Chapter 6: nucleic acid and protein synthesis Flashcards
what are examples of nucleic acid
DNA and RNA
what are nucleic acids
- polypeptides (monomer is a nucelotide)
- made up of C, H, O, N and P
- most complex and large molecules in living things
- form the hereditary genetic material
- the monomer of DNA and RNA
where are nucleic acids primarily found
in the nucleus
what are nucleic acids made up of
3 subunits that join up by condensation: sugar, phosphate and nitrogenous base
how are nucleotides linked to form nucleic acid (polynucleotides)
nucleotides are linked by condensation formed by phosphodiester bond
how are nucleotides linked to form nucleic acid (polynucleotides)
nucleotides are linked by condensation formed by phosphodiester bond
how are nucleotides linked to form nucleic acid (polynucleotides)
nucleotides are linked by condensation formed by phosphodiester bond
what is the sugar group of a nucleotide (see structure in notes)
pentose which can be
- ribose (OH group and used in RNA)
- (or) deoxyribose (H group and used in DNA)
what is the phosphate group of nucleotides
- PO4 (phosphate/phosphoric acid)
- negatively charged
what is the nitrogenous base of nucleotides
two types:
-purine bases (has 2 ring structure)
-pyrimidine bases (1 ring structure)
AGTUC
what are the purine bases
- adenine (A)
- guanine (G)
what are the pyrimidine bases
- thymine (T) only in DNA
- uracil (U) only in RNA
- cytosine (C)
what are the complementary base pairs
- C-G
- A-T in DNA
- A-U in RNA
what is the different between DNA and RNA
- RNA is single stranded
- DNA is double stranded and antiparallel
what are the types of RNA
- mRNA (codon)
- tRNA (anticodon)
- rRNA
what is the SP backbone in DNA structure
it is the 5’-3’ / 3’-5’ backbone of phosphate group bonded to sugar group
how are the complementary base pairs in dna sturcutre bonded
with hydrogen bonds
A-T is single hydrogen bond
C=G is double hydrogen bond
why are the complementary base pairs in dna bonded by hydrogen bonds
its a weak bond that is easily broken to expose the bases of both the polynucleotide chains for DNA replication or transcription
why are the complementary base pairs in dna bonded by hydrogen bonds
its a weak bond that is easily broken to expose the bases of both the polynucleotide chains for DNA replication or transcription
why must purine bases pair with pyrimidine bases
- the bases occupy the central position in DNA molecule
- purine (2 rings) must pair with pyrimidine (1 ring)
- so that the centre is spent by 3 rings’ width
- so that the 2 polynucleotide chains can be parallel
- allows DNA replication to occur by complementary base pairing
what happens if there is a wrong pairing of bases during DNA replication
mutation, a change in the base sequence of the DNA strands
what does the watson crick dna model state
DNA is made up of 2 long polynucleotide chain of antiparallel nucelotides in which opposite complementary bases pair up by hydrogen bonds to form a ladder-like construction which twists into the shape of a double helix
what does the double helix structure include
- double strands
- antiparallel
- complementary bases
- hydrogen bond
- ladder-like
- helix in shape
how does DNA replicate
- DNA is a double helix with two strands
- the two strands were capable of unwinding and separating from each other
- each strand will act as a template (act as a guide) during DNA replication (semi conservatively)
how did Meselson and stahl experiment prove dna replicates semiconservatively
emi-conservative replication was shown to be the method of replication by Meselson and Stahl in 1958. They used coli (a bacteria) and two nitrogen isotopes, a heavy form 15N and the ‘normal’ form 14N, to demonstrate how the density of DNA changes over generations as the 15N isotope was replaced with the 14N isotope
what does DNA replication require
Dna template, free DNA nucleotides and enzymes
what is a DNA template
double stranded DNA, each strand acts as a template
what are free DNA nucleotides
- 4 different dNTPs (deoxynucleoside triphosphate)
- 1 each for Adenine (dATP), Guanine (dGTP), Cytosine d(CTP), Thymine (dTTP)
- has 2 extra phosphate groups which are removed to releas energy to join the 2 nucleotides and form phosphodiester bond
which enzymes are used in dna replication
- helicase
- polymerase
- ligase
what does helicase do
- unwinds and unzips DNA double helix
- by breaking hydrogen bonds between complementary bases
- to form 2 straight chains (replication fork)
- using ATP
what does DNA polymerase do
runs along the DNA template strand and adds free DNA nucleotide one at a time by complementary base pairing
what does DNA ligase do
- will catalyse the joining of two nucleotides by phosphodiester bond
- links the nutrients/S-P backbones of both DNA fragments
what are the steps in the process of DNA replication
- DNA unzips
2. DNA replication
what are the 2 types of DNA replication
continuous and discontinuous replication
in which stage of cell division does DNA replication occur
interphase
what is the full process of DNA replication
The DNA double helix unwinds and ‘unzips’ as the hydrogen bonds between the bases break by helicase.
