Chapter 2 - Nucleic Acids and Proteins Flashcards
protein
a biomacromolecule made of amino acid chains folded into a 3D shape
polypeptide
a long chain of amino acids. Proteins can be made of one or many polypeptides
proteome
all the proteins that are
expressed by a cell or organism at a given time
enzyme
an organic molecule,
typically a protein, that catalyses (speeds up) specific reactions
peptide hormone
a protein signalling molecule that regulates
physiology or behaviour
antibody
a protein produced by
plasma cells during the adaptive immune response that is specific to an antigen and combats pathogens in a variety of ways. Also known as immunoglobulin
carboxyl group
the functional group on amino acid molecules that contains a hydroxyl group
(OH) and an oxygen
double-bonded to a carbon atom
amino group
the functional group on amino acid molecules that is made up of one nitrogen and two hydrogens (NH2)
R-group
the variable portion of an amino acid molecule. It can
be one of twenty variations and determines the identity of the amino acid
hydrophobic
having a tendency to repel and be insoluble in water
hydrophilic
having a tendency to be attracted to and dissolve in water
monomer
a molecule that is the smallest building block of a polymer
polymer
a large molecule that is made up of small, repeated monomer subunits
condensation reaction
a reaction where two monomers join to form a larger molecule, producing water as a by-product
peptide bond
the chemical bond linking two amino acids
primary structure
the first level of protein structure, which refers to the sequence of amino acids in a polypeptide chain
secondary structure
the level of protein structure where the amino acid chain forms either alpha-helices, beta-pleated sheets, or random coils
tertiary structure
the functional 3D shape of a polypeptide chain
quaternary structure
the level of protein structure where multiple polypeptide chains bond together, or other non-protein groups are added to form a fully functional protein
alpha helix
an organised coiled secondary structure of proteins
beta-pleated sheet
an organised folded secondary structure of proteins
disulphide bond
a strong covalent bond occurring between two sulphur atoms
random coil
an irregular secondary structure of proteins that is neither an alpha helix nor a beta-pleated sheet
prosthetic group
a non-protein group bound to a protein. For example, a vitamin or ion
nucleic acid
the class of macromolecule that includes DNA and RNA. All nucleic acids are polymers made out of nucleotide monomers
polymer
a large molecule that is made up of small, repeated monomer subunits
nucleotide
the monomer subunit of nucleic acids. Made up of a nitrogen-containing base, a five-carbon sugar molecule (ribose in RNA and deoxyribose in DNA), and a phosphate group
monomer
a molecule that is the smallest building block of a polymer
DNA (deoxyribonucleic acid)
a double-stranded nucleic acid chain made up of nucleotides. DNA carries the instructions for proteins which are required for cell and organism survival
RNA (ribonucleic acid)
a singlestranded nucleic acid chain made up of nucleotides. Includes mRNA, rRNA, and tRNA
phosphodiester bond
a strong covalent bond linking a five-carbon sugar to a phosphate group
condensation reaction
a reaction where two monomers join to form a larger molecule, producing water as a by-product
sugar-phosphate backbone
a strong covalently linked chain of five-carbon sugar molecules and phosphate groups in a nucleic acid chain
chromosome
a structure made of protein and nucleic acids that carries genetic information
gene
a section of DNA that carries the code to make a protein
genome
the complete set of DNA housed within an organism
antiparallel
a characteristic of DNA strands describing how each strand runs in an opposite direction to the other. One strand runs in a 3’ - 5’ direction and the other runs in a 5’ - 3’ direction
complementary base pairing
describes which nucleotides can form hydrogen bonds with each other. C pairs with G, A pairs with T (or U in RNA)
double helix
the structure of double-stranded DNA in the nucleus of eukaryotic cells, where each DNA strand wraps around a central axis
nuclear DNA
DNA that is located in the nucleus of a cell
messenger RNA (mRNA)
RNA molecules that are produced during transcription and carry genetic information from the nucleus to the ribosomes
transfer RNA (tRNA)
RNA that recognises specific
codons on the mRNA strand and adds the corresponding amino acid to the polypeptide chain during protein synthesis
ribosomal RNA (rRNA)
RNA that is a key structural component of ribosomes, which assemble proteins
transcription
the process whereby a sequence of DNA is used as a template to produce a complementary sequence of mRNA
translation
the process where an mRNA sequence is read to produce a corresponding amino acid sequence to build a polypeptide
genetic code
the set of rules by which information is encoded in genetic material
triplet
the sequence of three nucleotides in DNA coding for one amino acid
codon
the sequence of three nucleotides in mRNA coding for one amino acid
start codon
the sequence of three nucleotides in mRNA that signals the start of translation
stop codon
the sequence of three nucleotides in mRNA that signals the end of translation
promoter
the sequence of DNA to which RNA polymerase binds
