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Exam 1 Material
Chapters 1,10,11,12, 13, 14
118
Biology
Undergraduate 3
08/28/2014

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Term
Deoxyribonucleotide
Definition
basic building block of DNA, consisting of deoxyribose, a phosphate, and a nitrogenous base
Term
Deoxyribose
Definition
five-carbon sugar in DNA; lacks a hydroxyl group on the 2'-carbon atom
Term
Ribonucleotide
Definition
nucleotide containing ribose; present in RNA
Term
Ribose
Definition
five-carbon sugar in RNA
Term
Transforming Principle
Definition
substance responsible for transformation
- DNA
Term
Chargraff's Rules
Definition
rules developed by Erwin Chargraff and his colleagues concerning the ratios of bases in DNA
Term
Nucleotide
Definition
repeating unit of DNA or RNA made up of a sugar, a phosphate, and a base
Term
Inheritance of Acquired Characteristics
Definition
early notion of inheritance proposing that acquired traits are passed to descendants
Term
Pangenesis vs. Germ-plasm Theory
Definition
Pangenesis - proposes that particles carry genetic info
from different parts of the body to the reproductive
organs

Germ-plasm Theory - states that cells in the reproductive
organs carry a complete set of genetic info
Term
Evolution
Definition
genetic change taking place in a group of organisms
Term
Population Genetics
Definition
study of the genetic composition of population (groups of members of the same species) and how a population's collective group of genes changes with the passage of time
Term
Molecular Genetics
Definition
study of the chemical nature of genetic information and how it is encoded, replicated, and expressed
Term
Transmission Genetics
Definition
field of genetics that encompasses the basic principles of genetics and how traits are inherited
Term
Genome
Definition
complete set of genetic instructions for an organism
Term
Phenotype
Definition
appearance or manifestation of a characteristic
Term
Genotype
Definition
the set of genes possessed by an individual organism
Term
Allele (and relationship to gene)
Definition
1 or 2 or more alternate forms of a gene

Ex: coat color gene --> orange allele
Term
Purine
Definition
type of nitrogenous base in DNA and RNA
- adenine and guanine
Term
Pyrimidine
Definition
type of nitrogenous base in DNA and RNA
- cytosine, thymine, and uracil
Term
Nucleoside
Definition
ribose or deoxyribose bonded to a base
Term
Phosphate
Definition
a phosphorous atom attached to four oxygen atoms; one of the three components of a nucleotide
Term
Phosphodiester Linkage
Definition
phosphodiester bond connecting two nucleotides in a polynucleotide strand
Term
5' end
Definition
end of the polynucleotide chain where a phosphate is attached to the 5'-carbon atom of the nucleotide
Term
3' end
Definition
end of a polynucleotide chain where an OH group is attached to the 3'-carbon atom of the nucleotide
Term
Antiparallel
Definition
refers to a characteristic of the DNA double helix in which the two polynucleotide strands run in opposite directions
Term
Complementary DNA strands
Definition
the relation between the two nucleotide strands of DNA in which each purine on one strand pairs with a specific pyrimidine on the opposite strand
- A pairs with T; C pairs G
Term
Transcription
Definition
process by which RNA is synthesized from a DNA template
Term
Translation
Definition
process by which a protein is assembled from information contained in messenger RNA
Term
Replication
Definition
process by which DNA is synthesized from a single-stranded template
Term
Central Dogma
Definition
concept that genetic information passes from DNA to RNA to protein in a one-way information pathway
Term
DNA methylation
Definition
modification of DNA by the addition of methyl groups to certain positions on the bases
Term
Mitochondrial DNA (mtDNA)
Definition
has some characteristics in common with eubacterial DNA and typically consists of a circular molecule that lacks histone proteins and encodes some of the rRNAs, tRNAs, and proteins found in the organelle
Term
Chloroplast DNA (cpDNA)
Definition
has many characteristics in common with eubacterial DNA and typically consists of a circular molecule that lacks histone proteins and encodes some the rRNAs, tRNAs, and proteins found in the organelles
Term
Negative Supercoiling
Definition
coiled tertiary structure that forms when strain is placed on a DNA helix by underwinding of the helix
