Chapter 8: The Molecular Basis of Inheritance Flashcards
DNA
-makes up chromosomes which have genes at specific loci
protein as the heritable factor
- proteins are a major component of all cells
- complex macromolecules with lots of variety and specificity of function
- know a lot about structure of protein
Griffith (1927)
- some strains streptococcus pneumoniae are virulent, others are harmless
- discovered transformation: bacteria have the ability to transform harmless cells into virulent ones by transferring some genetic factor
Avery, MacLeod, McCarty (1944)
-identified Griffith’s transforming factor as DNA
Hershey and Chase (1952)
- tagged bacteriophages with radioactive phosphorous and sulfur
- proteins contain sulfur, but no phosphorous
- DNA contains phosphorous and no sulfur
- phosphorous labeled DNA of phages while S labeled protein coat
- radioactive P always entered bacteria when infected, so DNA from the viral nucleus was the genetic material
Rosalind Franklin (1950-53)
-carried X-ray crystallography analysis of DNA that showed the helix structure
Watson and Crick (1953)
-proposed the double helix structure of DNA using Erwin Chargaff’s Rule (equal amounts of C and G, A and T because of 1:1 pairing) and Franklin’s research
Meselson and Stahl (1958)
- proved that replication was in a semiconservative fashion
- cultured bacteria in heavy N and then in light N, bacteria were then spun in a centrifuge and found to be in between heavy and light bacteria (one heavy and one light strand)
purines
A, G
pyrimidines
C,T
structure of DNA
- double helix with two antiparallel strands (one runs 3’ to 5’, other 5’ to 3’)
- deoxyribose, phosphate group, and nitrogenous base
- nitrogenous bases of opposite strands form hydrogen bonds (A and T form double hydrogen bond, C and G form triple hydrogen bond)
chromatin
-DNA packed with histones (protein) during replication
nucleosome
-formed when double helix DNA wraps twice around a core of histones
RNA
-single stranded helix with A,G,C,U and ribose
semiconservative model
-each strand of DNA serves as a template for the formation of new strand of DNA
origin of replication
-where replication begins by the separation of the strands of DNA, creating a replication bubble
replication bubble
- speed up replication
- expands as replication occurs in both directions at once
replication fork
-Y-shaped region where new strands of DNA are elongating
DNA polymerase
-catalyzes the antiparallel elongation of new DNA strands by adding nucleotides to the 3’ end of the chain (so the strand is built from the 5’ to 3’ direction)
RNA primer
-short nucleotide sequence that initates synthesis
primase
-enzyme that makes the primer
leading strand
-formed towards the replication fork in an unbroken, linear fashion
lagging strand
-forms away from the replication fork with Okazaki fragments
Okazaki fragments
-eventually joined by DNA ligase to make one continuous strand
helicase
-enzymes that untwist the double helix at the replication fork
-topoimerase
-lessen the tension on the tightly wound helix
single-stranded binding proteins
-hold two unwound strands appart
mismatch repiar
-proofreading that corrects errors
DNA nuclease
-excises damaged regions of DNA
telomeres
-protective nonsense nucleotide sequence ends that prevent nucleotides at the end of chromosomes from being lost every time DNA replicates (no genes lost)
telomerase
-creates and maintains telomeres
codon
triplet code of mRNA
DNA to protein
-process of transcribing information in the DNA sequence into a complementary RNA sequence in the nucleus, leading to the RNA being translated into an amino acid sequence (polypeptide) in the cytoplasm at the ribosome
pre-RNA
RNA before processing
anitcodon
3 nucleotide sequence of tRNA that is complementary to the mRNA
mRNA
holds genetic info for protein, complementary to DNA
rRNA
makes up the ribosome with other proteins
ribosome structure
- on large subunit, one small subunit
- one mRNA binding site
- 3 tRNA binding sites (A,P,E)
tRNA
- one amino acid attachment site
- one mRNA binding site, with the tRNA anticodon
transcription
DNA –> RNA
- initiation
- elongation
- termination
initiation (transcription)
- RNA polymerase recognizes and binds to DNA at the promoter region
- promoter region: tells RNA polymerase where to begin and which of the two strands to transcribe
- transcription factors recognize key area within the promoter, or the TATA box (repetitive A and T nucleotides) and mediate the binding of RNA polymerase to DNA
- transcription initiation complex: completed assembly of transcription factors bound to the promoter, which also signals the transcription of DNA
elongation (transcription)
- RNA polymerase pries two strands apart and adds nucleotides to the 3’ end
- transcription unit: stretch of DNA that is transcribed into mRNA molecule, which consists of codons (specific sequences for amino acids)
- RNA can be transcribed by many RNA polymerases at once
- proofreading because errors are more harmful as the RNA strand is short
termination (transcription)
- RNA polymerase transcribes the termination sequence (AAUAAA)
- mRNA is cut away from DNA template
RNA processing
- 5’ cap added (helps mRNA bind to the ribosome)
- poly A tail added to 3’ (protects strand from degredation by hydrolytic enzymes, facilitates release of mRNA into the cytoplasm)
- noncoding region (introns) removed by snRPs (small nuclear ribonucleproteins) and spliceosomes, leaving exons (expressed region)
alternative splicing
-different RNA molecules can be produced depending on what is treated exons and what is introns
