Chapter 1: Nucleic Acids and Proteins Flashcards
Define proteins
- Proteins are molecules made up of amino acids
Describe the difference between polypeptides and proteins
- A polypeptide is a sequence of amino acids
- One polypeptide may need to join with another to have a function and, thus, be a protein
- A protein is a sequence of amino acids with a function
Define nucleic acids
- Nucleic acids are biomolecules found in all organisms
- There are two kinds of nucleic acids: DNA and RNA
- They provide information and are involved in protein synthesis
- All have a sugar-phosphate backbone (deoxyribose/ribose)
- They are polymers made up of monomers
Define nucleotide
- Nucloetides are the basic building blocks (monomers) of DNA and RNA consisting of a phosphate group, a base and a five-carbon sugar
- Adjacent nucleotides are held together by phosphodiester bonds
Draw and label the monomers of nucleic acids
- Diagram should include
- Phosphate
- Five-carbon sugar
- Nitrogenous base
State the DNA and RNA base pairings
-
DNA
- Adenine and thymine (straight letters)
- Cytosine and guanine (curved letters)
-
RNA
- Adenine and uracil (vowels)
- Cytosine and guanine (curved letters)
Compare DNA and RNA
-
DNA
- Contains deoxyribose sugar
- Contains adenine, cytosine, guanine and thymine
- Double stranded
- Deoxyribose-phosphate backbone
-
RNA
- Contains ribose sugar
- Contains adenine, cytosine, guanine and uracil
- Single stranded
- Ribose-phosphate backbone
NOTE: The sugar in RNA contains one additional oxygen atom, compared to deoxyribose.
State the function and location of the three main forms of RNA
-
Messenger RNA (mRNA) carries genetic material in DNA from the nucleus to ribosomes
- Located in the nucleus
-
Ribosomal RNA (rRNA) work with other proteins to make ribosomes found in the cytosol
- Located in the ribosomes
- rRNA and its associated proteins create a binding site for mRNA in translation
-
Transfer RNA (tRNA) carries amino acids to ribosomes to be used for translation
- Located in the cytoplasm
- Anticodon on tRNA binds to complementary codon on mRNA
Draw and label a eukaryotic gene
- Diagram should include
- Flanking regions
- Coding region
- Upstream and downstream
- Direction of transcription
Describe the difference between introns and exons
- Introns interfere → do not provide the code for amino acids
- Exons are expressed → provide the code for amino acids
Define operator
- The operator is a region in an operon that provides a binding site for a repressor (to stop transcription)
Define gene regulation
- Gene regulation is the process of turning genes on and off
Define and provide examples of structural genes
- Structural genes are genes that code for proteins that contribute to the structure or functioning of an organism
- E.g. Keratin and collagen
Define and provide examples of regulatory genes
- Regulatory genes code for proteins that control the activity/expression of other genes (transcription factors)
- Produce factors that alter the expression of a gene
- E.g. Repressor proteins
Describe 2 ways that regulatory genes work
- Regulatory genes can work directly by producing DNA binding proteins
- These proteins bind to a region of DNA to directly turn genes on or off
- They can also work indirectly by producing signalling proteins
- These proteins trigger reactions that lead to a gene being turned on or off
Explain the importance of gene regulation
- Organisms can conserve energy and resources
- Enables organisms to adapt to changing conditions by making substances when none are available from the environment
- Allows for the expression of appropriate genes at suitable times
Draw and label a prokaryotic gene structure
- Diagram should include
- Regulatory gene
- Operon consisting of a promoter, operator, leader and structural genes
Define operon
- A cluster of structural genes in bacteria controlled by the same promoter and, thus, operates as a coordinated unit
Define tryptophan
- Tryptophan is an amino acid that is used to make proteins
- E-coli ingests it from surroundings or produces it when required
Define trp operon
- A cluster of genes in bacteria that code for the enzymes needed in the production of tryptophan
Describe the difference between repression and attenuation
-
Repression is a form of gene regulation that occurs prior to transcription
- It involves a repressor binding to the operator
-
Attenuation is a form of gene regulation that occurs during transcription
- It involves the formation of hairpin loops in the leader region
Outline the process of repression when tryptophan is present
- Tryptophan binds to the repressor protein causing changes in its shape which allows it to be active
- This allows the repressor to bind to the operator
- RNA polymerase cannot bind to the promoter and transcription does not occur
- Thus, the operon is off
NOTE: The repressor in its active form is bound to two tryptophans.
