Chapter 4: Molecular Biology Flashcards
MCAT Mnemonics/Concepts I need to review
Why are DNA and RNA called nucelic acids?
It’s because they are found in the nucleus and possess many acidic phosphate groups
What is the dNTP?
The building block of DNA, stands for deoxyribonucleoside 5’ triphosphate where N represents one of the four basic nucleosides.
What is dATP?
Deoxyadenosine 5’ triphosphate
What makes up a nucleoside?
a sugar (deoxyribose for DNA, ribose for RNA), an aromatic, nitrogenous base, and 1-3 phosphate groups.
What are purines?
G and A
What are pyrimidines?
C, T, and U
What is the difference between a nucleoside and a nucleotide?
Nucleoside: ribose or deoxyribose w/ pyrimidine linked to the 1’ carbon.
Nucleotide: phosphate esters of nucleosides w/ 1,2, or 3 phosphate groups joined to the ribose ring by 5’ hydroxy group.
What is nucleoside triphosphate? (NTP)
When nucleotides contain 3 phosphate residues.
In individual nucleosides what is N replaced by?
A,G,C,T, or U
Mnemonic: Cut the Py
Pyrimidines: C, U,T
What is the backbone of DNA?
The sugar + phosphate portion of the nucleotide (invariant or unchanging) while the nitrogenous base is the variable portion of the building block.
What are the aromatic nitrogenous bases? Classify each as a purine or pyrimidine.
Adenine - purine
Cytosine - pyrimidine
Thymine - pyrimidine
Uracil - pyrimidine
Guanine - purine
What links nucleotides together to form polynucleotides and make up the DNA?
How specifically are two nucleotides bonded?
Phosphodiester bonds
3’ OH group of one deoxyribose bonds to the 5’ phosphate group of the next deoxyribose
What is the difference between an oligonucleotide and a polynucleotide?
Oligonucleotide = only several nucleotides linked together
Polynucleotide = many nucleotides linked together
What is the Watson-Crick Model?
Cellular DNA is right right-handed double helix held together by hydrogen bonds between bases. The strands run antiparallel
What is Chargoff’s Rule?
A=T
G=C
A+G = C+T
How many Hydrogen bonds between bases in a dsDNA?
AT = 2 H bonds
GC = 3 H bonds
A hydrogen-bonded pair always consists of a ____ plus a ______
purine plus a pyrimidine
What does annealing/ hybridization mean?
The binding of two complementary strands of DNA into a double stranded structure
What does melting/ denaturation mean?
The separation of two complementary strands of DNA from the double stranded structure
Which of the following is/are true about dsDNA?
I. If the amount of G in a double helix is known, the amount of C can be calculated
II. If the fraction of purine nucleotides and the total molecular weight of a double helix are known, the amount of cytosine can be calculated
III. The two chains in a piece of dsDNA containing mostly purines will be bonded together more tightly than the two chains in a piece of dsDNA containing mostly pyrimidines
IV. The oligonucleotide ATGTAT is complementary to the oligonucleotide ATACAT
I, IV are true
I is true because for every G there is a C and for every A there is a T.
II is false because the ratio of purines to pyrimidines is always 50:50 since a purine is always paired with a pyrimidine. To calculate the amount of any base you have to know the AT and GC pairs..
Item III is false because the ratio of purines to pyrimidines is always the same. However, two chains containing mostly GC pairs will bind more tightly than two chains containing mostly AT pairs, since GC are held together by 3 H bonds while AT pairs only have 2.
IV is true because the 5’ end is always written first unless specified otherwise, and the strands are antiparallel: A and T pair, G and C pair.
What is a genome?
The sum total of an organism’s genetic information
What is a chromosome and how many do humans have?
A chromosome is a large piece of linear dsDNA that make up the eukaryotic genome
Humans have 46 chromosomes (23 pairs, one from each parent)
What is the difference between eukaryotic, prokaryotic, and viral genomes?
eukaryotic contains chromosomes
prokaryotic contains one circular chromosome
viral can be linear or circular DNA or RNA
How many base pairs does the human genome have vs the bacterial genome?
humans have 10^9
bacterial have 10^6
What is DNA gyrase? Describe the steps.
An enzyme that requires ATP to twist the circular DNA in prokaryotes
Breaks the DNA and twists the two sides of the circle around each other, resulting in a twisted circle that is composed of dsDNA
Creation of supercoils
What are histones?
Globular proteins where DNA is wrapped around it
What are nucleosomes?
Made up of an octamer of histones with DNA wrapped around it
What is linker DNA?