Term
Positive Supercoiling
Definition
coiled tertiary structure that forms when strain is placed on a DNA helix by overwinding of the helix
Term
Topoisomerase
Definition
enzyme that adds or removes rotations in a DNA helix by temporarily breaking nucleotide strands; controls the degree of DNA supercoiling
Term
Euchromatin
Definition
chromatin that undergoes condensation and decondensation in the course of the cell cycle
Term
Heterochromatin
Definition
chromatin that remains in a highly condensed state throughout the cell cycle; found at the centromeres and telomeres of most chromosomes
Term
Nucleosome
Definition
Basic repeating unit of chromatin, consisting of a core of eight histone proteins (two each of H2A, H2B, H3, and H4) and about 146 bp of DNA that wraps around the core about two times
Term
Polytene chromosome
Definition
giant chromosome in the sailvary glands of Drosophila melanogaster. Each polytene chromosome consists of a number of DNA molecules lying side by side
Term
Chromosomal Puff
Definition
localized swelling of a polytene chromosome; a region of chramtin in which DNA has unwound and is undergoing transcription
Term
Epigenetic Change
Definition
stable ateration of chromatin structure that may be passed on to other cells or to an individual organism
Term
Centromere
Definition
constricted region on a chromosome that stains less strongly than the rest of the chromosome; region where spindle microtubules attach to a chromosome
Term
Telomere
Definition
stable end of a chromosome
Term
Telomeric Sequence
Definition
sequence found at the ends of a chromosome; consists of may copies of short, simple sequences repeated one after the other
Term
C-value
Definition
haploid amount of DNA found in a cell of an organism
Term
C-value Paradox
Definition
the absence of a relationship between genome size and complexity in eukaryotic organisms and the question of what is the function of extra DNA in species with large genome sizes
Term
Denaturation (melting)
Definition
process that separates the strands or double-stranded DNA when DNA is heated
Term
Renaturation/Hybridization/Reannealing
Definition
the process by which two complementary single-stranded DNA molecules pair
Term
Melting Temperature
Definition
midpoint of the melting range of DNA
Term
Unique Sequence DNA
Definition
sequence present only once or a few time in a genome
Term
Moderately Repetitive DNA
Definition
DNA consisting of sequences that are from 150-300 b in length and are repeated thousands of times
Term
Highly Repetitive DNA
Definition
DNA that consists of of short sequences that are present in hundreds of thousands to millions of copies clustered in certain regions of chromosomes
Term
Tandem Repeat DNA
Definition
DNA sequences repeated one after another; tend to be clustered at specific locations on a chromosome
Term
Interspersed Repeat DNA
Definition
repeated sequence at multiple locations throughout the genome
Term
Endosymbiotic Theory
Definition
states that some membrane-bounded organelles, such as mitochondria and chloroplasts, in eukaryotic cells originiated as free-living eubacterial cells that entered into and endosymbiotic relation with a eukaryotic host cell and evolved into the present-day organelles; supported by a number of similarities in structure and sequence between organelle and eubacterial DNAs
Term
Heteroplasmy
Definition
presence of two or more distinct variants of DNA within the cytoplasm of a single cell
Term
Homoplasmy
Definition
presence on only one version of DNA within the cytoplasm of a single cell
Term
D-Loop
Definition
region of mitochondrial DNA that contains an origin of replication and promoters; it is displaced during the initiation of replication, leading to the name displacement, or D, loop
Term
Mitochondrial DNA (mtDNA)
Definition
has some characteristics in common with eubacterial DNA and typically consists of a circular molecule that lacks histone proteins and encodes some of the rRNAs, tRNAs, and proteins found in the organelle
Term
Semi-Conservative Replication
Definition
replication in which the two nucleotide strands of DNA separate, each serving as a template for the synthesis of a new strand; all DNA replication is of this nature
Term
Origin of Replication
Definition
site where DNA synthesis is initiated
Term
Replication Fork
Definition
point at which a double-stranded DNA molecule separates into two single strands that serve as templates for replication
