Cr 5 - Molecular Biology Flashcards
2 types of living things
Non-Cellular & Cellular
Non cellular
Prions & viruses
Cellular
Prokaryotic & Eukaryotic
Necessary features of an organism
Movement
Respiration
Sensing stimuli
Growth
Reproduction
Excretion
Nutrition
Prokaryotes
Definition: Organism whose cells lack a nucleus and other organelles
Features:
- Nucleoid region
- No membrane bound organelles
- Generally smaller
- Smaller ribosomes
- Naked DNA
- Plasmid - small, circular double-stranded DNA molecule
Examples: Bacteria, Archaea
Eukaryotes
Definition: Organisms whose cells have a membrane bound nucleus.
Features:
- nucleus
- membrane bounds organelles
- generally larger
- larger ribosomes
- DNA associated with proteins
- no plasmid
Plant Cells
Features:
- Cell wall present
- chloroplasts present
- large central vacuole
- centrioles may be absent
- generally larger
Animal Cells
- Cell wall absent
- chloroplasts absent
- vacuoles small or absent
- centrioles present
- generally smaller
ORGANELLES - Mitochondria
Definitions:
Site of aerobic respiration
Site of ATP production (ATP is an energy source “currency” of the cells and is Adenosine Triphosphate)
ORGANELLES - Smooth & Rough ER.
Smooth ER:
Site of lipid and carbohydrate synthesis
Rough ER:
Site of protein synthesis
ORGANELLES - Nucleus
The nucleus contains the DNA and controls the activities of the cell
ORGANELLES - Golgi body (apparatus)
Site of processing / packaging of protein and lipid molecules, especially proteins to be exported from the cell.
ORGANELLES - Ribosomes
Site of protein synthesis
- Synthesise proteins in cells by linking amino acids together in the order specified by messenger RNA.
ORGANELLES - Cell Membrane
Controls entry and exit of substances in and out of the cell
ORGANELLES - Cell Wall
Provides structure and rigidity (plant cells only)
ORGANELLES - chloroplasts
Site of photosynthesis (plant cells only)
ORGANELLES - Vacuole
Storage of nutrients/water
Metabolism
The sum of all chemical reactions that occur in an organism.
ENZYMES
Function: Are able to speed up a reaction without being chemically altered.
Features:
- Are specific to particular substrates
- Are reversible
- Are only needed in small amounts
- Usually end in ‘ase’
- Are globular (spherical proteins)
- Have an active site to which the substrate binds
Substrate + Enzyme = Product + Enzyme
Substrate + Enzyme = ?
Product + Enzyme
ENZYMES - Catabolism
Substances are broken down
ENZYMES - Anabolism
Substances are built up
FACTORS EFFECTING ENZYME ACTIVITY - Temperature
*See physical card for reference graph
- Low temp = low kinetic energy. Less collisions, less enzyme-substrate complexes, decreased enzyme activity
- Increased temperatures = Increased kinetic energy. More collisions, more enzyme-substrate complexes, increased enzyme activity.
- Optimum temperature (Turning point)
- At too high temperatures, the enzyme denatures. i.e. the bonds of the active site break. This causes the shape of the active site to change so that it can no longer bind to substrates.
Because they are made of proteins (amino acids vibrate too vigorously, breaking the hydrogen bonds that hold the 3d structure together) the enzymes denature (break down).
FACTORS EFFECTING ENZYME ACTIVITY - pH
*See physical card for reference graph
1. Optimum pH (turning point)
- pH is too acidic: enzyme denatures due to an abundance of hydrogen ions which interact with the amino acids, changing the shape of the active site
- pH is too alkaline: enzyme denatures
Optimal pH depends on where the enzyme works in the body. i.e. pepsin works in the stomach (acidic)
https://www.youtube.com/watch?v=IoDEjeRZ0xE
FACTORS EFFECTING ENZYME ACTIVITY - Substrate concentration
As substrate concentration increases, enzyme activity will also increase.
- Low substrate concentration = free active sites
- Saturated substrate concentration = no active sites. i.e. they are all filled with substrate, causing the enzyme activity to plateau flat.
Graph roughly looks like this.
/────
No matter how much more substrate is added, there are no free active sites to increase the rate during the flat concentrations.
https://www.youtube.com/watch?v=5bIOwLlT3IA
INHIBITION - competitive
-Inhibitor is chemically similar to substrate
- Inhibitor binds to the active site (preventing substrate from binding to active site), therefore decreasing the number of enzyme-substrate complexes.
- However, an increased concentration of substrate, the effect of the inhibitor is reduced.
https://www.youtube.com/watch?v=jJUoQMLMV2E
INHIBITION - non-competitive
- Inhibitor is not chemically similar to substrate
- It binds to the allosteric site of the enzyme (not active site)
- Induces a conformational change as it changes the shape of the active site
- Substrate cannot bind which results in decreased enzyme activity.
https://www.youtube.com/watch?v=jJUoQMLMV2E
INHIBITION - information
Enzyme inhibitors can be beneficial in controlling biochemical pathways or they can be poisonous. Inhibitors can be both irreversible and reversible.
4 Biomolecules
- Proteins
- Lipids
- Carbohydrates
- Nucleic Acids
Cofactors (and coenzymes)
- Non-protein components of an enzyme.
