chapter 16 and 17 Flashcards
what does the central dogma of biology describe. how is it important to determine an organism’s phenotype
the flow of information in cells. An organism’s phenotype is a product of the proteins it makes
why does genetic code use a triplet codon
because a group of 3 bases (codon) code for one particular amino acid
define transcription
the process of using a DNA template to make a complementary RNA
define translation
the process of using the information in mRNA to synthesize proteins
alleles of the same gene differ in their _____ sequence
DNA
the protein produced by different alleles of the same gene frequently differ in their ____ sequence
amino acid
what are some exceptions in the central dogma
many genes code for RNAs that do not function as mRNAs and are not translated into proteins. These RNAs still perform important functions
Infor flow DNA –> RNA
Sometimes info flows from RNA back to DNA. Some viruses have reverse transcriptase which synthesizes DNA from an RNA template
what happens during transciption
one of the 2 DNA strands called the template strand provides a template for ordering the sequence of nucleotides in an RNA transcript
what happens during translation
the mRNA base triplets called codons are read in the 5’ to 3’ direction
- each codon specifies the amino acid to be placed at the corresponding position along a polypeptide
-each codon specifies the addition of one of the 20 amino acids
what is genetic code
specifies how a sequence of nucleotides code for a sequence of amino acids
what is a group of 3 bases called
a codon
what is a triplet code
a series of non-overlapping, three nucleotide words
why does a codon have three bases and not more or less
DNA only has 4 different letters: A, T, C, and G. But a protein can have 20 different amino acids. This is where codons come in — they help translate the DNA code into a protein code.
The triplet codon is a “sweet spot” that nature landed upon. It’s just enough to cover all the possible amino acids.
how many codons are there and what do they code for
there are 64 in total 61 code for amino acids, 1 codes for a start (signals where protein synthesis)
3 are stop codons that signal to end translation
Explain what is meant by the statement, ‘The genetic code is redundant but not ambiguous.’
The genetic code is a degenerate code, which means that there is redundancy so that most amino acids are encoded by more than one triplet combination (codon). Although it is a redundant code, it is not an ambiguous code: under normal circumstances, a given codon encodes one and only one amino acid.
how is the genetic code conservative
if several codons specify the same amino acid, the first two bases are identical and the third is different
why is the genetic code universal
because genes can be transcribed and translated after being transplanted from one species to another
how is the genetic code non overlapping
codons are read one at a time
how is the genetic code unambiguous
one codon never codes for more than one amino acid
define mutations.
what are the different kinds of mutations
a mutation is any permanent change in an organism’s DNA
point mutations resulting from one or a small number of changes. Chromosomal-level mutations are larger in scale
what is a beneficial mutation?
increases the fitness of an organism
what is a deleterious mutation
decreases the fitness of an organism
most mutations are _____ or _____
neutral or deleterious
what is a base pair substitution mutation? what kind of mutation is it?
Base-pair substitution mutations occur
when a mistake during DNA synthesis
or DNA repair results in a different
base at a particular location on the
gene
its a point mutation
what are missense mutations
when code for a different amino acid
explain the difference between a silent mutation and a missense mutation
give 2 examples of missense mutations
missense mutation changes the amino acid sequence, but silent mutations have no effect on the amino acid sequence
siamese cats and Himalayan mice
what are nonsense mutations?
nonsense mutations change an amino acid codon into a stop codon
what is a truncated polypeptide? are they functional
a polypeptide that is smaller than normal. Nearly all truncated proteins are nonfunctional and unstable
which type of base pair mutatuon is least likely to be harmful? most likely to be harmful?
silent mutations are least harmful. Nonsense mutation is most harmful
why are insertion or deletion mutations so harmful
they alter the reading frame and produce a frameshift mutation
will a frameshift mutation result in a functional protein
no because every other amino acid after point of insertion or deletion will be different
why are chromosomal mutations harmful
can change chromosome number or structure
what are the 4 types of different chromosomal mutations
inversion: a segment of chromosome breaks off, flips around and rejoins
Translocation: a section of a chromosome breaks off and becomes attached to another chromosome
Deletion: a segment of chromosome is lost
Duplication: a segment of a chromosome is present in multiple copies
-duplication and divergence results in the formation of new genes from duplicated of old ones
define gene family
a group of genes with related function
list the types of proteins and their functions
- hemoglobin carries oxygen
2.enzymes speed up chemical reactions - actin helps with muscle movements
what are the 3 structural differences between DNA and RNA
- RNA is made of ribose sugar DNA is made of deoxyribose
- RNA consists of one strand but DNA consists of 2
- RNA uses uracil and DNA used thymine
How does transcription occur?
