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169 Cards in this Set

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  • Back
What is a Genome?
The full DNA sequence for an organism.
What is a Gene?
The entire DNA sequence needed to encode a protein.
What is a Chromosome?
A single DNA strand with associated proteins.
What are Prokaryotes?
No nucleus, usually only one chromosome.
What are Eukaryotes?
1. Have a nucleus bounded by a nuclear membrane.
2. Contain 1 or more chromosomes
3. Chromosome # specific to each species.
How many chromosomes can an organism have?
Organisms may be haploid (one set of chromosomes) or diploid (2 sets) or polyploid (more than 2 sets).
Are Vertebrates diploid, haploid, or polypoid.
Vertebrates are diploid which focuses scientific interest on diploid organisms.
Where did the chromosomes come from on a diploid organism?
Each set in a diploid organism came from one parent.
What are "non-sex" related chromosomes referred to as?
Autosomes
Autosomes are present in how many pairs?
They are present in homologous pairs.
What is the female sex chromosome called?
X chromosome
The male sex chromosome is called?
XY chromosome
Genes on homologous pairs are normally present in how many copies?
Two copies (also called alleles), one at the same location (locus) on each chromosome.
What do genes produce?
Proteins
What do proteins determine?
Proteins determine how cells function.
What does cell function determine?
Cell function determines appearance or function of an organism (trait).
What is the Central Dogma?
Translation, Transcription, Protein Synthesis
DNA directs the synthesis of?
RNA (transcription)
RNA directs the synthesis of?
Protein (translation) by ribosomes.
DNA base sequences encode?
The base sequences for RNA.
RNA base sequences encode?
The amino acid sequence of the protein.
DNA coding sequences are called?
Genes
What does gene expression refer to?
The production of the protein (or RNA) coded for by that gene.
What do detectable traits represent?
They represent the phenotype of an organsim.
The actual genes carried at a locus are?
The organisms genotype.
How does genetic variation occur?
Mutations, Recombination, Selection
How can mutations change genes?
By deletion, insertion, and point change.
Are mutations harmful or beneficial?
Most mutations can be damaging or lethal, but some may improve function (i.e. improve binding by a signal to a receptor).
What is the most common source of variation in complex eukaryotes?
Recombination by chromosome exchanging regions.
Viruses are often the source for a special type of recombination:
Transposition
Water makes up how much of the cell?
~ 70%
Ions and small organic molecules make up how much of the cell?
~ 10%
What is the core element of the organics?
Carbon
Polar groups are hydrophobic, hydrophilic, or both?
Hydrophilic
Non-polar groups are hydrophobic or hydrophilic?
Hydrophobic
What are the chemical components of the cell?
Water, ions, small organic molecues, and macromolecules.
Give examples of macromolecules assembled from small organic molecules (subunits).
Nucleic acids, proteins, polysaccharides, and lipids.
How are nucleic acids assembled?
Nucleic acids are assembled from nucleotides.
Macromolecules are usually characterized by a:
A repetitious specific covalent bond between the small molecular components
What type of bonds are in nucleic acids?
Phosphodiester bonds
Macromolecules are often stabilized by:
Non-covalent (weak) bonds formed between parts of the macromolecule.
What type of bonds bind DNA strands?
Hydrogen bonds
How do covalent bonds form?
Covalent bonds form as a result of electrons being shared between atoms.
What type of bonds allow for free rotation?
Carbon-carbon (or O, N) single bonds
What type of bonds are rigid?
Double and triple bonds.
What allows for specific orientation around the carbon atom?
Single, double, and triple bonds.
How do non-covalent bonds form?
Non-covalent bonds form as a result of magnetic like attraction between charged or partially charged elements or by water exclusion.
How do Van der Waals bonds form?
Van der Waals bonds form between atoms in close proximity as a result of transient dipoles forming.
How do Hydrogen bonds form?
Hydrogen (H-) bonds form between an electronegative atom (O, N) and a H covalently bound to another electronegative atom.
Hydrogen has what kind of charge?
A partial positive charge.
Electronegative atoms have what kind of charge?
A partial negative charge.
How do Ionic bonds form?
Between charged (+/-) groups.
How do hydrophobic interactions form?
Hydrophobic interactions form as a result of hydrophobic regions coming close enough to exclude water.
How do hydrophobic regions come close enough to exclude water?
By becoming forced by the disruption of the water lattice when it tries to interact with non-polar groups.
What are proteins?