Outline the process of repression when tryptophan is absent
- The repressor is inactive and does not bind to the operator
- This allows RNA polymerase to bind to the promotor and initiate transcription
- Thus, the operon is on
Outline the process of attenuation when tryptophan is present
- The leader region is translated quickly
- This allows for the production of the termination hairpin loop
- The terminator hairpin loop causes RNA polymerase to detach from the DNA
- Transcription is stopped and the structural genes in the trp operon are not transcribed or translated
NOTE: The active tryptophan repressor that blocks RNA polymerases access to the operator and the downstream structural genes is not 100% effective. It will occasionally disconnect and allow RNA polymerase to transcribe the structural genes and therefore produce tryptophan. To overcome this, the LEADER SECTION (trp L) AND ATTENUATORS (hair pin folds) are used.
Outline the process of attenuation when tryptophan is absent
- The leader region is translated slowly
- The terminator hairpin loop cannot form and an antiterminator hairpin forms instead
- RNA polymerase remains attached to the trp operon
- Transcription and translation of the trp operon continues and the proteins from the structural genes are produced
State an advantage and disadvantage of using an operon
-
Advantage
- Operons allow protein synthesis to be controlled in response to the needs of a cell
- By producing proteins only when they are required, the cell can conserve energy and resources
-
Disadvantage
- Should mutations occur (in the regulatory genes, promoter, operator or leader regions), none of the genes will be expressed leading to cell death
State 3 examples of proteins and what they do
- ATP synthase is an enzyme that catalyses reactions
- Collagen is a structural protein that supports tissue in skin
- Insulin is a peptide hormone that regulates blood glucose
Define proteome
- A proteome is a complete set of proteins produced by a single cell or organism in a particular environment
Define gene
- A section of DNA that codes for a protein
Define the 3 important features of the genetic code
- Degenerate/redundant → more than one sequence of nucleotides (triplet of bases) can code for the same amino acid
- Universal → genetic code is the same in bacteria, plants and animals
- Unambiguous → the same codon will always code for the same amino acid
Define gene expression
- Gene expression is the the process by which the information from a gene is turned into a functional product such as a protein
List the steps of gene expression
-
Transcription (DNA to pre-mRNA)
- Transcription is the process in which genetic instructions from DNA are copied into a form that is able to leave the nucleus, known as messenger RNA (mRNA)
-
RNA processing (pre-mRNA to mRNA)
- RNA processing, also known as post-transcription modification, is the process that occurs after transcription in which pre-mRNA is altered to become mature mRNA
-
Translation (mRNA to protein)
- Translation is the process in which the mRNA is translated into a protein chain by the addition of corresponding amino acids
NOTE: In eukrayotes, transcription occurs in the nucleus while translation occurs in the cytoplasm. In prokaryotes, transcription and translation occur simultaneously within the cytoplasm.
Outline the steps in transcription
- RNA polymerase binds to a promoter sequence of DNA in the upstream region of the template strand
- The double stranded DNA unwinds and exposes the bases of the template strand
- RNA polymerase reads the template strand
- RNA polymerase moves along the DNA strand in a 3’ (downstream) to 5’ (upstream) direction adding complementary nucleotides to form an RNA chain
- When RNA polymerase moves past the coding region and has reached the downstream region of the gene, transcription stops and pre-mRNA is released
NOTE: The template strand is also known as the non-coding strand. The other strand is called the coding strand, because its sequence is the same as the resultant RNA sequence (with the exception of U replacing T).
State the transcription base pairings
- There is no thymine in mRNA
- A and U
- T and A
- C and G
- G and C
Outline the steps in RNA processing (CAS)
- Capping → a methyl cap is added to 5’ end of the pre-mRNA
- Adding a tail → poly A tail is added to the 3’ end of the pre-mRNA
- Splicing → introns are removed and exons are spliced together
State the importance of RNA processing
- Capping the 5’ end and adding a poly-A tail on 3’ end prevents mRNA from being damaged or broken as it moves out of the nucleus
- Splicing involves the removal of introns which allows for all genes to be expressed
- Errors in RNA processing can lead to different proteins being produced in translation
Outline the steps in translation
- mRNA leaves nucleus and enters a ribosome where it is read in groups of three (codons)
- Amino acids are carried to the ribosome by tRNA molecules (each tRNA molecules has an anticodon at one end)
- Each codon on mRNA is complementary to an anti-codon found on tRNA molecules
- The ribosome moves along the mRNA and tRNA molecules to deliver amino acids that are then joined by peptide bonds
- A STOP codon is reached and the polypeptide is released from the ribosome
NOTE: The translation start codon is commonly AUG which is translated into the amino acid Met. The stop codon does not produce an amino acid. Therefore, 100 codons will be translated into 99 amino acids.
