chap 2- nucleic acids Flashcards
What are nucleic acids
biomacromolecules. They are like proteins and are essential for all forms of life and are found in all cells
what are biomacromolecules
bio- produced by organisms
macro- large
molecules- a group of atoms bonded together
What are the two types of nucleic acids
DNA and RNA
nucleic acids are polymers, what are their monomers?
nucleotides
What are polymers
large molecules made of a chain of monomers that are chemically bonded
What are monomers
the building blocks of polymers
What does a nucleotide consist of
a phosphate group, a 5- carbon pentose sugar, a nitrogen base
What are the nitrogen bases
A,G,C,T,U
Where is uracil found
only in RNA
What does uracil replace in RNA
thymine
What structure are purines
a 2 ring structure. one that is 6 membered the other is 5 membered
what structure are pyrimidines
they have a 6 membered ring
what are the purines
guanine and adenine
what are pyrimidines
cytosine, thymine, uracil
Why is there a base pairing rule
so that a smaller pyrimidine will pair with a larger purine. forming hydrogen bonds between them to ensure they have a fixed distance between them
what is a hydrogen bond
an attraction between a hydrogen atom and an electronegative atom of nitrogen, oxygen and fluorine.
what is the base pairing rule
A-T
C-G
what does condensation polymerization involve
the synthesis of a polymer and releases water as a byproduct
what is condensation polymerization
how nucleotides join to form nucleic acids
how does condensation polymerization work
the hydroxyl (OH) group on the 3’ end of sugar combines with hydrogen from hydroxyl group of the phosphate. creating H2O. holds monomers together
is DNA stable
Yes
What does DNA do
carry and pass on genetic information of organisms through generations
what do DNA molecules consist of
2 strands of nucleotide polymers wound around eachother
what does the order of DNA code determine
which products are synthesized
how do you label 3’ and 5’ carbons on DNA
count clockwise from oxygen at top of pentose sugar
What sugar does DNA have
deoxyribose sugar
What sugar does RNA have
ribose sugar
What is the antiparallel nature of DNA
one strand will run in the 5’ to 3’ direction with the carbon pointing upwards. the other stand will run 3’ to 5’ direction with the 5’ carbon pointing downwards.
what are histones
small proteins that DNA winds around
what are nucleosomes
consist of 8 histone proteins which coil DNA
what do nucleosomes do
fold up to form chromatin fiber which forms loops
what is the chromatin in a chromosome made up of
loops that are compressed folded and tightly coiled
What is the process gene expression for
the process which the info used to direct the assembly of a protein molecule
what is a gene
a small section of DNA that is a basic unit of heredity
what does gene regulation do
conserve energy and materials within a cell
for a gene to be expressed it needs to be:
transcribed, processed in the nucleus, translated in the cytoplasm with ribosomes help
what do upstream and downstream sections of DNA indicate
where transcription should begin and end
what is the structure of a gene
stop/start triplet sequences, promoter regions, exons and introns
what does the start triplet indicate
where transcription will begin
what does a stop triplet indicate
where transcription ends
where are promoter regions of a gene found
before start at the 5’ end of the site where RNA polymerase attaches ready to begin transcription
what are promoter regions
binding regions upstream of the gene where RNA polymerase can bind in order for transcription to occur
what are exons
regions of the gene that code for an amino acid and are usually expressed as proteins or RNA
what do exons make up when joined together
mature mRNA
what are introns
non-coding regions of a gene
when are introns taken out of mRNA
during RNA processing
What is protein synthesis
a smaller single stranded mRNA molecule is created through transcription so that a section of DNA can leave the nucleus
what is RNA structure
single stranded, ribose sugar, uracil,
what are the 3 types of RNA
mRNA, rRNA, tRNA
when/where are mRNA molecules formed
in the nucleus during transcription
what is mRNA responsible for
carrying a copy of the nucleotide sequence of DNA that specifies the amino acid sequence out of the nucleus to a ribosome where the message can be translated
what structure does tRNA have
folded structure
what does tRNA do
match an mRNA codon with the amino acid it codes for
where is rRNA synthesised
in the nucleolous
what does rRNA do
with help of proteins forms organelle ribosome
what do ribosomes do
where info in mRNA is translated into chain of amino acids which can then be folded into a protein
what is the template strand of DNA
RNA polymerase reads template strand during transcription so that mRNA is same as DNA coding strand but it has U instead of T
what does transcription do
make an RNA copy of the DNA code
what are the 3 steps of transcription
initiation, elongation, termination
what happens during initiation (transcription)
RNA polymerase attaches to promoter region and unwinds DNA strand by breaking hydrogen bonds that hold the 2 strands together exposing nitrogenous bases
What happens during elongation (transcription)
RNA Polymerase moves along template strand in 3’ to 5’ direction. free nucleotides are attached to their complimentary base pairs and as RNA P moves along strand mRNA is produced
at what end are nucleotides added
3’ end
what happens during termination (transcription)
when RNA polymerase reaches stop tiplet transcription ends. this releases chemicals that signals termination and the RNA polymerase detaches releasing the mRNA strand and allowing DNA to reform
what does the finished product of transcription carry
the same base sequence as coding strand of DNA except U instead of T
What does RNA processing do
turns pre-mRNA into mature mRNA which is ready to leave the nucleus.