regulatory proteins
-control intron-exon choices by binding to regulatory sequences
translation
mRNA codons are changed into amino acid sequence
- initiation
- elongation
- termination
GTP (guanosine triphosphate)
-provides energy for process of tRNA bringing amino acid to the amino acid sequence
aminoacyl-tRNA synthetase
-enzyme that helps amino acid joined with the correct tRNA
methionine
- start codon
- AUG
stop codon
-UAG, UAA, UGA
wobble
-relaxation of base pairing because pairing rules for the third base of a codon are not as strict as they are for the first two bases (one tRNA for multiple codons)
initiation (translation)
-mRNA attaches to the subunit of a ribosome
elongation (translation)
-continues as tRNA brings amino acids to the ribosome and a polypeptide chain is formed
polyribosomes
-ribosome clusters that translate mRNA
termination (translation)
- complete when mRNA reaches one of its stop codons
- release factor: breaks bond between tRNA and the last amino acid in the polypeptide chain
genetic code
-has redundancies, but doesn’t have ambiguity in proteins
gene mutation
- spontaneous and random permanent changes to genetic material
- can be caused by mutagenic agents (radiation)
- somatic: disrupt normal cell function
- gametic: mutations that can be passed to offspring and change the gene pool of a population
- raw material for natural selection
point mutation
- base-pair substitution, may be harmless
- ex: sickle cell
insertion and deletion
- loss or addition of a nucleotide in the DNA
- causes a frameshift
nonsense mutation
-any changes to a codon causing a stop codon nonsense mutation
missense mutation
-any changes to a codon that causes a different amino acid
virus
- parasite that can live only inside another cell by commanding the host cell to transcribe and translate viral proteins
- infects specific cell type bc it binds to specific receptors
- bacteriophages, retrovirus
capsid
-viral protein coat that encloses DNA and RNA
viral envelope
- derived from membrane of host cells
- surrounds the capsid
- aids in infection
host range
-range of organisms that a virus can infect
bacteriophages
- lytic cycle: phage enters the host cell , replicates itself, and causes the cell to burst and release a new generation of infectious phages
- lysogenic: phage virus DNA is incorporated into the host cell (prophage: dormant DNA in the host genome) and is replicated with the bacterial DNA
- environmental cue causes change from lysogenic to lytic
- temperate viruses: able to enter both lytic and lysogenic
retroviruses
- contain only RNA, not DNA
- after infecting the host, the retrovirus RNA serves as a template for DNA (cDNA) through reverse transcriptase
- inserts itself in the host genome, becomes a prophage, and makes several copies of viral genome
transduction
- phage virus acquires bits of bacterial DNA as they infect cells, leading to genetic recombination
- generalized: moves random pieces of bacterial DNA as phage lyses and infects another in the lytic cycle
restricted: transfer of specific pieces of DNA during the lysogenic cycle (incorporate phage DNA into the genome of the host, and when the cell ruptures, phage with host DNA inserts host DNA into the next host)
nucleoid
- bacterial chromosome that is circular, double-stranded DNA that is tightly condensed
- no nuclear membrane surrounding
bacterial replication
-in both directions from a single point of origin
binary fission
-asexual replication, spontaneous, produces identical genes
bacterial transformation
-small pieces of extracellular DNA are taken up by living bacterium, leading to a change in the DNA
plasmid
- small, circular, foreign, self-replicating DNA molecule that inhabits bacterium
- bacteria can harbor many plasmids
F plasmid
- first discovered, fertility, bacterias with called F+, don’t have: F-
- -contain genes for production of pili (cytoplasmic bridges that allow DNA to be transferred between two adjacent cells… process called conjugation)
R plasmid
- makes the cell it is carried in antibiotic resistant
- can be transferred through conjugation
operon
- discovered in E. coli by Jacob and Monod
- only found in bacteria
- mode of negative gene regulation by switching genes on/off
- inducible (lac)
- repressible (tryptophan): always on unless repressor is activated
tryptophan operon
- consists of promoter and 5 structural genes that code for 5 enzymes that help synthesize the amino acid tryptophan
- if RNA pollymerase binds to the promoter, one strand of mRNA is produced
- if enough tryptophan is present, it acts as a corepressor activating the repressor
- repressor binds to the operator, preventing RNA polymerase from binding to promoter
- tryptophan absent, repressor inactive, operon on, produces tryptophan
lac operon
- 3 enzymes that break down lactose into glucose and galactose are coded for by 3 genes in the lac operon
- to transcribe: repressor must be prevented from binding to operator and RNA polymerase must bind to promoter
- allolactose (isomer of lactose): inducer that facilitates this process by binding to the active repressor and inactivating it
- drink milk, get more allolactose
- lactose present, repressor inactive, operon on
CAP and cAMP
- attachment of CAP directly regulates gene expression
- ex. of positive gene regulation
- lactose is only energy source when glucose levels are low
- CAP: allosteric regulatory protein
negative gene regulation
- genes in the operon are expressed unless they are switched off by a repressor protein.
- operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated
- inducer-repressor control of lac operon
positive gene regulation
- transcription factor is required to bind at the promoter in order to enable RNA polymerase to initiate transcription
- the genes are expressed only when an active regulator protein is present
- operon will be turned off when the positive regulatory protein is absent or inactivated
RNA polymerase
-enzyme that transcribes new RNA chain by linking ribonucleotides to nucleotides on a DNA template
operator
- sequence of nucleotides near the start of an operon that the active repressor can match
- binding of repressor prevents RNA polymerase from binding to the promoter
promoter
- nucleotide sequence in DNA sequence that is binding site of RNA polymerase
- positions RNA polymerase to begin at the right position
repressor
-inhibits gene transcription by binding to the operator
regulator gene
- gene that codes for a repressor
- located away from operon and has its own promoter
prions
- misfolded protein (not virus!!) found in the brain
- mad-cow disease
human genome
-24,000 genes but only 2% code for proteins
tandem repeats
- back-to-back repetitive sequences
- make up telomeres
- ex: tandem repeats in genes of Huntington’s Disease
recombinant DNA
- taking DNA from 2 or more sources and combining them
- viral transduction, bacterial transformation, conjugation, transposons
transposons
-transposable element that is a small piece of DNA that inserts itself into another place in the genome
biotechnology or genetic engineering
- manipulate and engineer genes in vitro
- used for gene therapy: replace nonfucntioning gene in someone’s cells using vector (nonviral virus that carries and transduces the gene)
- produce protein product (insulin)
- prepare multiple copies of a gene
- engineer bacteria
gene cloning
- insert gene into the plasmid
- insert plasmid in vector that is competent (able to take up a plasmid)
- clone the gene through fission
tools and techniques of recombinant DNA
- resriction enzymes
- gel elctrophoresis
- DNA probe
- polymerase chain reaction (PCR)
- restriction fragment length polymorphisms
restriction enzymes
- cut DNA at specific recognition sequences in bacteria to fend off bacteriophages
- often staggered, leaving sticky ends
- resulting fragments are known as restriction fragments
- useful for gene cloning
gel electrophoresis
- separates long molecules of DNA (must be cut by restriction enzymes so small enough to move) on the rate of movement in a agarose gel in an electric field
- DNA can be sequenced with DNA probe or compared to other DNA samples
- concentration of gel can be altered to allow finer separation of molecules
- used to separate proteins and amino acids
DNA probe
- radioactively labeled single strand of nucleic acid molecule used to tag a specific sequence in a DNA sample
- binds to complementary sequence, allowing for the detection of the location
polymerse chain reaction (PCR)
- billions of copies of fragment DNA can be made by placing Taq polymerase with the DNA and a supply of nucleotides and primers necessary for DNA synthesis
- limitations: must know a little about the nucleotide sequence of target DNA, size must be small, contaminate the target DNA
restriction fragment length polymorphism (RFLPs)
- RFLP: the difference in restriction fragment patterns across individuals
- used for DNA fingerprinting
- inherited Mendelian (used for paternity suits)
complimentary DNA (cDNA)
-bacteria do not have introns, so to clone a human gene in bacteria, must use reverse transcriptase to make cDNA transcripts of RNA
