Plasma Membrane
The selective barrier composed of lipid bilayer and embedded proteins that surrounds a living cell (CH.1)
Enzyme
A protein that ca... [Show More] talyzes a specific chemical reaction (CH.1)
Transcription
Copying of one strand of DNA into a complimentary RNA sequence by the enzyme RNA polymerase (CH.1)
Translation
Process by which the sequence of nucleotides in an mRNA molecule directs the incorporation of amino acids into proteins (CH.1)
Gene
Region of DNA that controls a discrete hereditary characteristic of an organism, usually corresponding to a single protein or RNA (CH.1)
Messenger RNA (mRNA)
RNA molecule that specifies the amino acid sequence of a protein (CH.1)
Amino acid
Organic molecule containing both an amino group and a carboxyl group. Those in which the amino and carboxyl groups are linked to the same carbon atom serve as the building blocks of proteins (CH.1)
Genome
The total genetic information carried by a cell or an organism (or the DNA molecules that carry this information) (CH.1)
T or F: Genes and their encoded proteins are co-linear, that is, the order of amino acids in proteins is the same as the order of the codons in the RNA and DNA
True. Even in eucaryotes where the coding regions of a gene are often interrupted by non-coding segment, the order of codons in the DNA is still the same as the order of amino acids in the protein (CH.1)
T or F: DNA and RNA use the same four-letter alphabet
False. The nucleotide subunits of RNA and DNA differences in two key ways. First, the backbone in RNA uses the sugar ribose instead of deoxyribose, which is used in DNA. Second, RNA uses the base uracil in place of the base thymine, which is used in DNA. Three of the four bases -A,C, and G- are the same in RNA and DNA. (CH.1)
In the 1940s, Erwin Chargaff made the remarkable observation that in samples of DNA from a wide range of organisms the mole percent of G [G/(A+T+C+G)] was equal to eh mole percent of C, and the mole percents of A and T were equal. This was an essential clue to the structure of DNA. Nevertheless, Chargaff's 'rules' were not universal. For example, in DNA from the virus omegaX174, which has a single-strand genome, the mole percents are A = 24, C = 22, G = 23, and T = 31. What is the structural basis for Chargaff's rules, and how is it that DNA from omegaX174 doesn't obey the rules?
In double-stranded DNA, which forms the genomes in all cellular life, G pairs with C, and A pairs with T. It is this requirement for base-pairing that necessitates that the number of Gs will equal the number of Cs, and that the numbers of As and Ts will be the same. In bulk samples of DNA, this translates into equivalent mole percents of G and C and of A and T.
The virus omega174 does not obey the 'rules' because its genome is single-stranded DNA. In the absence of a requirement for systematic base pairing there is no constraint on the relative amounts of G and C or of A and T. (CH.1)
Which of the following correctly describe the coding relationships (template --> product) for replication, transcription, and translation?
A. DNA --> DNA
B. DNA --> RNA
C. DNA --> protein
D. RNA --> DNA
E. RNA --> RNA
F. RNA --> protein
G. Protein --> DNA
H. Protein --> RNA
I. Protein --> protein
A. During replication, parental DNA serves as a template for synthesis of new DNA.
B. During transcription, DNA serves as a template for synthesis of RNA.
F. During translation, RNA (mRNA) serves as the template for synthesis of protein.
Two other processes, D. RNA --> DNA, called reverse transcription, and E. RNA --> RNA, called RNA replication, occur in the life cycles of RNA viruses such as HIV and poliovirus. (CH.1)
Virus
A small packet of genetic material that has evolved as a parasite on the reproductive and biosynthetic machinery of host cells (CH.1)
Model organism
Organism selected for intensive study as a representative of a large group of species (CH.1)
Archaea
One of the two divisions of procaryotes, typically found in hostile environments such as hot springs or concentrated brine. (CH.1)
Homolog
A homologous chromosome or, more generally, a macromolecule that has a close evolutionary relationship to another (CH.1)
Eucaryote
Living organism composed of one or more cells with a distinct nucleus and cytoplasm (CH.1)
Procaryote
Major category of living cells distinguished by the absence of a nucleus (CH.1)
T or F: The human hemoglobin genes, which are arranged in two clusters on two chromosomes, provide a good example of an orthologous set of genes.
False. The clusters of human hemoglobin genes arose during evolution by duplication from an ancient ancestral globin gene; thus, they are examples of paralogous genes. The human hemoglobin alpha gene is orthologous to the chimpanzee hemoglobin alpha gene, as are the human and chimpanzee hemoglobin beta genes, etc. All the globin genes, including the more distantly related gene for myoglobin, are homologous to one another. (CH.1)
Thought problem: The genes for ribosomal RNA are highly conserved (relatively few sequence changes) in all organisms on Earth; thus, they have evolved very slowly over time. Were such genes 'born' perfect?
