Chapter 5 Flashcards
building block of DNA
dNTP
nucleoside
ribose with a purine or pyrimdine linked to the 1’ carbon
nucleotides
phosphate esters of nucleosides
deoxynucleoside triphosphate (dNTP)
when nucleotides contain three phosphate residues
backbone of DNA
ribose and phosphate portion of the nucleotide
Oligonucleotide
a polymer of several nucleotides linked together
Polynucleotide
A polymer of many nucleotides linked together
Watson and Crick model
Cellular DNA is a right-handed double helix held together by hydrogen bonds between bases.
The helix pattern resets itself once every 34 angstroms, which is every 10 base pairs. Width is always 20 angstroms.
H-bonded pair always consists of a
Purine plus a pyrimidine
Annealing/Hybridization
The binding of two complementary stands of DNA into a double-stranded structure
Melting/Denaturation
Speration of strands
Tm
Temperature at which a solution of DNA molecules is 50% melted
Tm is (higher/Lower) in pairs of AT
lower, it takes less kinetic energy to disrupt 2 hydrogen bonds than 3
Genome
sum total of an organisms genetic information
Chromosome
each piece of ds-DNA
Is there a correlation between genome size and evolutionary sophistication?
No
Organisms with the largest genome
amphibians
DNA gyrase
uses energy of ATP to twist the gigantic circular molecule and then breaks the DNA and twists the sides of the circle around each other
Supercoils
Created by DNA gyrase; coils of a structure that’s already coiled
Histones
because eukaryotic DNA needs denser packing, DNA is wrapped around these gobular proteins
Nucleosomes
composed of DNA wrapped around an octamer of Histones
Chromatin
Fully packed DNA
Histones are composed of
Basic amino acids; Arginine & Lysine
Histones need to be basic since they must be attracted to acidic DNA
How does DNA affect cells
it contains sequences of nucleotides known as genes that serve as templates for the production of another nucleic acid known as RNA
Transcription
Process of reading DNA and writing the information as RNA
Once DNA is converted to RNA, RNA serves as a
messenger from the nucleus to the cytoplasm
Once the RNA reaches the cytoplasm
it is read and the information is written down as protein
Translation
production of proteins from RNA
Central Dogma
mechanism where inherited information is used to create actual objects; enzymes and structural proteins
Exception to the Central Dogma
certain viruses (retroviruses) which make DNA from RNA
How DNA orchestrates protein synthesis
DNA is copied into a messenger RNA
mRNA travels to the cytoplasm where it encounters the ribosomes and other components of protein synthesis
The ribosome synthesizes polypeptides according to the DNA’s original orders
Genetic Code
language used by DNA and mRNA to specify the building blocks of proteins
Alphabet used by the genetic code
A, T, C, G
Codon
nucleic acid word ( nucleotide letters)
Three stop codons
UAA, UAG, UGA
How many codons are there
64
All four of the codons with the same first two nucleotides
encode the same amino acid
Although an amino acid may be specified by several codons
each codon specifies only a single amino acid
Each piece of DNA can be interpreted only one way, meaning the code has no
ambiguity
Causes of mutation
mistakes in replication of the genome during cell division
chance chemical malformations (such as spontaneous deamination; loss of nitrogen group)
environmental agents such as chemicals and ultraviolet light
Intercalating
Purines and pyrimidine a with large flat aromatic ring structures cause mutations by inserting themselves between base pairs
Mutagen
any compound that can cause mutations
Three kinds of mutations
(1) point mutations, (2) insertion mutations, (3) deletions mutations
Point mutations
single base pair substitutions
Three types of point mutations
missense mutations: cause one amino acid to be replaced with a different amino acid
nonsense mutations: cause a stop codon to replace a regular codon
silent mutations: change a codon into a new codon for the same amino acid
Conservative mutations
missense mutations that lead to little change in the structure and function of the gene product
Insertion
refers to the addition of one more extra nucleotide into the DNA sequence
Deletion
the removal of nucleotides from the sequence
Frameshift mutations
mutations causing a change in the reading frame
Switching the 3rd nucleotide in the majority of the codons
will not have any effect
Replication
Duplication of the DNA; required by cell division
Daughter cells have the
same genome as the parents
Replication occurs during
S (synthesis) phase in the interphase of the cell cycle
Replication occurs by
Pulling apart the individual strands of the double-stranded parent,then a new daughter strand is synthesized using the parental DNA as a template to copy from
Semiconservative DNA replication
One strand of the newly synthesized DNA is from the parent and one is from the daughter
DNA polymerase (DNA pol)
the enzyme catalyze a the elongation of the daughter strand using the parental template