RNA polymerase
the enzyme responsible for constructing a pre-mRNA sequence from a DNA sequence during transcription
enzyme
an organic molecule, typically a protein, that catalyses (speeds up) specific reactions
TATA box
a type of promoter region
introns
non-coding regions of DNA that do not code for proteins. They are spliced out during RNA processing (only found in eukaryotes)
exons
regions of DNA that code for proteins and are not spliced out during RNA processing
termination sequence
a sequence of DNA that signals the end of transcription
operator
a short region of DNA that interacts with repressor proteins to alter the transcription of an operon
repressor protein
a protein coded for by a regulatory gene that prevents gene expression by binding to its operator
gene expression
the process of reading the information stored within a gene to create a functional gene product, e.g.: a protein or non-coding strand of RNA
leader region
the segment of DNA or mRNA that immediately precedes the coding region. Also known as the leader segment or leader sequence
precursor messenger RNA
(pre-mRNA)
the immediate product of transcription of a DNA sequence. Requires modifications before it can undergo translation
transcription factor
proteins that bind to the promoter region and control the functioning of RNA polymerase
template strand
the strand of DNA transcribed by RNA polymerase to produce a complementary pre-mRNA strand
coding strand
the strand of DNA not transcribed by RNA polymerase, contains an identical sequence to the mRNA strand produced (except thymine is replaced with uracil in mRNA)
ribosome
an organelle made of rRNA and protein that is the site of protein synthesis. Can be free in the cytosol or attached to the rough endoplasmic reticulum
5’ methyl-G cap
a molecule added to the 5’ end of pre-mRNA during RNA processing
3’ poly-A tail
a chain of adenine nucleotides added to the 3’ end of pre-mRNA during RNA processing
splicing
process where introns are cut out of a pre-mRNA molecule, and exons are joined together
spliceosome
the enzyme that removes introns from the premRNA molecule and joins exons together during RNA processing
alternative splicing
the process where different exons may be spliced, resulting in a single gene producing multiple different mRNA strands
anticodon
the sequence of three nucleotides on a tRNA molecule that recognises a specific sequence of three nucleotides (codon) on an mRNA strand
peptide bond
the chemical bond linking two amino acids
condensation reaction
a reaction where two monomers join to form a larger molecule, producing water as a by-product
exocytosis
a type of bulk transport that moves large substances out of a cell
gene regulation
the control of gene expression, typically achieved by switching transcription on or off
structural gene
a segment of DNA that doesn’t code for regulatory proteins, but instead codes for proteins that play a role in the structure or function of a cell or organism
regulatory gene
a segment of DNA responsible for producing proteins that control the expression of other genes
repressor protein
a protein coded for by a regulatory gene that prevents gene expression by binding to its operator
activator protein
a protein coded for by a regulatory gene that increases gene expression
promoter
the sequence of DNA to which RNA polymerase binds
operator
a short region of DNA that interacts with repressor proteins to alter the transcription of an operon
operon
a cluster of linked genes that all share a common promoter and operator and are transcribed at the same time
trp operon
a series of genes within certain species of bacteria that encode for the production of the amino acid tryptophan (A low level of transcription and translation
of the trp operon will occur regardless of the regulation. This is important as it ensures
that a cell is never completely without tryptophan. Still, repression and attenuation are
critical for the cell to function efficiently.)
trp operon repression
mechanism for gene regulation within the trp operon whereby repressor proteins stop the initiation of transcription when tryptophan levels are high (tryptophan binds to repressor protein -> protein undergoes conformational change and is now complementary to the operator - binds - blocks RNA polymerase)
conformational change
a change in the three-dimensional shape of macromolecules such as proteins
trp operon attenuation
mechanism for gene regulation within the trp operon whereby the premature ceasing of translation stops transcription when tRNA-bound tryptophan levels are high - (When tryptophan levels are high in a cell (i.e. the cell does not want to waste energy
making more tryptophan), the process of attenuation works as follows (Figure 5):
1. The processes of transcription and translation of the trp operon begin and occur simultaneously.
2. The ribosome involved in translation arrives at the two tryptophan codons in a row (found in the leader region).
The tRNA-bound tryptophan that is present in the cell travels to the ribosome and is added to the protein that is being made by the ribosome.
3. This causes the mRNA molecule being read by the ribosome to fold in a specific way via hydrogen bonds and form a terminator hairpin loop (sections 3 and 4 bind as the ribosome is overlapping section 2).