In the nucleus, there are nucleotides to which two extra phosphates have been added to activate the nucleotides, enabling them to take part in the reaction.
Each of the bases of the activated nucleotides pairs up with its complementary base on each of the old DNA strands, DNA polymerase ensures this and links adjacent nucleotides to each other by catalysing phosphodiester bonds. The two extra phosphates are broken off and released into the nucleus.
on the lagging strand, the replication occurs in fragments known as Okazaki fragments. All these fragments are joined together by DNA ligase.
what is the leading strand
it is synthesized continuosly in the 5’ -> 3’ direction by DNA polymerase
what is the lagging strand (with Okazaki fragments)
its synthesized discontinuously
-primase synthesizes a short RNA primer, which is extended by DNA polymerase to form an Okazaki fragment
what is gene expression
- gene expression is when a gene (DNA) is translated into a polypeptide
- based on central dogma
what happens in gene expression
- DNA codes for the synthesis of DNA and RNA (has thymine group)
- mRNA codes for the synthesis of polypeptides (has uracil group)
- polypeptide does not code for the synthesis of polypeptides, RNA or DNA
what are the steps in gene expression
- transcription
- processing
- transport to cytoplasm
- translation
- modification
what is a gene
a length (segment) of DNA
what is transcription (stage of gene expression)
copying from primary RNA transcript
what does the processing in gene expression
Mrna/trna/rrna
Which RNAs are transported to where?
- The rRNA is transported to the ribosomes
- the t RNA and m RNA (base sequences) are transported to the cytoplasm
What happens in translation (in gene expression)?
RNAs form polypeptide chains
How many polypeptide chains are there in 1 protein
I or more polypeptide chains
What happens in modification?
Polypeptide chains fold to form secondary/tertiary structure which then joins with other polypeptide chains to form quaternary structures and then complexes with non protein components (prosthethic group)
What are prosthetic groups
Proteins that form complexes with non- protein component
What is a gene
A gene is a length of DNA that codes for a specific polypeptide chain. each living cell carries the full set of gene.
What does a gene consist of?
A gene consists of a specific sequence of nucleotide (or bases)
What does a gene determine?
It determines the structural, physiological and biochemical characteristics of an organism
Why are genes different in each cell
In different cells, different genes are switched because different cells in the body take up different structures and functions
How is a specific sequence of bases on mRNA formed
When transcription of a specific sequences on a gene occurs by complementary base paining
How is a specific sequence of amino acids on a polypeptide formed?
By translation of a specific sequence of bases on mRNA
How is an amino acid formed
Triplet code joins with triplet codon (complementary base pairing)
What are the features of genetic code?
- triplet bases
- universal
- Degenerate
- punctuated
- non-overlapping
What is a triplet of bases
- triplet code for DNA
- Triplet codon for mRNA
- a triplet of bases on the dna/rna codes for one amino acid in a polypeptide chain
What is the triplet of bases for DNA called?
A triplet code
What is the triplet of bases for mRNA called?
Triplet codon
Why are triplet bases a feature of genetic code?
In order to form 20 amino acid groups with 4 bases, 3 possible arrangements of code are needed
Why is universal a feature of genetic code
The same triplet code codes for the same amino acids in all organisms except for a few triplet codes in mitochondrial DNA and ancient bacteria
Why is degenerate a feature of genetic code?
1 amino acid may be coded by more than 1 codon so that point mutation does not change the amino acid coded by it so that the amino acid sequence in the polypeptide chain will not change so that the tertiary structure of the protein will not change and the function is not affected
What is point mutation?
Change in the base sequence by only one base
Why is punctuated a feature of genetic code?
- has 1 start codon (translates to amino acids) Aug
- 3 stop codons ( does not translate to amino acids)
- the 3 stop codons are uag, uaa and uga
Why is non-overlapping a feature of genetic Cade?
Read 3 bases by 3 bases
What is transcription?
- synthesis of mRNA
- Mechanism by which the base sequence of a gene is converted into complementary base sequence of mRNA
What is the first step of transcription
DNA unzips at the beginning of a gene
What is the second step of transcription?
RNA polymerase uses DNA template strand/transcribed strand and adds RNA nucleotides by complementary base pairing 5’ -> 3’
What happens at the end of transcription?
RNA leaves the DNA at the end of the gene
What are the 3 types of RNA that are used in translation?
- messenger RNA (mRNA)
- ribosomal RNA (rRna)
- transfer RNA (trna)
What is messenger RNA?
- A transcript (copy) from the DNA template strand
- carries coded instructions from the nucleus to ribosomes to direct the synthesis of a polypeptide
- Carries triplet codons that code for amino-acid sequence in a polypeptide chain
- 3.5% of total cell RNA
What is ribosomal RNA?
- forms part of the ribosome structure
- makes up 80% of total cell RNA
- Base sequence is similar in all organisms
How are ribosomes formed and where
In nucleolus: rRNA + protein → ribosome
What is the role of ribosomes
Ribosomes are the site for protein synthesis and helps in locating tRNA onto mRNA for the efficient assembly of amino acids on the growing polypeptide chain.
