Chapter 11 Flashcards
DNA structure
composed of nucleotides, which are covalently linked to form DNA strands. Two DNA strands are held together by hydrogen bonds between the bases to form a double helix.
DNA associates with various proteins to form
A chromosome
Nucleotides have 3 parts
Nucleotides are composed of a phosphate, a sugar, and a nitrogenous base. The sugar can be deoxyribose (DNA) or ribose (RNA).
Purine and pyrimidine
The purine bases are adenine and guanine, and the pyrimidine bases are thymine (DNA only), cytosine, and uracil (RNA only).
In DNA sugars are connected by a Colvalent bond in which direction
in a 5′ to 3′ direction (Figure 11.6).
DNA structure
• The X-ray diffraction data of Franklin, the data of Chargaff (that is, the amounts of A and T and those of G and C are approximately equal), and the ball-and-stick modeling of Pauling helped reveal the structure of DNA (Figure 11.7, Table 11.1).
4 criteria of genetic material
Irtv
Information
Replication
Transmission
Variation
1920s to 1940/ scientist though what would be the genetic material
The protein portion of chromosomes
Griffith bacterial transformation of streptococcus pneumoniae bacteria
What happened, what did it mean, what did he call it
Smooth(s) strain fatal in mice. Rough (r) are not fatal in mice. Heat killed S type did not kill mice, heat killed S type and living R type did kill mice
This meant some genetic material from type S had transferred to the living type R and provided it with a new trait. He called this the transformation principle.
How did Griffiths findings gir into the 4 criteria of genetic material
- Information: the transformed bacteria acquired the information to make a polysaccharide capsule from the S type
- for the bacteria to be able to kill the mouse it would have has to replicate
- The mactsria had to transmit the genetic material to the daughter cells
- VAriation existed in the ability of the two strains to either form a capsule or not form a capsule
Hershey and chase bacteriophage experiment t2 virus that infects escherichia coli
What they did what the learned
First part phage produced with sulfur 35, a radioactive amino acid.let phage infect bacteria but none of s35 got in. Part 2 involved phosphorus 32 labeled deoxyribonucleotides.resulted in the p32 showing up in the bacteria cell which told them that DNA is the genetic material
Levels of DNA structure (5)
- Nucleotides- the building blocks
- Strand- a linear polymer
- Double helix- 2 strands of DNA
- Chromosomes - DNA with An array of protein
- Genome- complete complement of genetic material
DNA Nucleotide
RNA nucleotide
5 carbon sugar, deoxyribose, a phosphate group and a nitrogenous base
4 carbon sugar, ribose, a phosphate group and a nitrogenous base
Eukaryotes have DNA in
Nucleus, mitochondria and chloroplasts
Purine bases
Pyrimidine bases
Have a double ring structure; adenine and guanine
Have a single ring structure; cytosine. Thymine in DNA and uracil in RNA
How are nucleotides bonded
Covalently
Phosphodeister bond
The bond that links the two sugars in the DNA backbone. They are linked by the phosphate group of the first nucleotide
Nucleotide numbering system
Base attaches to
Phosphate attaches to
Sugar carbons are numbered 1-5
Base attached to 1’ carbon
Phosphate attaches to 5’ carbon
What charge does the backbone of DNA/RNA have?
Negative due to the phosphate groups
Base pairs
Adenine and thymine in DNA
Adenine and uracil in RNA
And guanine and cytosine
How X-ray diffraction pattern works
When something’s exposed to X-rays the atoms in the substance cause the X-rays to be scattered. If t has a repeating structure, the X-ray will scatter in an arrangement related to the substances structure
How Rosalind franklin used d pattern
She used mathematics to conclude that DNA had a helical structure that has a uniform diameter and is too large to be single stranded.
Base composition by Erwin chagroff
Analyzed base composition of DNA from many species and realized the amount of adenine is always equal to the amount of thymine. And same with g&c.
Linus Pauling
Protein model building, proposed some regions of proteins fold into an x helix
Built ball and stick units
Watson and crick
2 ways they got it wrong
2 things they finally got right
- thought the bases were on the outside instead of Inside
- thought a would pair with a, g with g and so on
- its a double stranded helix
- A with t and g with c
Who won the novel
Prize in 62 for the ball and stick model
James Watson, Francis crick and Maurice Wilkins
Features of DNA:
Antiparallel strands
Complementary strands
How many nucleotides per helical turn
DS BI BP HB BB
- One strand goes from 5’- 3’, the other goes from 3’- 5’
- 5’- GCGGATTT -3’
3’- CGCCTAAA -5’ - 10
Double stranded,Bases inside,Base pairing
Hydrogen bonding,Sugar phosphate backbone
Major groove. Minor groove
Proteins bind to affect gene expression
Narrower
Semi conservative replication mechanism
The right one
A double stranded DNA seperates into two single strands to serve as template strands. the new DNA contains one parental strand and one daughter strand
Conservative mechanism
Dispersive mechanism
2 parental stay together and 2 daughters stay together
Segments of parental and daughter DNA are intertwined into both strands
The replication fork
How the nucleotides and backbone bond
Once the strands are seperated individual nucleotides have access to the template strands in this region
the nucleotides hydrogen bond according to the AT/GC rule
Then then the phosphodeister bond occurs allowing the phosphate of one nucleotide and the sugar of the next nucleotide to covalently bond
DNA helicase
How it does it
What it can cause
What fixes that
Binds to DNA and travels 5’ to 3’ using ATP to seperate base pairs
Uses energy from ATP to break hydrogen bonds between base pairs.
