Chapter 1: Review Flashcards
adenine
Adenine (A, Ade) is a nucleobase (a purine derivative). Its derivatives have a variety of roles in biochemistry, including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA.
centromere
The centromere is the part of a chromosome that links sister chromatids. During mitosis, spindle fibers attach to the centromere via the kinetochore. Centromeres were first defined as genetic loci that direct the behavior of chromosomes.
(shown: In this diagram of a duplicated chromosome, (2) identifies the centromere—the region that joins the two sister chromatids, or each half of the chromosome. In prophase of mitosis, specialized regions on centromeres called kinetochores attach chromosomes to spindle fibers.)
Additional reading:
The physical role of the centromere is to act as the site of assembly of the kinetochore - a highly complex multiprotein structure that is responsible for the actual events of chromosome segregation - i.e. binding microtubules and signalling to the cell cycle machinery when all chromosomes have adopted correct attachments to the spindle, so that it is safe for cell division to proceed to completion and for cells to enter anaphase.
There are, broadly speaking, two types of centromeres. “Point centromeres” bind to specific proteins that recognise particular DNA sequences with high efficiency. Any piece of DNA with the point centromere DNA sequence on it will typically form a centromere if present in the appropriate species. The best characterised point centromeres are those of the budding yeast, Saccharomyces cerevisiae. “Regional centromeres” is the term coined to describe most centromeres, which typically form on regions of preferred DNA sequence, but which can form on other DNA sequences as well.[3] The signal for formation of a regional centromere appears to be epigenetic. Most organisms, ranging from the fission yeast Schizosaccharomyces pombe to humans, have regional centromeres.
Regarding mitotic chromosome structure, centromeres represent a constricted region of the chromosome (often referred to as the primary constriction) where two identical sister chromatids are most closely in contact. When cells enter mitosis, the sister chromatids (the two copies of each chromosomal DNA molecule resulting from DNA replication in chromatin form) are linked along their length by the action of the cohesin complex. It is now believed that this complex is mostly released from chromosome arms during prophase, so that by the time the chromosomes line up at the mid-plane of the mitotic spindle (also known as the metaphase plate), the last place where they are linked with one another is in the chromatin in and around the centromere.[4]
chromatin
Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells (cells with defined nuclei). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore and is localized within the nucleoid region).
In general terms, there are three levels of chromatin organization:
DNA wraps around histone proteins forming nucleosomes; the “beads on a string” structure (euchromatin).
Multiple histones wrap into a 30 nm fibre consisting of nucleosome arrays in their most compact form (heterochromatin). (Definitively established to exist in vitro, the 30-nanometer fibre was not seen in recent X-ray studies of human mitotic chromosomes.)
Higher-level DNA packaging of the 30 nm fibre into the metaphase chromosome (during mitosis and meiosis).
There are, however, many cells that do not follow this organisation. For example, spermatozoa and avian red blood cells have more tightly packed chromatin than most eukaryotic cells, and trypanosomatid protozoa do not condense their chromatin into visible chromosomes for mitosis.
codon
Groups of three nucleotides, called codons, constitute the three-letter “words” of the genetic coding language. Every combination of three stands for one of the 20 specific amino acids. The codons in mRNA are “read” consecutively starting at one end by the translational machine, called the ribosome.
Shown: A series of codons in part of a messenger RNA (mRNA) molecule. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosometo synthesize a protein according to this code.
cytosine
Cytosine (C) is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine.
deoxyribonucleic acid
Deoxyribonucleic acid (DNA) is a molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are known as polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of a nitrogen-containing nucleobase—either cytosine (C), guanine (G), adenine (A), or thymine(T)—as well as a monosaccharide sugar called deoxyribose and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. According to base Watson-Crick pairing rules (A with T, and C with G), hydrogen bonds bind the nitrogenous bases of the two separate polynucleotide strands to make double-stranded DNA.
diploid
Diploid is a cell or organism that has paired chromosomes, one from each parent. In humans, cells other than human sex cells (called somatic cells), are diploid and have 23 pairs of chromosomes. Human sex cells (egg and sperm cells) contain a single set of chromosomes and are known as haploid.
DNA cloning
DNA cloning involves taking a DNA fragment and replicating it many times over until there are many copies so that essentially it can be treated like a reagent in a test tube. The process of replicating a DNA sequence is called “amplifying,” in the same way as a guitar amplifier multiplies the volume of sound.
epigenetic
Epigenetics is the study, in the field of genetics, of cellular and physiological phenotypic trait variations that are caused by external or environmental factors that switch genes on and off and affect how cells read genes instead of being caused by changes in the DNA sequence.
Functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These epigenetic changes may last through cell divisions for the duration of the cell’s life, and may also last for multiple generations even though they do not involve changes in the underlying DNA sequence of the organism; instead, non-genetic factors cause the organism’s genes to behave (or “express themselves”) differently.
One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. In other words, as a single fertilized egg cell – the zygote – continues to divide, the resulting daughter cells change into all the different cell types in an organism, including neurons, muscle cells, epithelium, endothelium of blood vessels, etc., by activating some genes while inhibiting the expression of others
extranuclear
outside of the nucleus, ex. mitochondrial DNA is not nuclear DNA
forward genetics
The starting point of forward genetics is to treat cells of the normal wild-type form of the organism with some agent such as X rays or certain chemicals that causes mutations. Then descendants of these cells (usually organisms growing from them) are screened for abnormal manifestation of the function in question. For example, if we are interested in the biological function “color” and the wild type is purple, then we might look for mutations producing any other color (blue, red, pink, and so on) or even the absence of color (white). The first question asked is, Are these properties inherited as a single mutated gene? That question can be answered by crossing each presumptive mutant organism to a wild-type organism, then inspecting the ratios of wild-type to mutant progeny in the subsequent generations of descendants. The ratios indicating single-gene inheritance were originally established by the “father of genetics,” Gregor Mendel, in the 1860s. A gene discovered in this way can be mapped or isolated, often leading to its DNA sequence.