What is transfer RNA?
- acts as specific amino acid carriers and transfers specific amino acids from cytoplasm to ribosome
- Different tRNA carries different amino acids based on the anticodon of the tRNA and uses its anticodon to translate the triplet codon on mRNA to amino acids on polypeptide
- small, made up of less than 100 nucleotides and makes up 15% of total cell RNA
- Around 60 types of tRNA in the cytoplasm, each having the same basic structure of 3 rings
How does tRNA carry a specific amino acid?
- tRNA anticodon forms complementary base pairings with mRNA codon to bring in the required amino acid to fit in the appropriate place on mRNA template
- type of amino acid carried depends on the anticodon
What is translation?
Translation is the mechanism by which the sequence of bases in mRNA is converted to a sequence of amino acid to form a polypeptide chain
What are the three steps in translation?
- Initiation
- Elongation
- Termination
How are multiple polypeptide chains formed at a time during translation?
Many polypeptide chains can be made at a time as many ribosomes move along the mRNA
What is an mRNA with many ribosome units called
Polyribosomes
What happens in the initiation stage of translation?
- ribosomes bind to the 1st start codon ( Aug) on mRNA
- 2 codons of mRNA are exposed in a ribosome
- met-trna (methionine carryingtrna) binds to the 1st triplet codon by complementary base pairing with its anticodon
How does met tRNA do complementary base paining in initiation?
- 1 codon in p-site (where the tRNA holds poly peptide chain)
- 1 codon in a-site (where the tRNA brings in new amino acid)
What happens in the elongation stage of translation?
- the 2nd triple codon in a-site is exposed to tRNA
- tRNA carrying the 2nd amino acid sits into A site by complementary base pairing between its anticodon with mRNA codon in A site
- Peptidyl transferase catalysts the formation of peptide bonds between the amino acids when they are side by side
- t RNA in p-site leaves the ribosome to pick up another specific amino acid from the cytoplasm
- the ribosome moves along the mRNA for distance of 1 triplet codon
- The next triplet codon is now exposed in a-site for the appropriate tRNA to bind in
- Specific sequence of amino acids is assembled as the ribosome moves along the mRNA
What happens in the termination stage of translation?
- When the ribosome encounters the stop codon, there is no amino acid to bind to it
- The completed polypeptide is released from the ribosome and mRNA
Why does gene mutation occur?
Gene mutation can occur due to mistakes during DNA replication or dna damages by mutagens/ radiations and misrepair
What is gene mutation?
A change in the base sequence of gene structure
What are the types of gene mutation
- Insertion (of extra codons)
- Deletion
- substitution (replacement)
- inversion
- duplication
How are the base sequences in DNA and RNA read during gene expression?
The base sequences in DNA and RNA is read during gene expression as 3 bases that codes for one amino acid, so every triplet code (in DNA) is considered as one reading frame
What is frame shift mutation?
- Frame shift/ reading frame shift/framing error occur when the grouping of the original 3 bases has changed
- Usually caused by insertions or deletions of a number of nucleotides /bases in a DNA sequence that is not divisible by 3
What is the effect of frame shift mutation?
- The frameshift mutation will also alter the first stop codon (uaa, uga or uga) encountered in the sequence
- the poly peptide being created could be abnormally short or long and will most likely not be functional
What are the immediate consequences of gene mutation if there is a degenerative codon?
Silent mutation: even after mutation the degenerative codon codes for the same amino acid so the intended protein is produced
What is the immediate consequence of gene mutation if there is no degenerative codon?
- Non - sense mutation i.e. Mutation leads to a stop codon being coded which leads to a short protein
- mis-sense mutation i.e. Mutation codes for different codons which leads to different proteins
What may genetic mutation lead to?
Mutation → different mRNA → different primary structure → different secondary/tertiary /quaternary structure → ineffective /non-functional protein → change in phenotype
What is an example of phenotypic mutation caused by frame shift mutation?
- sickle cell anaemia
- caused by substitution in gene coding for beta chain of haemo globin
- haemoglobins with 2 abnormal beta chains each will stick together to form long fibre when blood 02 level is Low
- bi concave red blood cell becomes sickle shaped
What are the consequences of sickle cell anaemia
- fibrous haemoglobin cannot carry o2 or co2
- block capillaries and small arteries
What does a centromere consist of
Repeated base sequence of DNA which are not transcribed
What are non coding DNA
- structural DNA in the centromere and telomere
What is a intron?
- a non coding nucleotide sequence found inbetween the exon (coding sequence of gene)
- Found only in eukaryotes
- transcribed by RNA
- subsequently removed by RNA splicing (cutting and joining) to leave a functional mRNA or other RNAs
What are the transcription regulators?
Promoter and operator
What does the promoter do in transcription regulation?
Upstream of the gene where RNA polymerase will bind to start transcription
What does the operator do in transcription regulation?
Segment of DNA that controls where RNA polymerase binds to the promoter and doesn’t bind