Term
DNA Polymerase
Definition
Enzyme that synthesizes DNA
Term
Continuous Replication
Definition
replication of the leading strand in the same direction as that of unwinding, allowing new nucleotides to be added continuously to the 3' end of the new strand as the template is exposed
Term
Discontinuous Replication
Definition
replication of the lagging strand in the direction opposite that of unwinding, which means that DNA must be synthesized in short stretches (Okazaki fragments)
Term
Leading Strand
Definition
DNA strand that is replicated continuously
Term
Lagging Strand
Definition
DNA strand that is replicated discontinuously
Term
Okazaki Fragments
Definition
short stretch of newly synthesized DNA; produced by discontinuous replication on the lagging strand, these fragments are eventually joined together
Term
DNA Helicase
Definition
enzyme that unwinds double-stranded DNA by breaking hydrogen bonds
Term
DNA Gyrase
Definition
E.coli topoisomerase enzyme that relieves the torsional strain that builds up ahead of the replication fork
Term
Primase
Definition
enzyme that synthesizes a short stretch of RNA on a DNA template; functions in replication to provide a 3'-OH group for the attachment of a DNA nucleotide
Term
RNA Primer
Definition
short stretches (about 10-12 nucleotides long) of RNA nucleotidesq2
Term
DNA Polymerase I
Definition
bacterial DNA polymerase that removes and replaces RNA primers with DNA nucleotides
Term
DNA Polymerase III
Definition
bacterial DNA polymerase that synthesizes new nucleotide strands by using the 3'-OH group provided by the primer
Term
DNA Ligase
Definition
enzyme that catalyzes the formation of a phosphodiester bond between adjacent 3'-OH and 5'-phosphate groups in a DNA molecule
Term
Proofreading
Definition
ability of DNA polymerase to remove and replace incorrectly paired nucleotides in the course of replication
Term
Mismatch Repair
Definition
process that corrects mismatched nucleotides in DNA after replication has been completed; enzymes excise incorrectly paired nucleotides from the newly synthesized strand and use the original nucleotide strand as a template when replacing them
Term
G Overhang
Definition
a guanine-rich sequence of nucleotides that protrudes beyond the complementary C-rich strand at the end of a chromosome
Term
Telomerase
Definition
enzyme that is made up of both protein and RNA and replicates the ends (telomeres) of eukaryotic chromosomes; the RNA part of the enzyme has a template that is complementary to repeated sequences in the telomere and pairs with them, providing a template for the synthesis of additional copies of the repeats
Term
DNA Repair
Definition
1. Proofreading
2. Nucleotide Selection
3. Mismatch Repair
Term
Heteroduplex DNA
Definition
DNA consisting of two strands, each of which is from a different chromosome
Term
Ribozyme
Definition
RNA molecule that can act as a biological catalyst
Term
Ribosomal RNA (rRNA)
Definition
RNA molecule that is structural component of the ribosome
Term
Messenger RNA (mRNA)
Definition
RNA molecule that carries genetic information for the amino acid sequence of a protein
Term
Pre-messenger RNA (pre-mRNA)
Definition
Eukaryotic RNA molecule tha is modified after transcription to become mRNA
Term
Transfer RNA (tRNA)
Definition
RNA molecule that carries an amino acid to the ribosome and transfers it to a growing polypeptide chain in translation
Term
Template Strand
Definition
the strand of DNA that is used as a template during transcription; the RNA synthesized during transcription is complementary and antiparallel to the template strnd
Term
Non-template Strand
Definition
the DNA strand that is complementary to the template strand; not ordinarily used as a template during transcription
Term
Transcription Unit
Definition
protein that binds to DNA sequences in eukaryotic cells and affects transcription
Term
Promoter
Definition
DNA sequence to which the transcription apparatus binds so as to initiate transcription; indicates the direction of transcription, which of the two DNA strands is to be read as the template, and the starting point of transcription
Term
RNA-coding Region
Definition
Sequence of DNA nucleotides that encodes an RNA molecule
Term
Terminator
Definition
sequence of DNA nucleotides that causes the termination of transcription
Term
Ribonucleoside Triphosphate (rNTP)
Definition
