Packet flashcards
Chromosomes
Complex of DNA and proteins
Genes
Made of DNA and act as instructions to make proteins
2 major features of DNA
The backbone made of sugar and phosphate groups.
Series of bases that project from each sugar in the backbone
Hershey-Chase Experiment
Studied how the T2 virus infects and replicates in the bacterium Escherichia coli
T2 infection of E. coli begins when:
The virus injects its genes into the cell and they direct the production of new virus particles.
What was the conclusion of the Hershey-Chase experiment
DNA can replicate
Structure of DNA
Double-stranded
Each strand consists of deoxyribonucleotides (deoxyyribose sugar, phasphate group, and nitrogenous base)
Phosphodiester linkage
Covalent bond
The hydroxyl group on 3’ carbon of one deoxyribose joined by a covalent bond to the phosphate group attached to 5’ carbon of another deoxyribose.
DNA directionality
5’ to 3’ direction
Semiconservative replication
Parental strands separate and each is template for a new daughter strand.
Each daughter has one old and new strand.
Conservative replication
The parental molecule serves as an entirely new molecule.
One daughter has both old strands; other has both new strands.
Dispersive replication
Parent molecule is cut into small pieces
Each daughter has an old and new DNA interspersed.
What did Watson and Crick propose
Proposed existing DNA strands of DNA served as a template.
Deoxyribonucleotides were added to new strands according to complementary base pairings.
Meselson-Stahl Experiment
Experiment done by Mehselson and Stahl that demonstrated that DNA replicated semi-conservatively.
Grew bacteria in a heavy isotope of Nitrogen (15N), then transferred to light nitrogen. Put in medium and spun.
DNA Polymersase
Enzyme that catalyzes DNA synthesis
What direction does DNA synthesis proceed
It only works in one direction which means the 5’ –> 3’ direction
Origin of replication
Sequence of bases on a chromosome where DNA replication starts
How many origin of replications are in bacterial chromosomes
1
How many origins of replications are there in eukaryotes
Multiple orgins of replication along each chromosome
What forms as DNA is synthesized
Replication bubble
Where do replication bubbles form
specific sequence of bases called the origin of replication.
Where does active DNA synthesis take place?
Replication forks of each replication bubble
DNA helicase
Protein that breaks hydrogen bonds between two DNA strands to separate them
Single-strand DNA-binding proteins
Attach to separating strands of DNA during replication. It prevents them from reforming the double helix
Topoisomerase
An enzyme that unwinds DNA double helix
3 limitations of DNA polymerases
- Can only synthesize DNA in the 5’–> 3’ direction
- DNA polymerases cannot start synthesis from scratch on a template strand
- DNA polymerases can only extend from the 3’ end of an existing strand that is hydrogen-bonded by complementary base pairings to the template
Primer
a short nucleic acid sequence that provides a starting point for DNA synthesis
Primase
An enzyme that synthesizes a short stretch of RNA to use as a primer during DNA replication
RNA polymerase
Enzyme that synthesizes RNA molecules from a DNA template through transcription
Difference between RNA and DNA polymerase
RNA polymerase can start synthesis from scratch
Leading strand
Strand of DNA that is synthesized towards the replication fork
Lagging strand
Strand synthesized away from the replication fork
Discontinuous replication hypothesis
Proposed to explain how the lagging strand is synthesized.
Held that primase synthesizes new RNA primers for lagging strands, and that DNA polymerase synthesizes short DNA fragments from these primers
Ozaki fragments
Short segments of DNA produced during replication of lagging strand template
Okazaki fragments are eventually linked together to produce the lagging strand in newly synthesized DNA
Synthesis of lagging strand
Priming: The lagging strand is synthesized in the 3’ to 5’ direction, which is opposite to the direction of the DNA replication fork. To initiate synthesis, an RNA primer is synthesized by the enzyme primase.
Initiation of Okazaki Fragment: DNA polymerase III adds nucleotides to the RNA primer, synthesizing a short DNA fragment called an Okazaki fragment. This process is initiated at the RNA primer.
Extension of Okazaki Fragment: DNA polymerase III continues to add nucleotides, extending the Okazaki fragment in the 5’ to 3’ direction.
Removal of RNA Primer: The RNA primer of each Okazaki fragment is removed by the enzyme RNase H, leaving a gap.
Fill-in by DNA Polymerase I: The gap left after primer removal is filled in by DNA polymerase I. This enzyme has both 5’ to 3’ polymerase activity and 5’ to 3’ exonuclease activity.
Ligation: DNA ligase seals the nick between adjacent Okazaki fragments by catalyzing the formation of a phosphodiester bond, producing a continuous lagging strand.
DNA ligase
An enzyme that joins pieces of DNA by catalyzing the formation of a phosphodiester linkage between the pieces.