The string-like DNA between nucleosomes that is bound by a single linker histone
What is a chromatin?
Heterochromatin?
Euchromatin?
Fully packed DNA that is composed of closely stacked nucleosomes
When staining, it is the darker region that is more dense and rich in repeats
When staining, it is the lighter region that is less dense and therefore has higher transcription rates and higher gene activity because the looser packing makes DNA accessible to enzymes and proteins
What is the centromere?
What is it made of?
The region of the chromosome that spindle fibers attach to during cell division
Made of heterochromatin and repetitive DNA sequences
What is a kinetochore?
Multiprotein complexes that act as anchor attachment sites for spindle fibers
What types of arms do chromosomes have?
What are the different centromere positions called? Name and describe each.
short arm (p)
long arm (q)
- Metacentric - p and q are equal
- Submetacentric - q is slightly longer than p
- Acrocentric - q is a stalk while p is bulb-like
- Telocentric - there is only one arm because the centromere is at the end of the chromosome
What is a telomere? Be specific.
The ends of linear chromosomes that have repeated nucleotide sequences (about 50-several hundred times)
Can be single or double stranded DNA about 300 BP long
Acts as a disposable buff that blocks the ends of chromosomes to prevent deterioration and also prevents fusion with neighboring chromosomes
On average, how long is one repeated unit in telomeres and what is it rich in?
6-8 BP long repeated unit
Guanine rich
How many BP is the human genome?
3.2 billion BP
How many genes does the human genome code for?
21,000
What are intergenic regions?
What is their purpose?
What are some important things in the intergenic region?
Non-coding DNA
Can direct assembly of specific chromatin and can contribute to regulation of nearby genes
Intergenic regions includes tandem repeats and transposons
What is SNP’s? Give details.
How often does it occur?
Single Nucleotide Polymorphisms which are single nucleotide changes/ mutations that mostly occur in the non-coding regions of the genome. However, some SNPs lead to specific traits and phenotypes.
Occurs once in every 1,000 BP
If the size of the human genome is just over 3 billion base pairs, approximately how many human SNPs are there?
3 mill base pairs are human SNPS
Since SNPs happen once every 1000 BPs
3 billion BP / 1000 BP = 3 mill human SNPs
What is CNV?
Misalignment of repetitive DNA sequences during synapsis of homologous chromosomes in meiosis leads to different copies of DNA.
How big is a region of CNV?
10^3 to 10^6 BP
Where is CNV commonly seen?
0.4% of the genome
Associated with cancer and other diseases
Immune system function
Brain development and activity
What is a tandem repeat?
short sequences of nucleotides repeated (3-100 times) one after the other
What constitutes as an unstable tandem repeat?
What are the effects of an unstable tandem repeat?
When the repeating unit is short (di- or tri-nucleotides) or when the repeat itself is very long
Unstable tandem repeats can lead to chromosome break and disease
What is transcription and what can it make?
Reading DNA and writing the information as RNA
Can make a final gene product (all non-coding RNA)
Can make a messenger molecule
What is translation? What enzyme does it involve?
The synthesis of proteins using mRNA as a template
Ribosome is the massive enzyme that is composed of many proteins and rRNA
____ encodes and transmits the genetic info passed down from parent to offspring not _____
1) DNA
2) protein
What is the Central Dogma?
Inherited information used to create enzymes and structural proteins
DNA –> RNA –> proteins
What is the genetic code?
The language used by DNA and mRNA
A,G,T,C
What is a codon?
A 3 letter nucleotide sequence that codes for a particular amino acid.
How many possible different codons are there and how can that be calculated?
64 codons (enough to specify 20 unique amino acids)
4 nucleotides
3 nucleotides per codon
4^3 = 64 different combinations
Why is uracil shown in the chart and why is thymine absent? (pg 74)
This is because RNA is the nucleic acid that encodes protein during translation. RNA has a U instead of a T.
The codon GTG in DNA is transcribed in RNA as _____, which the ribisome translates into what amino acid?
G =C
T= A
G= C
The RNA codon was transcribed from DNA as CAC coding for histidine.
What is a stop codon?
What is another name for it?
Does not code for a specific amino acid, but instead notifies the ribosome that the protein is complete. Causes it to stop reading the mRNA
Also called nonsense codons
If the last nucleotide in the codon CUU is changed in a gene that codes for a protein, will the protein be affected?
No since CUN codes for leucine, regardless of what N is. Notice that switching the third nucleotide in the majority of codons will have no effect.