RNA polymerases synthesize the mRNA version of the instructions stored in DNA
-only one strand of DNA is copied (the template strand)
as a region of DNA unwinds, one strand is used as a template for the RNA transcript to be made
-nucleoside triphosphate (NTPs) are used to produce an RNA transcript that is complementary to the template strand
which direction is DNA and RNA read and which direction is it made?
read from 3’-5’
synthesized in 5’-3’ direction
during transcription which direction is the strand growing in?
grows in the 5’-3’ direction
what happens during initiation
RNA polymerase and associated proteins bind to the DNA duplex at promoter sequence
what is the promoter sequence and where are they found
sequence that indicate where a gene starts and which DNA strand is the template strand
promoters are located upstream of the transcription start site
what bone holds DNA nucleotides together?
What bond holds amino acids together
phosphodiester bonds
peptide bonds
What is the name of the bond between amino acids? What type of bond is that? What is the name of the reaction that joins two amino?
peptide bonds are a type of covalent bonds
dehydration synthesis
what happens during elongation?
RNA polymerase opens up the DNA double helix, creating a transcription bubble.
The template strand is threaded through RNA polymerase active site
NTPs pair with complementary DNA bases, and polymerization begins
how are nucleotides added to the growing RNA polymer
RNA polymerase catalyzes the synthesis of phosphodiester bonds
What happens during termination? how is it different in prokaryotes and eukaryotes
RNA polymerase transcribe a transcription termination signal. In prokaryotes this codes for RNA that forms a hairpin structure. This causes the RNA polymerase to separate from the RNA transcript
In eukaryotes, a poly(A) signal is transcribed rather
than a hairpin, and the RNA downstream is cut.
what is the primary transcript and what is it needed for
RNA transcript that comes off the template DNA
-it contains information needed to direct the ribosome to produce proteins
what is mRNA
The RNA molecule that combines with the ribosomes to direct protein synthesis
true or false in prokaryotes primary transcript is the mRNA. Why?
true because both processes occur in the cytoplasm and the is no nuclear envelope to spatially separate transcription from translation
true or false in eukaryotes primary transcript is the mRNA. Why?
false because in eukaryotes there’s a barrier (the nuclear membrane) between transcription and translation.
The primary transcript goes through a complex process of chemical modification known as RNA processing
what are the 3 types of chemical modifications that occur before the mRNA is translated by the ribosome
- RNA splicing
- addition of a 5’ cap
- polyadenylation
what happens during RNA splicing
one modification of the primary transcript is the excision of a certain sequences known as introns leaving intact the exons
- about 90% of all human genes contain at least one intron
why does RNA splicing occur
splicing allows different mRNAs and proteins to be produced from one gene
one primary transcript can code for multiple proteins. which protein is formed depends on how the transcript is spliced
what is alternative RNA splicing
when from slicing which protein is formed depends on how the transcript is spliced
what is the 5’ cap that is added to primary RNA transcripts
a modified guanine nucleotide that enables ribosomes to bind and protect from degradation
what is the 3’ cap that is added to primary RNA transcripts
a 100-250 adenine nucleotides that is needed for translation and protects from degradation
what is the product after splicing and the addition of a cap and tail
a mature mRNA that contains untranslated regions at both ends
during transcription what is the template strand
provides a template for ordering the sequence of nucleotides in an RNA transcript
during translation the mRNA base triplets called ____ are read in the ___ to ___ direction
codons
5’ to 3’
each codon specifies which amino acid will be placed at the corresponding position along a polypeptide
what happens during translation?
in translation, the sequence of bases in an mRNA is decoded to synthesize the amino acid sequence in a protein. Ribosomes catalyze translation of the mRNA sequence into protein
tRNAs bind to amino acids and then transfer them to the growing polypeptide
how does translation occur in bacteria vs in eukaryotes
in bacteria, ribosomes often begin translating an mRNA before transcription is complete
in eukaryotes transcription and translation are separated. mRNAs are synthesized and processed in the nucleus.