Polymers of amino acid subunits.
What groups do amino acids have?
An amino group, carboxylic acid group, & side chain
How many side chains are there?
There are 20 different side chains that make up 20 different amino acids.
How are amino acids joined?
They are joined together in proteins by covalent peptide bonds.
What is a sequence of amino acids called?
The Primary structure.
What type of shapes do proteins fold into?
3 Dimensional shapes.
Two proteins bound together form
a quaternary structure
A tertiary structure that is repeated in many proteins is called
a Domain
How many domains do most proteins have?
2 or more
What are Transcription Factors?
Proteins that control RNA transcription.
How many domains do Transcription Factors have?
Usually 3 Domains
Name the Transcription Factor Domains .
a DNA binding domain,
a transcription regulating domain,
a protien-protein binding domain
DNA binding domains are also called
Motifs
Motifs are grouped into
Families
Give examples of motif families.
Zn finger, helix-loop-helix
DNA and RNA binding proteins can recognize
Specific sequences or General Structural elements
Single strand binding proteins recognize
DNA backbone
Transcription Factors recognize
Specific DNA sequences
How is Inheritance maintained in a stable manner?
Because of the chemical nature of DNA and RNA.
What are Nucleic Acids?
Long chain polymers
Monomers are also called
Nucleotides
What are Monomers (nucleotides)?
Organic bases attached to 5 carbon sugars (pentoses) which are phosphorylated
How do Phosphodiester bonds join monomers into long chain polymers?
Via a phosphate-pentose backbone.
An antiparallel double helical poly-nucleotide
DNA
A single stranded polynucleotide
RNA
The Pentose Deoxyribose lacks
An OH on the 2nd Carbon
Native structure is
a Ring
Name the bases
adenine, guanine, thymine, cytosine
Name the purines
Adenine and Guanine
How many rings do purines have?
Two rings
Name the pyrimidines.
Thymine and cytosine
How many rings do pyrimidines have?
One ring
Where do bases attach to?
To Carbon 1 of deoxyribose
Where are Phosphates attached to?
The C 5 of deoxyribose in an ester linkage.
How are Nucleotides joined together?
By an Ester linkage between the phosphate on C5 of one nucleotide and the C3 OH on the next.
What is a Phosphate?
A sugar polymer with bases as side chains.
The terminal C5 (5') end has a
Phosphate
The C3 (3')end has a
Hydroxyl Group
How do Nucleic Acids grow?
By addition of Nucleotides to the 3' (three prime) end .
dNTP's adds to
DNA
NTP's adds to
RNA
How does DNA exist?
As a Double Strand
How are the DNA backbone and bases situated?
Backbone outside and Bases inside
DNA strands are situated in what way?
Anti-parallel
The 2 DNA strands are wrapped in what direction?
In a right handed helix
How many base pairs are there per turn?
10.5 base pairs per turn
Base pair occurs by what type of bonding?
Hydrogen bonding
Adenine and Thymine bond by
2 Hydrogen bonds
Guanine and Cytosine bond by
3 Hydrogen bonds
What is Chargaff's rule?
The quantity of adenine equals the quantity of thymine and the quantity of guanine equals the quantity of cytosine.
How are New Strands built?
Using Old Strands as Templates.
What forces major and minor grooves in the helix?
Base pairing that is tilted from Axis
Describe a Hydrated DNA Helix
B form and with 10 base pairs per turn
Describe a Dehydrated DNA Helix
A form, is right handed, and has 11 base pairs per turn
Describe a Z Form Helix
Left handed, 12 base pairs per turn, and zig-zag shape
How can Bends form in the cellular helix?
Via Protein binding or long A-T stretches (4+)
What contributes to bends in the cellular helix?
Propeller twists between base pairs.
How can DNA strands be separated?
By heating, melting, or denaturation.
What is Melting Temperature (Tm) dependent on?
The number of G-C pairs (due to the 3 H-bonds).
How can DNA strand renature (hybridize)?
Via slow cooling if they are complementary.
What makes RNA more labile?
The Ribose sugar
What is the sugar in RNA?
Ribose (has C2 OH)
Name the bases in RNA
Adenine, guanine, Uracil, and cytosine
What is Uracil?
A Pyrimidine in RNA
Where are RNA bases attached to?
The ribose at C1
Where are RNA Phosphates attached to?
C5
RNA structure normally exists as a
Single Strand. But may form RNA:RNA or RNA:DNA double helices.
