosome is used), while female diploid genomes (found in somatic cells) have twice the DNA content.

This sequence identified 19,969 protein-coding sequences, accounting for approximately 1.5% of the genome, and 63,494 genes in total, most of them being non-coding RNA genes.

Model of hydrogen bonds (1) between molecules of water

Hydrogen bond

2 links

Primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group, and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac).

Primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group, and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac).

Model of hydrogen bonds (1) between molecules of water
AFM image of naphthalenetetracarboxylic diimide molecules on silver-terminated silicon, interacting via hydrogen bonding, taken at 77  K. ("Hydrogen bonds" in the top image are exaggerated by artifacts of the imaging technique. )
An example of intermolecular hydrogen bonding in a self-assembled dimer complex. The hydrogen bonds are represented by dotted lines.
Intramolecular hydrogen bonding in acetylacetone helps stabilize the enol tautomer.
Examples of hydrogen bond donating (donors) and hydrogen bond accepting groups (acceptors)
Cyclic dimer of acetic acid; dashed green lines represent hydrogen bonds
Crystal structure of hexagonal ice. Gray dashed lines indicate hydrogen bonds
Structure of nickel bis(dimethylglyoximate), which features two linear hydrogen-bonds.
The structure of part of a DNA double helix
Hydrogen bonding between guanine and cytosine, one of two types of base pairs in DNA
Para-aramid structure
A strand of cellulose (conformation Iα), showing the hydrogen bonds (dashed) within and between cellulose molecules

Intramolecular hydrogen bonding is partly responsible for the secondary and tertiary structures of proteins and nucleic acids.

For example, the double helical structure of DNA is due largely to hydrogen bonding between its base pairs (as well as pi stacking interactions), which link one complementary strand to the other and enable replication.