State the base pairings between codons and anticodons
- A and U
- U and A
- C and G
- G and C
Determine the difference between triplets, codons and anticodons
- A triplet is a group of 3 nucleotide bases in DNA
- Codons are in mRNA and anticodons are in tRNA
Describe how a gene codes for the correct number and sequence of amino acids
- DNA is read in groups of 3 nucleotides giving specificity to the order of amino acids (sequence) in the protein
- Translation begins at the start codon and ends at the stop codon
- The number of codons between the start and stop codons determine the correct number of amino acids to be coded for
Explain how the expression of a single gene can lead to the production of different proteins
- Post-transcriptional modification(s) of pre-mRNA
- Alternative splicing (exon shuffling) whereby exons are rearranged to have different orders
- Post-translational changes to the protein such as alternative folding in the golgi apparatus
- Different nucleotide or mRNA sequences code for different proteins
- These processes result in different mRNA sequences or different folds in the sequences that allow the same piece of genetic material to produce a variety of proteins
Define and outline the structure of amino acids
- Amino acids are monomers of proteins
- They vary only in their R-group
- The R-group determines the chemical properties of the amino acid (e.g. hydrophobic, hydrophilic, positively charged or negatively charged)
- Amino and carboxyl group remains the same
Describe condensation polymerisation
- Condensation polymerisation is the process in which amino acids join to make a polypeptide chain and water is released
- Condensation refers to the release of water
- Polymerisation refers to monomers combining to form a polymer
- Water is an output and energy is an input
- Carboxyl groups bind with the amino group (OH of carboxyl group joins with H of the amino group to form water)
Define and provide examples of polymer
- Polymers are large molecules made up of small monomers
- Proteins (polymers) are made up of amino acids (monomers)
- DNA (polymer) is composed of nucleotides (monomers)
Describe the primary structure of a protein
- The primary structure is a linear sequence of amino acids joined together via peptide bonds
Describe the secondary structure of a protein
- The secondary structure is where three different folds can occur in amino acid chains; alpha helices (spiral shape), beta-pleated sheets (folded or represented as arrows) and random coils
- Alpha helices form due to hydrogen bonding between the peptide backbones of the polypeptide chain
- Beta pleated sheets result from hydrogen bonding between peptide strands that run alongside each other
- Random coils appear due to irregular or non-repetitive hydrogen bonding patterns
Describe the tertiary structure of a protein
- The tertiary structure is the 3D shape of a protein, involving further folding of the secondary structure
- Proteins become functional at this level
- E.g. Fibrous enzymes and hormones
Describe the quaternary structure of a protein
- Quaternary structures are made up of two or more polypeptide chains
- E.g. Haemoglobin, antibodies
State why the shape of a protein is important to its function
- A protein’s structure is important because it allows it to perform a particular function
State the importance of the primary structure of a protein
- The primary structure of a protein is important because it influences the way that the polypeptide folds
State (in order) the role of the organelles involved in the protein secretory pathway
- The nucleus stores genetic material and synthesises mRNA
- The rough ER contains ribosomes that synthesises protein (via the mRNA code) which it then folds and modifies
- Transport vesicles move resultant proteins from the rough ER to the golgi apparatus
- The golgi apparatus further modifies and packages proteins into secretory vesicles
- Secretory vesicles take the proteins to the plasma membrane
- The plasma membrane fuses with secretory vesicles allowing them to expel the proteins via exocytosis
TIP TO REMEMBER: Never Really Trust Grumpy Singing Penguins.
Explain the likely impact of a nonsense mutation in the regulatory region of the trp operon
- A nonsense mutation occurs as a result of a point mutation that produces a STOP codon
- This can result in a shortened, non-functional protein (repressor)
- The repressor does not bind to the operator
- The impact of this would be the continuous production of the amino acid tryptophan
NOTE: The repressor protein is sysnthesised by the regulatory region.
Leader region
- The 5’ untranslated region between the promoter and operon genes