DNA polymerase III
Extends leading strand and creates okazaki fragments by extension of RNA primers
Sliding clamp
Holds DNA polymerase in place during strand extension
Replisome
macromolecular machine that copies DNA; includes DNA polymerase, helicase, primase, and other enzymes
Telomeres
Region at the end of the eukaroyitc chromosome
Problem with copying telomeres
The lagging strands become too short as an enzyme that degrades the ribonucleotides removes the primer. As a result the single-strand DNA remains single stranded
Telomerase
Enzyme that adds DNA to the ends of chromosomes (telomeres) to prevent them being shortened by DNA synthesis
Where are telomerase found and not found
Found in gametes and stem cells and are not found in somatic cells
What happens to chromosomes of somatic cells without telomerase
Gradually shortens with every mitotic division and becomes shorter as an individual ages
Dark side of telomere
Cancer cells have active telomerase that allow unlimited division of cancer cells
How accurate is DNA synthesis
Very accurate as, it only inserts an incorrect base once every 100,000 bases
What happens to incorrect bases
Repair enzymes remove defective bases and replace them with the correct one
Two sources of where DNA polymerase’s ability to select correct deoxyribonucleotide to add to a growing strand
- Correct base pairs are energetically favorable
- Shape of an incorrect base pairs differs from correct ones
Proofreading
Process where DNA polymerases “check their work,” fixing the majority of mispaired bases.
Exnuclease active site
Mismatched deoxyribonucletidfe moves to site where it does fit and the site catelazyes removal of incorect ribonucleotide
Mismatch repair enzymes
Recognizes mismatched pairs, incorrect base and fills in correct bases.
Nucleotide excision repair
DNA repair that removes damaged regions in one strand of DNA and replaces it with a correct seqence using the undamaged strand as a template.
Xeroderma pigmentosum
Rare autosomal recessive disease in humans
Causes extreme sensitivity to UV light that increases chances of skin cancer
Gene expression
Process of converting information in DNA into functioning molecules within the cell
one-gene, one-enzyme hypothesis
Each gene contains information to make an enzyme
Mutant
modification of the gene to make it different
Genetic Code Hypothesis
Sequence of bases in DNA acted as a code
Messenger RNA
Intermediatary between genes and proteins that carries info from DNA to site of protein synthesis
RNA polymerase
Catalyzes synthesis of RNA from ribonucleotides using a template usually consisting of DNA
Central dogma
DNA codes for RNA, which codes for proteins
Transcription
the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA)
Translation
process of using information in mRNA to synthesize proteins
Organism’s genotype
Determined by sequences of bases in DNA
Organism’s phenotype
Product of proteins it produces
Reverse transcriptase
An enzyme that can synthesize DNA from an RNA template
genetic code
speicfies how a sequence of nucleotides code for a sequence of amino acids
triplet code
shortest genetic word to code for at least 20 amino acids
Codon
Group of three bases that specifies a particular amino acid
Reading frame
Sequence of codons that could be destroyed by adding or subtracting one or two bases
Mutation
PERMANENT CHANGE TO DNA BULLSHITTER
Point mutations
Result from one or small number of base changes
Chromosome-level mutations
larger in scale
Missense mutations
Change an amino acid in protein
Silent mutation
A point mutation that changes the sequence of a codon without changing the amino acid that is specified
Frameshift mutations
The addition or deletion of one or a few base pairs in a coding sequence that shifts the reading frame of the mRNA
nonsense mutation
Change codon that specifies an amino acid into stop codon
Beneficial mutations
Increase fitness (ability to survive and reproduce) of an organism
Neutral mutations
Do not affect an organism’s fitness
Deleterious mutations
Decreases the fitness of an organism
Chromosome mutations
May change chromosome number (polyploidy and aneuploidy) or structure
Four types of chromosome structural mutations
Deletion
Inversion
Duplication
Translocation
Inversion
Segment of chromosome breaks off, flips around, and rejoins
Deletion
Segment of a chromosome is lost
Duplication
segment of chromosome is present in multiple copies
Translocation
Section of chromosome breaks off and becomes attached to another chromosome
Karyotype
Complete set of chromosome in cell
Genetic code is
Redundant: All but two amino acids are encoded by more than one codon
Unambiguous: One codon never codes for more than one amino acid
Non-overlapping: Codons are read one at a time
Universal: All codons specify the same amino acids in all organisms
Conservative: If several codons specify the same amino acid, the first two bases are usually identical
Initiation
the first phase of transcription in bacteria where sigma protein must bind to the core enzyme to recognize sites where transcription should begin
Promoters
The sites that sima recognizes where transcription begins
sigma
Protein that binds to the core enzmye to recognize sites where transcription begins
Core enzyme
general term for the enzyme within a multipart holoenzyme that is responsible for catalysis
holoenzyme
What RNA polymerase core enzyme and sigma form
What is the core enzyme for bacteria
bacterial RNA polymerase
How many base pairs long are promoters
40-50 pairs long and had a series of bases on one strand of DNA identical or similar to TATAAT
-10 box
Six base pair sequence known as -10 box as it is centered 10 bases from the point where transcription starts
Downstream
Direction in which RNA polymerase moves along a DNA strand
Process: Initiating transcription in bacteria
- Initiation begins, sigma binds to promoter region of DNA
- Initiation continues, RNA polymerase opens the DNA helix and transcription begins
- Initiation is complete: Sigma is released from the core enzyme; RNA synthesis continues from DNA
Upstream
Opposite to the direction in which RNA polymerase moves along a DNA strand
Elongation
Process by which RNA lengthens during transcriptions as nucleotides are added to the 3’ end of the RNA
Termination
Ends transcription when RNA polymerase transcriptes a DNA sequence called a transcription-termination signal
Causes the RNA polymerase to separate from the RNA transcript
Process: One way of ending transcription in bacteria
Hairpin forms
RNA polymerase transcribes a trranscription terminal signal, which codes for RNA that forms a hairpin
Termination
If a hairpin is followed by a stretch of U nucleotides in the RNA, this leads to the RNA separating from RNA polymerase terminating transcription