It is unlikely that any gene came into existence perfectly optimized for its
function. It is thought that highly conserved genes such as ribosomal RNA
genes were optimized by more rapid evolutionary change during the evolution
of the common ancestor to archaea, eubacteria, and eucaryotes. Since
ribosomal RNAs (and the products of most highly conserved genes) participate
in fundamental processes that were optimized early, there has been no
evolutionary pressure (and little leeway) for change. By contrast, less conserved—
more rapidly evolving—genes have been continually presented
with opportunities to fill new functional niches. Consider, for example, the
evolution of distinct globin genes that are optimized for oxygen delivery to
embryos, fetuses, and adult tissues in placental mammals. (CH. 1)
Thought problem: Several procaryotic genomes have been completely sequenced and their genes have been counted. But how do you suppose one recognizes a gene in a string of Ts, As, Cs, and Gs?
It would be impossible to identify genes in a vast stretch of Ts, As, Cs, and Gs
if genes did not have some identifying characteristics. In the absence of any
knowledge of gene structure in procaryotes, you might imagine that the sites
where gene transcription begins and ends might be special and thus recognizable.
Similarly, you might imagine that sequences where protein synthesis
begins and ends might be distinctive and thus recognizable. In reality, it
is the signals for protein synthesis that have proven most valuable for identifying
procaryotic genes.
Genes that encode proteins, which are the vast majority, start with ATG
(corresponding to the start codon AUG in the mRNA) and end with TAA,
TAG, or TGA (corresponding to the three stop codons UAA, UAG, and UGA in
mRNA). One searches for an ATG and then proceeds three nucleotides at a
time (codon-by-codon) until a stop codon is reached. This procedure
defines an open reading frame, or ORF. Nearly all ORFs greater than 100
codons correspond to genes. Some smaller ORFs also encode proteins and
are therefore genes; however, many small ORFs occur by chance and do not
correspond to genes. In some cases real genes can be identified among the
smaller ORFs by virtue of other typical signal sequences that characterize
genes in procaryotes. Nevertheless, in gene counts derived from genomic
sequences an arbitrary cut-off is used so that the smallest ORFs are not
included in the count.
Gene identification in eucaryotic genome sequences is much more problematical.
The protein-coding regions of eucaryotic genes are often split into
segments that are not finally united until the initial RNA transcript is processed
to remove the noncoding RNA. Thus, the procedure used to count
genes in procaryotes is not useful for eucaryotes. Computer algorithms to
identify eucaryotic genes are still in their infancy and are not yet reliable. (CH. 1)
Thought problem: Which one of the processes listed below is NOT thought to contribute significantly to the evolution of new genes? Why not?
A. Duplication of genes to create extra copies that can acquire new functions.
B. Formation of new genes de novo from noncoding DNA in the genome.
C. Horizontal transfer of DNA between cells of different species.
D. Mutation of existing genes to create new functions.
E. Shuffling of domains of genes by gene rearrangement.
B. It is not thought that formation of genes de novo from the vast amount of
unused, noncoding DNA typical of eucaryotic genomes is a significant process
in evolution. Mutation to generate a coding sequence complete with
regulatory elements is too slow a process to account for the observed rates
of evolutionary change. (CH. 1)
Quaternary structure
Three-dimensional relationship of the different polypeptide chains in a multisubunit protein or protein complex (CH. 3)
alpha helix
Common folding pattern in proteins in which a linear sequence of amino acids folds into a right-handed coil stabilized by internal hydrogen bonding between backbone atoms. (CH. 3)
Primary structure
The amino acid sequence of a protein. (CH. 3)
Binding site
A region on the surface of a protein that can interact with another molecule through noncovalent bonding. (CH. 3)
Tertiary structure
Complex three-dimensional form of a folded protein. (CH. 3)
Polypeptide backbone
The chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein.
beta sheet
Common structural motif in proteins in which different sections of the polypeptide chain run alongside each other and are joined together by hydrogen bonding between atoms of the polypeptide backbone. (CH. 3)
Protein domain
Portion of a protein that has a tertiary structure of its own. (CH. 3)
Secondary structure
Regular local folding patterns in a protein, including alpha helix and beta sheet. (CH. 3)
What are the four weak (noncovalent) interactions that determine the conformation of a protein?
Hydrogen bonds, electrostatic attractions, van der Waals attractions, and the hydrophobic force. (CH. 3) [Show Less]