4. The folding of the terminator hairpin loop causes the mRNA molecule to separate from the template DNA at the attenuator sequence.
5. RNA polymerase detaches from the DNA, causing transcription to stop before any
structural genes are transcribed. Without these structural genes, new tryptophan cannot be synthesised. )
(When tryptophan levels are low in a cell, the cell does not want the process of attenuation to occur - it wants more tryptophan to be made. In this situation, the process occurs differently:
1. The processes of transcription and translation of the trp operon begin and occur simultaneously.
2. The ribosome involved in translation arrives at the two tryptophan codons in a row. Due to there being no tRNA-bound tryptophan in the cell, when the ribosome involved in translation arrives at the attenuator sequence that codes for two tryptophan amino acids it pauses. Meanwhile, the RNA polymerase involved in transcription continues
along the DNA.
3. This causes the mRNA molecule to fold in a specific way via hydrogen bonds and form
an antiterminator hairpin loop (sections 2 and 3 bind).
4. The antiterminator hairpin loop does not cause the mRNA to separate from the template strand at the attenuator sequence.
5. RNA polymerase continues to read the DNA template strand, transcribing the structural genes for proteins involved in the synthesis of tryptophan and translation can continue.)
attenuator sequence
part of the leader region within the trp operon that allows for attenuation
terminator hairpin
a loop formed in mRNA in the presence of tryptophan that ceases transcription of the trp operon
antiterminator hairpin
a loop formed in mRNA when tryptophan is not present that ensures the transcription of the structural genes in the trp operon
vesicle
a small fluid-filled organelle enclosed in a phospholipid membrane that transports substances around the cell
bulk transport
a type of active transport that uses vesicles to move large molecules or groups of molecules into or out of the cell
active transport
the movement of molecules across a semipermeable membrane requiring an energy input
secretory products
the substances inside a vesicle that are being transported out of the cell
plasma membrane
the phospholipid bilayer with embedded proteins which separates the intracellular environment from the extracellular environment
rough endoplasmic reticulum (RER)
a membranous organelle shaped like a series of connected, flattened cylinders that folds and transports proteins via its attached ribosomes
Golgi apparatus
an organelle made of flattened sacs of membrane involved in modifying, sorting, and packaging proteins. Also known as the Golgi body or Golgi complex
mitochondrion (pl. mitochondria)
a double-membrane-bound
organelle that is the site of the second and third stages of aerobic cellular respiration
What prime end are nucleotides added
nucleotides can only be added to the 3’ end as that is what forms the bond with the next phosphate. The 5’ end is attached to the phosphate of that nucleotide.
Four properties of genetic code
- Universal - Unambiguous - Degenerate - Non-overlapping
Universal
Nearly all living organisms use the same codons to code for specific amino acids
Unambiguous
Each codon is only capable of coding for one specific amino acid. For example, the codon UUA only codes for the amino acid leucine.
Degenerate
While each codon only codes for one amino acid (unambiguous), each amino acid may be coded for by multiple different codons (degenerate). For example, both the codons UUA and UUG code for the amino acid leucine. This provides a degree of redundancy, where changes to the original DNA sequence through mutations may not necessarily lead to the insertion of a different amino acid.
Non-overlapping
Each triplet or codon is read independently, without overlapping from adjacent triplets or codons.
Steps of transcription:
INITIATION - To begin transcription, specific proteins called transcription factors bind to the promoter region to initiate transcription. With the help of transcription factors, RNA polymerase binds to the promoter region. This signals for the weak hydrogen bonds between the two strands of DNA to break, resulting in the bases of each strand being exposed and the DNA helix being unwound and unzipped. RNA polymerase is then able to start transcription.
ELONGATION - RNA polymerase moves along the template strand of DNA, reading the nucleotide sequence and uses free-floating complementary RNA nucleotides to produce a new single-stranded RNA molecule known as pre-mRNA. The pre-mRNA molecule is synthesised in a 5’ to 3’ direction, so new RNA nucleotides are added to the exposed 3’ end. This pre-mRNA strand has a complementary nucleotide sequence to the DNA template strand. The strand of DNA that is not read by RNA polymerase is called the coding strand. As the coding strand is also complementary to the template strand, the coding strand is identical to the pre-mRNA strand (except the pre-mRNA includes uracil instead of thymine).