Can cause knots called supercoils to form just ahead of the fork,DNA topoisomerase relieves cooling ahead of replication fork
Single strand binding proteins
Coat each strand to keep parental strands open to act as templates
deoxynucleoside triphosphates
Nucleotides with three phosphate groups
DNA polymerase synthesizes DNA at how many nucleotides per second
500
DNA polymerase can’t
So it needs a
Begin synthesis on a bare template strand
A primer to get started
DNA polymerase only works from ____ to ____
5’ to 3’
DNA primase
Makes a primer from RNA
RNA primer is later removed and replaced with DNA
Leading strand
The leading strand is the one that’s going from 3’ to 5’, because the new strand that’s being made is the opposite of the template, the new strand for this one will be from 5’ to 3’ which convienantly is the way DNA polymerase goes. It is still started with an RNA primer but from that point on it replicated smoothly
Lagging strand
The lagging strand is from 5’ to 3’ so the daughter strand that’s being synthesized has to go from 3’ to 5’, which DNA polymerase can’t do. So the RNA primer is put down and then DNA polymerase comes and does a segment( going in the opposite direction as the first strand, this is going away from the unwinding)
DNA polymerase
What it does to the deoxynucleoside triphosphate
What it does with the resulting phosphate
(What type of bond)
Enzyme that covalently linksnucleotides to make DNA strands.
It does this by breaking the covalent bond at the catalytic site of the first and second phosphate from the deoxynucleoside triphosphates,
which gives it energy to connect the resulting nucleotide to the 3’ end of a growing strand
Using a phosphoester bond
Pyrophosphate
When two of the three phosphates of deoxynucleoside triphosphate has its bond with two of the phosphates broken this is what leaves, giving energy to connect the nucleotides
3 things that make DNA replication very accurate
Hydrogen bonding between AT N GC is more stable than mismatched combos //Active site of DNA polymerase unlikely to form bonds if pairs are mismatched //DNA polymerase proofread to remove mismatched pairs(DNA backs up&digests linkages, other DNA repair enzymes)
Telomere
3’ overhang
Short nucleotide sequences repeated at the end of chromosomes in eukaryotes
Telomere at 3’ doesn’t have a complementary strand
Telomerase enzyme
Attaches many copies of DNA repeat sequence to the ends of chromosomes
Shortening of telomerase is correlated with
Cellular senescence
What percent of human cancers have high levels of telomerase
99%
Typical eukaryotic chromosomes are how many base pairs long
Chromosomes are composed of
Hundreds of millions
Chromatin which is a DNA protein complex
Levels of DNA compaction
1.
Octomer of Histone is made of
And contains what amino acids
- DNA wrapping- DNA wraps around a group of proteins that make up an Octomer histone//Has 2 molecules and each contain 4 histone proteins, h2a, h2b or h3 and h4//Positively charged arginine and lysine which are attracted to the negative charge of the phosphate in DNA
DNA levels of compaction
- 30 mm fiber
- radial loop domains
Nucloesomes organize more compactly. But it comes out as an irregular fluctuating structure with stable nucleosome units connected by bendable linker regions //Compaction of the 30 mm fiber by interaction with the nuclear matrix
Nuclear matrix
Nuclear lamina
Filamentous network of proteins in the nucleus
Protein fibers that line the inner nuclear membrane
Heterochromatin
Contains
Euchromatin
Contains
Totally compacts chromosomes which helps then take the right shape for metaphase by making tighter radial loops. Contains centromeric and telomeric regions
Less condensed, contains genes
Three types of RNA and what they do
mRNA
mRNA is created when the DNA recipe is copied in the first step of the central dogma. The information found in mRNA can be interpreted by using two other forms of RNA in the second step of the central dogma.
.
Once there’s three okazakis who replaces the RNA primer with DNA
Then ______ links the okazakis
1 primer and DNA polymerase set= an Okazaki. Once there’s three okazakis DNA polymerase 1 replaces the RNA primer with DNA
Then DNA ligase links the okazakis
rRNA
mRNA is translated into protein at a cellular structure known as the ribosome. A second type of RNA helps form the structure of a ribosome. This type of RNA is called ribosomal RNA, or rRNA.
tRNA
Proteins can are made of amino acids, so the formation of any protein requires assembly of a chain of amino acids. Transfer RNA, or tRNA, molecules ferry amino acids to the ribosome for this assembly
