Genetics Flashcards
Nucleotide: monomer
A sugar (deoxyribose) with a phosphate group attached to it and a base
Deoxyribose bases
Adenine (A), Guanine (G), Cytosine (C), or Thymine (T)
Protein: polypeptide
Long chain of 20 types of amino acids, each linked by a covalent peptide bond
Protein: pH 7
Both the amino and carboxyl groups are ionized
optical isomers
Proteins consist of exclusively L amino acids
Lysine side chain
Basic NH3+ amide group
Arginine side chain
Basic NH2+ resonance
Histidine side chain
Basic NH+ weak pentagon
Deoxyribose sugar
H at the 2’ carbon position
Ribose sugar
OH at the 2’ carbon position
Purine bases
Adenine and Guanine with double rings
Pyrimidine bases
Thymine, Cytosine and Uracil with single rings
Nucleoside
A base attached to only a sugar: adenine+ribose–>adenosine
Adenosine triphosphate
ATP nucleotide containing adenine, ribose, and three phosphate groups
Guanosine triphosphate
GTP nucleotide containing guanine, ribose, and three phosphate groups
deoxyadenosine triphosphate
dATP nucelotide containing adenine, deoxyribose, and three phosphate groups
phosphodiester bond
two covalent phosphoester bonds with phosphate attached to 5’ carbon of one sugar and 3’carbon of another sugar
Chargaff’s rule
Equal amounts of A&T, G&C. A+G=T+C
DNA directionality
Phosphate group adds on to 3’ hydroxyl end
Complete helix turn
One helix turn is 3.4 nm and contains 10 nucleotides
Bases: hydrogen bonds
G and C -> 3 bonds. A and T -> 2 bonds
A DNA
Right handed helix and tilted on axis
B DNA
Predominant DNA in living cells, right handed helix
Z DNA
Left handed helix, may affect transcription and level of chromosome compaction
RNA helix
RNA can be single stranded or be double stranded at some points
Structural gene
Nucleotide sequences that encode proteins
Intergenic regions
nontranscribed regions of DNA located between adjacent genes
Bacteria chromosome
Mos bacteria contain circular chromosomal DNA and one chromosome with few million bp
Bacteria genes and origin
several thousand different genes and one origin of replication
Bacteria DNA compaction
DNA must be compacted about 1,000 fold
DNA gyrase
In bacteria travels in front of DNA helicase and relaxes positive supercoils
Topoisomerase I
In bacteria relaxes negative supercoils
Quinoline + coumarin
Drugs that inhibit gyrase and bacterial topoisomerases but not eukaryotic topoisomerase
Chromatin
DNA-protein complex found within eukaryotic chromosomes
Centromere
Recognition site for kinetochore proteins during mitosis and meiosis
Eukaryotic origin of replication
each chromosome contains OR every 100,00 bp
Eukaryotic Chromosome bp
Tens of millions to hundreds of millions bp
Telomeres
inhibit chromosomal rearrangements such as translocations
Nucleosome
double stranded segment of DNA wrapped around octamer of histone proteins
DNA:nucleosome
150 bp around histones + 20-100 bp linker region
Interphase compaction
Nucleosomes+zigzag 30 nm fiber+radial loops
Radial loops
Chromosome sequences matrix attachment regions attaching to nuclear matrix
Euchromatin
capable of gene transcription and forms radial loop domains during interphase
heterochromatin
compacted regions at centromere and telomere
Facultative heterochromatin
chromatin that can occasionally interconvert between heterochromatin and euchromatin
histone code hypothesis
Patterns involving phosphorylation of serine at first position in H2A and acetylation of 5th and 8th lysine in H4 may attract chromatin loosening proteins
Condensin
Enters nucleus at M phase and converts euchromatin in chromatids to heterochromatin
cohesin
promotes binding between sister chromatids after s phase through prophase along entire length
Separase
cohesins at centromere remain attached until anaphase
Semiconservative model
14N and 15N radioiosyptes showed DNA replication
bacteria ori
DnaA binds to ori and recriuts DNA helicase
DNA helicase
when this enzyme encounters double stranded regions it breaks the hydrogen bonds between the strands to generate single strands
Single strand binding proteins
binds to single DNA strands and prevents double helix
DNA primase
synthesizes short strands of RNA called RNA primers
DNA polymerase III
synthesizes DNA in leading and lagging strand
DNA polymerase I
removes RNA primers and fills in with DNA
okazaki fragment
1,000-2,000 fragments in length
bacterial primosome
DNA helicase+primase
bacterial replisome
2 DNA polymerase holoenzymes+primosome
DNA polymerase III fidelity
1 mistake in 100 million nucleotides
oriC regulation
DnaA protein amount and GATC methylation sites in oirigin
Eukaryotic origins
replication proceeds bidirectionally from many origins during S phase
ARS elements
50 bp and necessary to initiate chromosome replication
DNA polymerase y(gamma)
replication of mitochondria DNA
DNA polymerase a(alpha)
associates with primase to synthesize RNA primers followed by 20 DNA bp
DNA polymerase delta
possible greater role in lagging strand synthesis
DNA polymerase e(epsilon)
possible greater role in leading strand synthesis
telomerase
synthesizes additional repeats of telomeric sequences
homologous chromosomes
homologs - the maternal and paternal chromosomes of a pair
human karyotype
cytogeneticists use the 46 human chromosomes displayed at mitosis to view abnormalities
human genes
approximately 25,000
Avg gene size
27,000 nucleotide pairs or 9,000 amino acids
Avg # exons/gene
10
nuclease
breaks down DNA by cutting between the nucleosomes
histone octamer
two molecules each of H2A, H2B, H3, and H4
Histone
high salt dissociates the ionic (salt) linkages between DNA and histones
histone deacetylase complex
HDAC-removes acetyl groups (COCH3) from lysine and removing gene expression proteins