Mature mRNAs are transported to the cytoplasm for translation by ribosomes
what is aminoacyl tRNA
a tRNA linked to its amino acid
describe the structure of tRNA
relatively short: 75-85 nucleotides long.
flattened into one plant to reveal its base pairing, a tRNA molecule looks like a cloverleaf.
because of hydrogen bonds, tRNA actually twists and folds into a 3 dimensional molecule
what is found at the 3’ end of a tRNA
a CCA sequence that is the binding sequence for amino acids
what is the bottom loop end of the tRNA
forms the anticodon which has a sequence of 3 nucleotides that can base pair with the mRNA codon
what is aminoacyl- tRNA synthetases
they “charge” the tRNA by catalyzing the addition of amino acids to tRNAs
ATP is needed to attatch tRNA to an amino acid
for each of the 20 amino acids: there is a different aminoacyl tRNA synthetase; there are one or more tRNAs
what is the wobble hypothesis
there are 61 codons but only about 40 tRNAs in most cells
this is because the anticodon of tRNAs can still bind successfully to a codon whose third position requires a nonstandard base pairing.
one tRNA is able to base pair with more than one type of codon
what are the 2 subunits that make up ribosomes?
the small subunit holds the mRNA in place
the large subunit is where the peptide bonds form
how many tRNAs can line up within the ribosome
3
what is required for the tRNAs to fit
tRNAs can only fit when its anticodon binds to the corresponding codon in the mRNA
what are the 3 sites that tRNAs can fir into in the ribosome
the A site is the acceptor site for an aminoacyl tRNA
The P site is the peptidyl site where the peptide bond forms
The E site is where tRNAs without amino acids exit the ribosome
what is the 3 step sequence that occurs in ribosomes to build a polypeptide
- an aminoacyl tRNA carrying the correct anticodon for the mRNA codon enters the A site
- a peptide bond forms between the amino acid on the A site tRNA and the polypeptide on the P site tRNA
- the ribosome moves down the mRNA by one codon and all 3 tRNAs move down one position
- the tRNA in the E site exits
-the A site is available for another tRNA to bind
the protein grows by one amino acid with each repeat of the 3 steps
amino acids are always added to the ___ end of the poly peptide
carboxyl / C- terminous
what are the 3 phases of translation
- initiation
- elongation
- termination
where does the initiation phase of translation begin.
What happens here?
What is this process mediated by?
begins near the AUG start codon
The small ribosomal subunit binds to the mRNA at the ribosome binding site
the process is mediated by initiation factors
what is the initiator tRNA
the first tRNA that carries a modified methylamine
what are the 3 steps of translation initiation in bacteria
- the mRNA binds to a small ribosomal subunit
2.the initiator tRNA bearing f-met binds to the start codon - the large subunit binds so that the initiator tRNA is in the P site
what happens at the start of elongation
the initiator tRNA is in the P site; the E and A sites are empty
an aminoacyl tRNA binds to the codon in the A site
the amino acid on the P-site tRNA is connected to the amino acid on the A site tRNA forming a peptide bond
what is translocation and what does it accomplish
Translocation occurs when the ribosome slides one codon toward the 3’ end of the mRNA
-elongation factors help move the ribosome
- the uncharged tRNA from the P site moves to the E site and is ejected from the ribosome
- the tRNA attached to the growing protein moves into the P site
- opens the A site to expose a new codon which is available to accept a new aminoacyl tRNA
dehydration reaction vs hydrolysis
dehydration synthesis build molecules and hydrolysis breaks them down and releases energy in the process
what happens during termination in the ribosome
termination occurs when the A site encounters a stope codon
a protein called a release factor enters the A site
at the end, the newly synthesized polypeptide, tRNAs and ribosomal subunits separate from the mRNA
describe release factors? What do they do
resemble tRNAs in size and shape, but don’t carry an amino acid.
They hydrolyze the bond linking the P-site tRNA to the polypeptide chain
what is the post-translational modifications
most proteins go through an extensive series of processing steps called post-translational modification before they are fully functional
folding determines proteins shape and function
what are molecular chaperones for
to speed protein folding