Loops and hairpins can form becuase of
Base pairing, including some unusual pairs (G-U), U-A-U)
Loops and hairpins have functional relevance depending on the
type of RNA
Some RNA molecules function
as enzymes (ribozymes).
Ribozymes are usually attached to a protein but
the RNA is the catalyst.
Nucleic acid analysis is done by
DNA purification and DNA analysis
DNA purification is done by
isolating DNA from cell extracts using phenol extraction & ethanol precipitation or isolating DNA fragments by gel electrophoresis.
DNA analysis can be done by these methods:
By Size using gel electrophoresis .
Restriction fragment analysis.
Hybridization by complementary oligonucleotides.
Amplify by cloning or PCR
Sequence analysis.
Sequence analysis is done by
Sanger (dideoxy chain termination) method
Protein Purification is done by
1. Extracting by cell homogenization
2. Isolating proteins by size, shape, charge, etc
3. Sequencing by Edman degradation or by mass spectrometry
To isolate proteins by size, shape, charge, etc you must
1. Must have an assay to detect the protein of interest
2. Techniques involving precipitation by salt or acid, column chromatography, gel electrophoresis
3. You must not inactivate or distort the protein (problem with heat precipitation).
DNA is organized in cells as
Chromosomes
Chromosomes can be
Can be linear (as in eukaryotes) or circular (as in prokaryotes).
The amount of DNA varies with
Species
Prokaryotic chromosomes are usually
Are usually a SINGLE CIRCULAR CHROMOSOME and May carry additional genetic information in small circular plasmids
A single circular Prokaryotic Chromosome
1. Must be compressed to fit in cells
2. Circular DNA will have supercoiling in one region due to unwinding in an adjacent region
3. Binding to proteins may enable further compression into loops
Eukaryotic DNA is organized into
linear chromosomes in order to fit into cells (& nucleus)
Characteristics of Eukaryotic DNA:
1. Compact primarily due to associated proteins (histones, non-histones) & some supercoiling
2. Numbers of chromosomes (& genome size) relates to organism complexity with some anomalies
More complex organisms have a
Lower gene density
Genes are a small part of
genome-intergenic DNA increases
Examples of Non-linear genes are
Exons & Introns
Exons contain
coding information
Introns are
intervening sequences
Eukaryotic chromosomes have both stretches of
unique sequence DNA & repetitive sequence DNA
Unique sequence DNA occurs
only once (or only a few times) in a genome
Unique sequence DNA makes up about
55% of the Human Genome
Repetitive sequence DNA occurs in
many repeats
Repeats may be situated
in a scattered form (interspersed repeated DNA) or right next to each other (tandem repeat DNA)
Interspersed is from
transposons and retrotrasnposons
Simple sequence repeats (satellite) DNA account for
3% of the human genome
Tandem repeats of identical or near-identical sequences are
14-500 bp in regions 20-100 kbp long
Micro-satellites are
1-13 bases
Simple sequence repeats are usually
highly conserved in a species, but with many individual differences in number of repeats
The Human Genome Project invovled
Many government labs & commercial labs organized to determine the base sequence for the human genome
The Human Genome could only be sequenced
by automated dideoxy sequencing at >600 bp. So the genome was broken into small regions.
What were the two approaches to the Human Genome Project?
The Mapping Approach and the Whole Genome Shotgun (WGS)
The Mapping Approach required
genetic maps & physical maps to cut the genome into segments
What do Genetic Maps use to find genes?
Crosses or Pedigrees
What are Sequence tagged sites (STS)?
Unique sequences in the genome that are useful.
An example of good STS's are
Short tandem repeats
Expressed sequence tags (ESTs) are
STS determined from cDNA by RT-PCR from mRNA recovered from cultured cells
What are Physical maps?
Restriction maps using enzymes which cut rarely in the human genome (at about 8 base cutters)
Chromosomes were sheared and then cloned & mapped by STS probes in what type of mapping?
Physical Mapping
WGS fragments whole genome by shearing through
a hypodermic needle
Sequencing is often done by
PCR using fluorescently labeled dideoxy nucleotides
After shearing with a hypodermic needle, what is done with the WGS fragments?
Fragments are run on gel & ~2,000 bp fragments cloned into genome library
In the Genome Library each clone
is sequenced on both strands from each end
After each clone is sequenced from end to end, many overlaps occur resulting in
approximately 7x total genome sequenced so center regions are picked up in other fragments
Computer analysis arranges the
order of overlaps in clone sequencing