TERMINATION - Transcription ends when RNA polymerase reaches the termination sequence of a gene, signalling the end of transcription. RNA polymerase then detaches, releasing the premRNA molecule and the DNA molecule winds up again into a double helix. The pre-mRNA molecule is then processed to become mRNA, carrying the message for protein synthesis from DNA in the nucleus to the ribosomes located in the cytosol or attached to the rough endoplasmic reticulum of the cell.
The VCAA does not assess transcription in terms of the initiation, elongation, and termination stages.
Instead, those three stages are simply a framework for memorising the process of transcription.
(((When asked to outline the process of transcription on past VCAA Biology exams (e.g. 2016 Section B Q6b, 2013 Section B Q6ai) the following points were required:
* DNA unwinds/unzips
* RNA polymerase catalyses transcription through the joining of complementary RNA nucleotides
* transcription of the DNA template strand into pre-mRNA occurs
* pre-mRNA is complementary to the DNA template strand
* in the pre-mRNA, adenine (A) pairs with uracil (U), not with thymine (T).)))
Steps of RNA processing / post-transcriptional modifications:
(only occurs in eukaryotic cells as prokaryotes don’t possess introns)
- The addition of a methyl-guanine cap (methyl-G cap) at the 5’ end and a chain of adenine nucleotides (poly-A tail) to the 3’ end serve to stabilise the mRNA molecule, preventing it from degrading and allowing it to bind to ribosomes during translation.
- SPLICING - a complex molecule known as a spliceosome removes the introns and splices the exons together
- ALTERNATIVE SPLICING - Exons may also be removed during the splicing process. A single pre-mRNA strand can produce many different mRNA molecules depending on which exons are spliced out or kept. (allows for a single gene to give rise to many different mRNA strands and code for many different proteins)
Steps in translation:
INITIATION - The 5’ end of the mRNA molecule binds to the ribosome (with helps from the methyl-G cap) and is read until the start codon (AUG) is recognised. Then, a tRNA molecule with a complementary anticodon (UAC) binds to the ribosome and delivers the amino acid methionine, signifying the commencement of translation.
ELONGATION - After the first amino acid is attached, the mRNA molecule is fed through the ribosome so that the next codon can be matched to its complementary tRNA anticodon. Then, complementary tRNA molecules deliver specific amino acids to the ribosome, which bind to adjacent amino acids with a peptide bond via a condensation reaction. The first tRNA molecule then leaves the ribosome and is free to pick up another amino acid, and the next mRNA codon is exposed for more tRNA-delivered amino acids to add to the growing amino acid chain.
TERMINATION - The reading of mRNA, delivery of amino acids by tRNA, and the linking of amino acids in the polypeptide chain continues until the ribosome reaches a stop codon on the mRNA molecule. The stop codon signals the end of translation as there are no corresponding tRNA molecules. The polypeptide chain is then released by the ribosome into the cytosol or endoplasmic reticulum.
(((The VCAA does not assess translation in terms of the initiation, elongation, and termination stages. When asked to outline the process of translation on past VCAA Biology exams (e.g. 2018 Section B Q1a, 2014 Section B Q7a), the following points were required:
* ribosome binds to and reads the mRNA molecule
* tRNA anticodons are complementary to the mRNA codons
* tRNA brings the corresponding amino acids to the ribosome
* adjacent amino acids are joined together into a polypeptide chain via a condensation reaction.)))
Functions of key organelles in the protein secretory pathway
- Ribosome - synthesises proteins
- Rough endoplasmic reticulum - folds and transports proteins (If a protein is destined to be secreted, the ribosome synthesising it is usually attached to the rough endoplasmic reticulum rather than being free in the cytosol. The environment inside the rough endoplasmic reticulum allows for the correct folding of the newly formed polypeptide chain before being passed to the Golgi apparatus.)
- Transport vesicle - transports proteins (A transport vesicle containing the protein buds off the rough endoplasmic reticulum and travels to the Golgi apparatus. The vesicle fuses with the Golgi membrane and releases the protein into its lumen.)
- Golgi apparatus - Modifies and packages proteins (Proteins can have chemical groups (e.g. sugar molecules) added or removed at the Golgi apparatus, where they are often packaged into secretory vesicles for export or released directly into the cytosol for use by the cell.)
- Secretory vesicle - transports proteins (Secretory vesicles containing proteins for export bud off the Golgi apparatus and travel through the cytoplasm, fusing with the plasma membrane. This releases the proteins contained from within, into the extracellular environment through the process of exocytosis.)
ESSENTIALLY - Proteins are produced at ribosomes, folded in the rough endoplasmic reticulum, transported via transport vesicles to the Golgi apparatus, where they are modified and packaged into secretory vesicles, and then subsequently exported from the cell via the process of exocytosis.