what is step 1 of RNA processing
methyl cap added to 5’ end of pre-mRNA
what is step 2 of RNA processing
spliceosome removes introns from pre-mRNA strand and joins the exons together to make mature mRNA.
what is step 3 of RNA processing
poly-A-tail is added to 3’ end of mRNA molecule
what increases mRNA’s stability and prevents it from degrading
5’ methyl cap and 3’ poly-A-tail
what does a poly-A-tail consist of
a chain of up to 250 adenine nucleotides
What is alternative splicing
RNA processing, many ways to splice out the introns. results in different proteins arising from the same gene
what happens during translation
translating the message (mRNA) into a protein
what happens during inititation (translation)
small ribosomal subunit attaches to 5’ of a mature mRNA strand &moves along till it reaches start codon. tRNA molecule brings amino acid Met to mRNA &joins to mRNa start codon. large ribosomal subunit also attaches to tRNA & small ribosome subunit which allows 3 sites for the tRNA to bind
what happens during elongation (translation)
after Met has attached, another tRNA molecule with complimentary anticodon to next codon on the mRNA strand attaches by a peptide bond &adds its amino acid to the growing chain, ribosome releases tRNA molecule &moves further along mRNA strand &process repeats
what happens during termination (translation)
attachment of amino acids continues until stop codon is reached, & a release factor attaches. polypeptide chain is then released from ribosome into cytoplasm or ER.
What is ribosome A site
A site accepts incoming tRNA molecules with associated amino acid to match the anticodon that complementary pairs with the mRNA codon.
What is ribosome P site
P site where its associated amino acid is joined by peptide bonds into growing polypeptide chain
What is ribosome E site
E site is where tRNA molecules that have added their amino acids to the polypeptide chain move before they exit ribosome.
why is DNA considered universal
every known living organisms has genes make of DNA, and the 20 amino acids are the same in all organisms
what is the genetic code based off
triplets of nucleotides called codons which specify individual amino acids in a polypeptide or a stop signal
how many possible combinations of nucleotide sequences are there
64, 3 of which are stop codons
why is genetic code redundant/degenerate
as there is 61 codons but there are only 20 amino acids. some code for the same amino acid
what is the protein secretory pathway
1-nucleous (stores DNA, controls and regulates activities of cell)
2- Rough ER (production, folding, quality control and dispatch of proteins
3- Smooth ER (synthesis of lipids and steroid hormones)
4- Golgi (process/packages proteins and lipid molecules into vesicles to then be transported
what is exocytosis
the release of substances from inside to outside of the cell
how does exocytosis occur
fusion of vesicle membrane with plasma membrane
what is a protein
a type of biological polymer that has a diverse range of functions
what are proteins made of
amino acids, nitrogen, carbon, hydrogen and oxygen, some also contain sulphur & phosphate
motility protein function
allow movement of cells and their organelles
structural protein function
provide support, strength and protection
transport protein function
carry molecules from one location to another or across plasma membrane
cellular signaling protein function
signal between different cell types: stimulation or inhibition
cell-surface reception protein function
receive signals such as hormones and growth factors, transmission of nerve impulse
defense protein function
recognize and protect against foreign organisms
enzymes function
catalyze, or actively assist biochemical reactions
structure of amino acid
amino refers to NH2.
Acid refers to COOH
R group is part of molecule that varies and has a different chemical structure in different amino acids
what are polar amino acids
hydrophilic and tend to be on the surface of the protein
what are non-polar amino acids
hydrophobic and tend to fold away from the water molecules in the cell environment
what do the R groups of amino acids do
distinguish one amino acid from another and give them different chemical properties, some r groups make regions of the protein molecule polar or non-polar
how are the 9 essential amino acids obtained
from our diet
how are amino acids joined together
peptide bonds in condensation polymerization. The OH part of one amino acid joins with a H atom from the other amino acid
what does condensation polymerization produce
a growing polypeptide chain
what is the primary structure of a protein
linear sequence of amino acids in the polypeptide chain
what is the secondary structure of a protein
the coiling and folding of a protein chain
when is secondary structure deemed random coiling
when not alpha helices or beta pleated sheets
what are alpha helices
secondary structure. hydrogen bonds form between adjacent amine and carboxyl groups within the polypeptide chain causing it to coil and form a helical shape
what are beta pleated sheets
secondary structure, hydrogen bonds formed between amine and carboxyl parts of adjacent polypeptide chains causing the chains to fold back on each other
What is tertiary structure of a protein
the total irregular folding pattern of a protein forming a complex shape. now considered biologically functional as its a complex 3D shape
what is quaternary structure of a protein
two or more polypeptide chains interacting to form a single functioning protein
What are conjugated proteins
chains of amino acids join with other chemical groups. attached by covalent bonds or weak interactions
What is a proteome
the complex range of proteins produced by a single cell or organism in a particular environment
What is proteomics
the study of proteomes
what does denaturation do
results in the loss of function of a protein
are fully denatured proteins reversible
no
when is a protein said to be denatured
when the bonds that create the tertiary structure of the protein are broken and the shape of the protein is altered causing it to lose its function
what is a regulatory sequence capable of
increasing or decreasing the expression of specific genes within an organism.
what is the promoter region for
found before the start triplet on the 5’ end where RNA polymerase binds (determines site of transcription.