substrate of RNA synthesis; consists of ribose, a nitrogenous base, and three phosphates linked to the 5'-carbon atom of the ribose; in transcription, two of the phosphates are cleaved, producing an RNA nucleotide
Term
RNA Polymerase
Definition
enzyme that synthesizes RNA from a DNA template during transcription
Term
Consensus Sequence
Definition
compromises the most commonly encountered nucleotides found at a specific location in DNA or RNA
Term
-10 Consensus Sequence
Definition
consensus sequence (TATAAT) found in most bacterial promoters approximately 10 bp upstream of the transcription start site
Term
-35 Consensus Sequence
Definition
consensus sequence (TTGACA) found in many bacterial promoters approximately 35 bp upstream of the transcription start site
Term
Rho Factor
Definition
subunit of bacterial RNA polymerase that facilitates the termination of transcription of some genes
Term
Rho-dependent Terminators
Definition
sequence in bacterial DNA that requires the presence of the rho subunit of RNA polymerase to terminate transcription
Term
Rho-independent Terminators
Definition
sequence in bacterial DNA that does not require the presence of the rho subunit of RNA polymerase to terminate transcription
Term
Polycistronic mRNA
Definition
single bacterial RNA molecule that encodes more than one polypeptide chain; uncommon in eukaryotes
Term
Transcriptional Activator
Definition
protein in eukaryotic cells that binds to consensus sequences in regulatory promoters or enhancers and affects transcription initiation by stimulating the assembly of the basal transcription aparatus
Term
Core Promoter
Definition
located immediately upstream of the eukaryotic promoter, DNA sequences to which the basal transcription apparatus binds
Term
TATA box
Definition
consenssus sequence (TATAAAA) commonly found in eukaryotic RNA polymerase II promoters; usually located from 25 to 30 bp upstream of the transcription start site; the TATA box determines the start point for transcription
Term
TATA-box Binding Protein
Definition
polypeptide chain found in several different transcription factors that recognizes and binds to sequences in eukaryotic promoters
Term
Enhancer
Definition
sequence that stimulates maximal transcription of distant genes; affects only genes on the same DNA molecule (is cis acting), contains short consensus sequences, is not fixed in relation to the transcription start site, can stimulate almost any promoter in its vicinity, and may be upstream or downstream of the gene; the function of an enhancer is independent of sequence orientation
Term
Colinearity
Definition
concept that there is a direct correspondence between the nucleotide sequence of a gene and the continuous sequence of amino acids in a protein
Term
Exon
Definition
coding region of a split gene (a gene that is interrupted by introns); after processing, the exons remain in messenger RNA
Term
Intron
Definition
intervening sequence in a split gene; removed from the RNA after transcription
Term
Nuclear Pre-mRNA Intron
Definition
belongs to a class of introns in protein-encoding genes that reside in the nuclei of eukaryotic cells; removed by spliceosomal-mediated splicing
Term
Shine-Delgarno Sequence
Definition
consensus sequence found in the bacterial 5' untranslated region of mRNA; contains the ribosome-binding site
Term
Protein-coding Region
Definition
the part of mRNA consisting of the nucleotides that specify the amino acid sequence of a protein
Term
5' Cap
Definition
modified 5' end of eukaryotic mRNA, consisting of an extra nucleotide (methylated) and methylation of the 2' position of the ribose sugar in one or more subsequent nucleotides; plays a role in the biding of the ribosome to mRNA and affects mRNA stability and the removal of introns
Term
Poly(A) Tail
Definition
string of adenine nucleotides added to the 3' end of a eukaryotic mRNA after transcription
Term
Spliceosome
Definition
large complex consisting of several RNAs and many proteins that splices protein-encoding pre-mRNA; contains five small ribonucleoprotein particles (U1, U2, U4, U5, and U6)
Term
Lariat
Definition
looplike structure created in the splicing of nuclear pre-mRNA in which the 5' end of an intron is attached to a branch point in pre-mRNA
Term
Alternative Splicing
Definition
process by which a single pre-mRNA can be spliced in more than one way to produce different types of mRNA
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