Replication rules
Polymerization occurs in the 5’ to 3’ direction, without exception
DNA pol requires a template
DNA pol requires a primer
Helicase
the enzyme that unwinds the double helix and separates the strands
Origin of replication
the place where the helicase begins to unwind
Topoisomerase
cut one or both of the strands and unwrap the helix, releasing the excess tension created by the helicase
Single stranded binding proteins
Protect DNA which has been unpackaged in preparation for replication and help keep the strands separated
Replication forks
areas where the parental double helix continues to unwind
Leading strand
bottom daughter strand, elongates continuously right into the winning replication fork
Lagging strand
Must wait until the replication fork widens before beginning to polymerize, the top daughter strand
Okazaki fragments
small chunks of DNA comprising the lagging strand
Replication forks grow
away from the origin in both directions
All RNA primers are replaced by
DNA, and the fragments are joined by an enzyme called DNA ligase
In eukaryotic replication
each chromosome has several origins
Prokaryotes have only one
chromosome, this chromosome has only one origin. Since the chromosome is circular, partially replicated genome being to look like theta sign
RNA is chemically distinct from DNA in 3 ways
RNA is single stranded, except in some viruses
RNA contains uracil instead of thymine
The pentose ring in RNA is ribose rather than 2’ deoxyribose
The pentose ring in RNA being ribose rather than 2’deoxyribose causes RNA polymer to be
less stable
Three types of RNA
mRNA, rRNA and tRNA
mRNA
carries genetic information from the nucleus to the cytoplasm where it can translated into protein
Monocistronic
obeys the “one gene, one protein” principle. Each piece of mRNA encodes one and only one polypeptide
There are as many different mRNA’s as there are
proteins
Cells regulate
the amount of each particular protein they synthesize
Polycistronic
prokaryotic mRNA often codes for more than one polypeptide
rRNA
serves as components of the ribosome and many polypeptide chains.
Provides the catalytic function of the ribosome
tRNA
responsible for translating the genetic code
Transcription
synthesis or RNA using DNA as the template
Transcription has a lower
fidelity process than replication
Start site
the site where transcription starts
Promoter
Sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription
The amount of each protein are in every cell is controlled by
the amount of mRNA that gets transcribed
Template non-coding, transcribed or antisense strand
Strand which is actually transcribed and is complementary to the transcript
Coding or sense strand
same sequence as the transcript (expect it has a T in place of U)
Prokaryotes have no nucleus
transcription and translation occurs freely in the cytoplasm and simultaneously
Eukaryotes must transcribe their mRNA in the
nucleus, then modify it, then transport it across the nucleus membrane to the cytoplasm where it can be translated
Splicing
A way in which eukaryotic primary transcript is modified extensively before translation
Introns
Non-coding sequences intervening between the segments that actually code for proteins
Exons
protein-coding regions of the RNA and are actually expressed
5’ Cap
essential for translation. While both the cap and the poly-A tail are important in preventing digestion of the mRNA by exonucleases that are free in the cell
During translation, an mRNA molecule
attaches to a ribosome at a specific codon, and the appropriate amino acid is delivered by the tRNA molecule
Anticodon
responsible for recognizing the mRNA codon to be translated
Amino acid acceptor site
which is where the amino aid is attached to the tRNA
tRNA moves through how many sites?
3; A –> P –> E
Initiation
requires the formation of the 70S initiation complex. Initiator tRNA sits in the P site of the 70S ribosome, hydrogen-bonded with the start codon
Elongation
1st step: second amino acid-tRNA enters the A site and hydrogen bonds with the second codon
2nd step: peptidoglycan transferase activity of the large ribosomal subunit catalyzes the formation of a peptide bond between the 1st amino acid and the 2nd amino
3rd step: translocation: tRNA #1 (now empty) moves into the E site, tRNA #2 (holding the growing peptide) moves into the P site and the next codon will translated into the A site
Termination
occurs when a stop codon appears in the A site. Release factor now enters the A site
Eukaryotic translation
the ribosome is larger (80S, the mRNA must be processed before it can be translated, and the N-terminal amino acid is different
Eukaryotic mRNA
must not only be spliced, capped and tailed, but it also requires transport from nucleus to cytoplasm
transcription and translation cannot proceed simultaneously
Ratios of purine to pyrmidines is
Always 50:50 since each purine is paired with a pyrimidine
Which chain will be more tightly bound, CG or AT?
Chain containing mostly GC will bind more closely due to 3H bonds unlike AT with 2H bonds