What are synonyms for the genetic code and how does this affect the genetic code?
Synonyms are when two or more codons code for the same amino acid
The genetic code is degenerate because of this
What are some examples of molecular biology that is outside of the Central Dogma?
Retroviruses make DNA from RNA using the enzyme reverse transcriptase.
Info can be transferred in other ways such as DNA methylation and post-translational modification of proteins that can alter gene expression and convey information, even though they are not directly included in the Central Dogma.
Lastly, many final products are not proteins but rather RNA instead.
What is the Meselson-Stahl Experiment?
Semiconservative replication - One strand of the DNA is parental while the other strand is the daughter strand
Conservative replication - the parental dsDNA stays as is while an entirely new ds genome is created as the daughter
Dispersive replication - both copies of the genomes were composed of scattered pieces of new and old DNA
DNA replication is _____
semiconservative
Individual strands of the double-stranded parent are pulled apart and then a new daughter strand is synthesized using the parental DNA as a template to copy from. Each new daughter chain is perfectly complementary to its template or parent.
What is helicase?
An enzyme that requires ATP to break the hydrogen bonds and separate the dsDNA at the origin of replication
How do prokaryotes find the ORI?
Eukaryotes?
Prok: DnaA protein finds the ORI
Euk: three proteins cooperate to find the ORI
2 of the proteins are synthesized during M and G1 phase and destroyed in the S phase. These link DNA replication to the cell cycle to ensure DNA replication doesn’t initiate during other phases of the cell cycle
What is topoisomerase?
An enzyme that cuts one or both of the strands and unwraps the hel
What is SSBP?
Single stranded binding protein that protects the DNA that has been unpackaged in preparation for replication and to help keep the strands separated
What is an open complex?
Where the strands are separated during DNA replication
What is a primase?
An RNA polymerase that is part of the primosome. It synthesizes an RNA primer for each template strand during DNA replication
What is a primosome?
A set of proteins that help to synthesize an RNA primer for each template strand during DNA replication
How long is the average RNA primer?
8-12 nucleotides long
What is DNA polymerase?
Elongates the primer on the daughter strand by adding dNTP’s to its 3’ end
3’ OH group acts as a nucleophile in the polymerization reaction to displace 5’ pyrophosphate from the dNTP to be added.
What direction is the template strand read in?
3’ to 5’ because the daughter strand is made in the 5’ to 3’ direction and the two strands have to be antiparallel
What is a replisome?
A large complex of proteins that help DNA polymerase polymerize the DNA quickly
How many components does a prokaryotic replisome have?
Eukaryotic? Why?
13 components
27 components because it must also unwind the DNA from the histones
What is the driving force for the polymerization reaction?
Removal and hydrolysis of pyrophosphate (P2O7 4-) from each dNTP added to the chain
What direction does polymerization always happen in?
5’ to 3’ direction without exception
This means the existing chain is always lengthened by the addition of a nucleotide to the 3’ end of the chain. There is never 3’ to 5’ polymerase activity.
What does DNA polymerase require?
A template and a primer
It cannot make a DNA chain from scratch but must copy an old chain. This makes sense b/c it would be useless if DNA pol just made a strand of DNA randomly without copying a template.
Needs a primer since it cannot start a new nucleotide chain
Can DNA polymerase make the following partially double-stranded structure completely double-stranded in the presence of excess nucleotides using the top strand as a primer? (pg. 78)
No. The DNA strands are antiparallel meaning that the upper strand would have to be extended in a 3’ to 5’ direction which is impossible. (excess nucleotide is an extraneous phrase, typical MCAT smokescreen)
What is a replication fork?
The area where the parental double helix continues to unwind during DNA replication
Replication proceeds in both directions away from the origin of replication. Both template strands are read ___ to ___ while daughter strands are elongated ____ to ____
1) 3’ to 5’
2) 5’ to 3’
What is a leading strand?
Lagging strand?
Elongating continuously
Needs RNA primers constantly as the replication fork widens
What are Okazaki fragments?
Small chunks of DNA on the lagging strand
As the replication forks grow, does helicase have to continue to unwind the double helix and separate the strands?
Yes
Replication forks grow ____ from the origin in both directions. Each replication fork contains an _____ and a _____
1) away
2) leading strand
3) lagging strand
Replication of the leading strand is ____
continuous and leads into the replication fork
Replication of the lagging strand is ____
discontinuous
resulting in Okazaki fragments
Eventually all RNA primers are replaced by ____
DNA
What are the Okazaki fragments joined by?
DNA ligase, an enzyme