histone acetyl transferase
HAT-commonly adds acetyl group to lysine on histones and recruits proteins that turn on gene expression. Also adds acetyl to transcription factors
histone methyl transferase
adds methyl groups
acetylation vs methylation
A methylated lysine cannot be acetylated and vice versa
histone covalent modifications
acetylation+methylation of lysines, phosphorylation of serine+threonine, methylation of arginine, ubiquityl+sumoyl+biotin of lysine
Histone synthesis
synthesized during S phase
histone variants
synthesized during interphase binding to specific chromatin sites
histone code potential
signals that stretch of chromatin is newly replicated, chromatin damaged or needs repair
reader-writer complex
A gene regulatory protein will recruit a histone modifying enzyme, which attracts a code reader protein causing a repetitive effect
barrier sequence
cluster of proteins such as histone acetylase enzymes blocks chromatin condensing
lampbrush chromosomes
extended meiotically paired chromosomes in amphibian oocytes allows viewing of interphase chromosomes
polytene chromosome
all homologous chromosomes are side by side and allow viewing of dark heterochromatin DNA bands; first seen drosophila
Chromosome puff
duirng transcription, the DNA puffs out on a polytene chromosome
Heterochromatin types
different types of heterochromatin allow different levels of compaction
nucleus subcompartments
cajal bodies, nucleolus, and repair factories create specialized environments in nucleus
homologous gene
genes similar in nucleotide sequence and function because of common ancestry
pseudogene
one copy of a duplicated gene can be seen to have become irreversibly inactivated by multiple mutations
Globin gene duplications
The globin gene family has duplicated and diverged over eveolution from a single globin to variety of globins during development
point mutation
change in a single base pair within the DNA
base substitution
one base is substituted for another base
transition mutation
base substitution where a pyrimidine is substituted for a pyrimidine or purine for a purine
transversion mutation
base substitution where a pyrimidine is substituted for a purine
silent mutation
base mutation that does not alter the amino acid sequence even though the nucleotide has changed
missense mutation
base substitution where amino acid sequence changes from one amino acid to another with one nucleotide change
nonsense mutation
change from a normal codon to a stop codon
operon polarity
nonsense mutation occurs in a bacterial operon it might inhibit downstream gene expression
frameshift mutation
addition or deletion of a number of nucleotides not divisible by 3
neutral mutation
silent mutation and when a missense mutation has not detectable effect on protein
wild type genotype
relatively prevalent genotype and if multiple alleles could have mutliple wild type alleles
mutant allele
a rare mutation that changes the wild type genotype by altering DNA gene sequence
conditional mutants
affect the phenotype under a defined set of conditions such as temperature sensitivity
suppressor mutations
a second mutation that affect the phenotype expression of the first mutation by affecting protein
intragenic suppressor
when the second mutation is within the same gene (such as LacY) as the first mutation
intergenic suppressor
suppressor mutation the is in a different gene from first mutation
promoter mutations
up promoter or down promoter mutations affect transcription
splice mutation
mutations in eukaryotic genes can alter splice junctions and affect the order and/or number of exons that are contained within mRNA
trinucleotide repeat expansion
repeated sequence of 3 nucleotides can readily increase in number from one generation to the next
position effect mutation
Genes may be moved next to regulatory sequences such as promoters or heterochromatin regions
genetic mosaic mutation
somatic regions that are genotypically different from each other
spontaneous mutation
changes in DNA structure that result from abnormalities in biological processes
induced mutation
abnormalities caused by environmental agents
spontaneous mutation cause
molecular change in DNA caused by depurination, deamination, tautomeric shift
depurination
removal of a purine (adenine, guanine) from DNA which breaks covalent bond between deoxyribose and purine causing apurinic site
deamination
removal of an amino group from cytosine which produces uracil or changes 5-methylcytosine to thymine
T+G tautomers
common form is keto form and rare is enol form
A+C tautomers
common form is amino form and rare is imino form
tautomeric shift
if the base tautomers shift right before DNA replication a mutation can occur
deamination mutagen
nitrous acid replaces amino groups with keto groups in bases
hypoxanthine
deamination of adenine. hypoxanthine pairs with cytosine
5-bromouracil
base analogue that has tautomeric shifts commonly
UV mutagen
thymine dimers between bases in DNA
photolyase
in plants and yeast thymine dimers are split
alkyltransferase
protein removes methyl or ethyl groups from guanine bases mutated by alkylating agents
base excision repair
enzyme DNA glycosylase that recognizes abnormal bases and cleaves the bond to sugar
nucleotide excision repair
direct repair of nucleotides
homologous recombination repair
repairs double stranded breaks by exchanging DNA between broken and unbroken sister chromatids during S and G2 phase
nonhomologous end joining
repairs double stranded breaks by filling DNA gaps and ligates them together
bacteria origin of replication
bacterial chromosomes have a single origin of replication and proceeds bidirectionally