The next step is to determine the function of each gene that has been identified. Returning to our example, we would ask, How does that gene act to influence flower color? The biochemical properties of each mutant obtained are studied at the molecular level and the defective protein encoded by that gene deduced, an important step in piecing together the overall system of reactions responsible for color. Hence, overall forward genetics can be represented by the sequence
Mutation -> gene discovery -> DNA sequence and function
The relatively new field of genomics has facilitated this approach: once a gene for a specific property has been mapped in the genomic sequence, then that gene’s sequence is known, and if that gene has been studied in experimental organisms, then because of evolutionary homology, it is very likely that a function is already known for it. For example, human genes for proteins that promote transcription have been identified by their homology with the genes of fruit flies and yeast. Many heritable disorders have complex inheritance (heart disease, diabetes, and cleft palate are some examples) involving several genes; genomic analysis has begun identifying these genes too.
functional RNA
A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA (npcRNA), non-messenger RNA (nmRNA) and functional RNA (fRNA). The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene.
Non-coding RNA genes include highly abundant and functionally important RNAs such as transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as RNAs such as snoRNAs, microRNAs, siRNAs, snRNAs, exRNAs, piRNAs and scaRNAs and the long ncRNAs that include examples such as Xist and HOTAIR. The number of ncRNAs encoded within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest the existence of thousands of ncRNAs. Since many of the newly identified ncRNAs have not been validated for their function, it is possible that many are non-functional. It is also likely that many ncRNAs are non functional (sometimes referred to as Junk RNA), and are the product of spurious transcription.
(shown: The cloverleaf structure of Yeast tRNAPhe (inset) and its 3D structure determined by X-ray analysis.)
gene
A gene is a locus (or region) of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity. The transmission of genes to an organism’s offspring is the basis of the inheritance of phenotypic traits. Most biological traits are under the influence of polygenes (many different genes) as well as the gene–environment interactions. Some genetic traits are instantly visible, such as eye colour or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that comprise life.
Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypetraits. Colloquial usage of the term “having a gene” (e.g., “good genes,” “hair colour gene”) typically refers to having a different allele of the gene. Genes evolve due to natural selection or survival of the fittest of the alleles.
gene pair
Because homologous chromosomes are virtually identical, they carry the same genes in the same relative positions. Thus, in diploids, each gene is present as a gene pair. However, notice in Figure 1-6 (shown) that, although the nucleus in a body (somatic) cell contains pairs of chromosomes, they are not physically paired in the sense of being next to each other. The chromosomes of the ruptured nucleus shown in the lower part of the image reveal no pairing. Notice also that the upper part of the image shows an intact nucleus from another cell, and here again, the chromosomes are clearly not in a paired state; for example, the members of the violet pair are at opposite ends of the nucleus. However, the physical pairing of homologs does take place in the nuclear division known as meiosis.
genetic code
The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact some variant codes have evolved. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code.
genetics
Broadly, genetics is the study of all aspects of genes. In turn, genes are defined as the fundamental units of biological information.
Today, the term genetics embraces both molecular genetics and genomics.
genome
complete sets of genes within a cell
genomics
The study of complete gene sets (called genomes)
guanine
Guanine (G, Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. Being unsaturated, the bicyclic molecule is planar. The guanine nucleoside is called guanosine.
haploid
The nucleus of a eukaryotic cell is haploid if it has a single set of chromosomes, each one not being part of a pair. By extension a cell may be called haploid if its nucleus is haploid, and an organism may be called haploid if its body cells (somatic cells) are haploid. The number of chromosomes in a single set is called the haploid number, given the symbol n.
Gametes (sperm and ova) are haploid cells. The haploid gametes produced by most organisms combine to form a zygote with n pairs of chromosomes, i.e. 2n chromosomes in total. The chromosomes in each pair, one of which comes from the sperm and one from the egg, are said to be homologous. Cells and organisms with pairs of homologous chromosomes are called diploid. For example, most animals are diploid and produce haploid gametes. During meiosis, sex cell precursors have their number of chromosomes halved by randomly “choosing” one member of each pair of chromosomes, resulting in haploid gametes. Because homologous chromosomes usually differ genetically, gametes usually differ genetically from one another.
haploid number
The number of chromosomes in
the basic genomic set is called the haploid number
(designated n).
Human beings are diploid, having
two copies of 23 distinct chromosomes, so in our
case n = 23 and 2n = 46. Many eukaryotes such as
fungi are haploid; that is, their nuclei contain just
one chromosome set. For example, the bread mold
Neurospora is haploid, and n = 7. In a diploid, the
two members of a chromosome pair are called
homologous chromosomes or sometimes just homologs. The DNA sequences of the members of a homologous pair are virtually the same, even though minor variation in the nucleotide sequence is often present.
histone
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human cell has about 1.8 meters of DNA, (~6 ft) but wound on the histones it has about 90 micrometers (0.09 mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.
thymine
Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidinenucleobase. In RNA, thymine is replaced by the nucleobase uracil.
purine
Purines and pyrimidines make up the two groups of nitrogenous bases, including the two groups of nucleotide bases. Two of the four deoxyribonucleotides and two of the four ribonucleotides, the respective building-blocks of deoxyribonucleic acid - DNA, and ribonucleic acid - RNA, are purines.
pyrimidine
Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U).
uracil
Uracil (U) is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine. Uracil is a demethylated form of thymine. A pyrimidine.