What is the enhance/silencer
region where transcription factors can bind
what does UTR stand for
Untranslated Region
Where is the UTR located
each side of a coding sequence, this section is transcribed not translated.
What is the 5’ UTR for
recognized by the ribosome allowing it to bind to it but not translate it.
What is the 3’UTR for
plays a role in polyadenylation adding poly-A-tail and terminating translation.
Where is the 5’UTR found
between promoter and start triplet where the gene is transcribed not translated.
do eukaryotes contain both exons and introns
yes
do prokaryotes have introns
No, which is why their translated mRNA doesn’t need to undergo RNA processing before its translated.
What is gene expression
where the info in a gene is used to synthesise a functional gene product such as a protein or RNA.
why is the info in a gene being expressed.
the info in a gene is being expressed in the form of the product that is produced.
What is gene regulation
the process that controls gene expression by determining which genes are switched on and which genes are switched off
why is gene regulation important
for efficiency as otherwise every protein would be produced regardless of whether the cell needs it or not.
What are structural genes
genes that code for proteins that become pat of the structure and functioning of an organism
What are regulatory genes
involved in controlling the expression of one or more other ones. turns genes on or off determining the rate in which their products are made.
what do regulatory genes
proteins that do not control other genes
how do regulatory genes work
code for transcription factors that control gene expression at the transcription stage.
how do transcription factors work
bind to DNA sequences close to the promoter region of a gene or to the RNA polymerase to activate or repress the expression of specific genes.
what are transcription factors
proteins or functional pieces of RNA
What is E.Coli
a simple prokaryotic bacteria
what happens if trp is unavailable to E.Coli
produces enzymes for trp synthesis, otherwise they aren’t produced.
What is an operon
a group of genes transcribed as a single unit from one promoter
Are operons found in both prokaryotes and eukaryotes
found in prokaryotes but not eukaryotes
which direction does the trp operon move
left to right (5’ to 3’)
What is trp R
a regulatory gene, upstream of the operon that codes for a transcription factor called trp repressor. Expressed all the time which is why the trp repressor is always present
what is the operater
short DNA segment that forms the binding site for a transcription factor
what is the leader
a sequence of nucleotide bases with regulatory activity
what is the attenuator
a mRNA transcription termination site made up of multiple uracil-adenine base pairs.
What are trp e,d,c,b,a
structural genes that code for the enzymes needed for the biosynthesis of trp.
What happens during transcription repression when tryptophan is present
binds to repressor protein & alters its shape, so that is repressor can bind to the operator. repressor then covers part of the promoter, preventing RNA polymerase from binding to promoter & blocking transcription of the structural genes in the operon.
are structural genes made/transcribed during transcription repression when tryptophan is present
No
What happens during transcription repression when tryptophan is absent
repressor protein is inactive, and cant bind to operator. RNA polymerase can bind to the promoter & transcribe the 5 genes into a mRNA transcript. This in turn is translated into 5 enzymes used in the synthesis of trp.
what is attentuation
the 2nd regulatory mechanism in the trp operon. reduces expressiom of the trp operon when the levels of trp are high. doesn’t block initiation of transcription, it prevents the completion of transcription.
what happens in attenuation when trp is present on tRNA molecules
1- ribosome reads mRNA strand & quickly passes through region 1 where the 2 trp codons are located.
2- ribosome stops when it reaches stop codon 1&2 of the leader.
3- as ribosome is partially covering region 2, allows regions 3/4 to form a hairpin via complimentary base pairing
4- hairpin classed as terminator as it puts pressure of attenuator & breaks the hydrogen bonds holding together A&U.
5- causes mRNA to break away from DNA being transcribed & the ribosome detaches. RNA polymerase also detaches from DN strand ending transcription. the structural genes of the trp operon are therefore not produced.
what happens in attenuation when trp is absent
1- ribosome stalls/pauses in region 1 waiting for trp molecules to be carried by tRNA.
2- allows regions 2&3 to form a hairpin via complementary base pairing
3- hairpin is known as anti-terminator as its further away from the attenuator region meaning that the mRNA does not pull away from DNA.
4- means that RNA polymerase can continue transcribing the structural genes of the operon into an mRNA strand and translation of the enzymes needed for synthesis of trp will proceed.