- If the cofactor is organic, it is called a co-enzyme.
- Coenzymes are often vitamins, inorganic cofactors can be minerals.
- Cofactors & coenzymes may be permanent or temporary
- Cofactors & coenzymes often sit in the active site.
- Cofactors activate the enzyme
Apoenzyme
An inactive enzyme without the cofactor
Holoenzyme
Complete enzyme with cofactor
DNA (features)
- Double stranded
- 4 nitrogenous bases: adenine, thymine, cytosine, guanine
- Contains deoxyribose (sugar)
RNA (features)
- Single Stranded
- 4 nitrogenous bases
- Adenine, Cytosine, Guanine and Uracil
- Contains ribose (sugar)
Process of protein s___
Synthesis
DNA to mRNA
Transcription
mRNA to protein
Translation
Step one: Protein synthesis
DNA in the nucleus (not doing anything)
Step 2: Protein synthesis
DNA unwinds due to RNA polymerase, leaving exposed bases
Transcription bubble
Step 3: Protein synthesis
Free mRNA nucleotides form base pairs with ONE of the exposed strands
Step 4: Protein synthesis
The mRNA detaches, the DNA rewinds
Step 5: Protein synthesis
The pre-mRNA is spliced: the introns (intervening sequences) are removed and the exons (expressed sequences) are stitched together to form mature mRNA
Introns: Protein synthesis
Intervening Sequences: Sections of mRNA that do not code for a protein (are removed)
Exons: Protein synthesis
Expressed Sequences: Sections of mRNA that do code for a protein (are kept)
Step 6: Protein synthesis
The mature mRNA exits the nucleus through a nuclear pore. In the cytoplasm, it binds to a ribosome.
What is a ribosome made of
rRNA (ribosomal RNA)
Step 7: Protein synthesis
The mRNA binds to the small subunit of the ribosome
Step 8: Protein synthesis
In the cytoplasm, there are transfer RNA (tRNA) molecules which carry an amino acid at one end and have a corresponding anticodon.
Simplified: tRNA carries an amino acid at one end and a codon at the other, and the tRNA’s codon corresponds with the amino acid that a mRNA codon wants.
Example: If a codon in a chain was CUA, and its amino acid was amino acid X, a tRNA molecule would come and would have a codon of GAU and would have amino acid X on the other end.
Step 9: Protein synthesis
The tRNA with the amino acid that corresponds to the start codon will bind to the mRNA. A second tRNA binds to the second codon and a peptide bond forms between the two amino acids.
Step 10: Protein Synthesis
This process continues with two tRNA molecules in the ribosomes at a time, until the ‘stop’ codon is reached. The newly formed protein detaches.
True or False: The genetic code is universal
True
The genetic code is universal meaning…
All organisms use the same codons to encode amino acids and degenerate (multiple codons can encode a single amino acid)
Gene
A section of DNA that codes for a particular polypeptide
Codon
A triplet of nucleotide bases
Anticodon
A sequence of three nucleotides on a tRNA molecule that pairs with a complementary codon on mRNA during protein synthesis.
Functions of Proteins List
- Catalysis
- Immunity
- Transport
- Messaging
- Movement
- Structure
FUNCTIONS OF PROTEINS: Catalysis
Enzymes
FUNCTIONS OF PROTEINS: Immunity
Antibodies
FUNCTIONS OF PROTEINS: Transport
Throughout membrane/ across cell membrane
Example of a transport protein could be haemoglobin.
FUNCTIONS OF PROTEINS: Messaging
Hormones
FUNCTIONS OF PROTEINS: Movement
Muscle filaments
FUNCTIONS OF PROTEINS: Structure
Collagen, Keratin
Chlorophyll
photosynthetic pigment
Photo…
synthesis
Granum
a stack of thylakoid membrane
Thylakoid
membrane-bound compartments, with chlorophyll embedded in the membrane
Stroma
gel-like fluid, with lots of ribosomes
Photosynthesis Equation (words):
carbon dioxide +water (sunlight, chlorophyll) = glucose + oxygen
Photosynthesis Balanced Equation (Chemical)
6CO2 + 6H2O → (chlorophyll) C6H12O6 + 6O2
True or false - photosynthesis occurs in stages
true
Light dependant phase
- Takes place in the thylakoid membranes of the chloroplast.
- Requires light to excite electrons in chlorophyll.
- Splits water molecules (H₂O) to release electrons.
- Produces ATP and NADPH to power the Calvin Cycle.
- Byproduct: Oxygen (O₂) is released into the atmosphere.
Hydrogen produced in this step moves to the stroma and oxygen is released into the atmosphere. As the bonds holding water together are broken, the energy released is converted into energy carrier molecules (ATP, NADPH), which also move to the stroma to provide energy for the dark stage.
Light independent phase
Takes place in the stroma of the chloroplast.
Uses ATP and NADPH from the light-dependent phase.
Carbon dioxide (CO₂) is converted into glucose.
RuBisCO enzyme helps fix CO₂.
Does not require light directly.
Regenerates molecules to keep the cycle going.
The importance of Photosynthesis
- converts solar energy into chemical energy
- ‘fixes’ carbon, creating an organic molecule from an inorganic molecule
- produces oxygen
Factors effecting photosynthesis
- Water availability
- CO2 consumption/concentration
- Light intensity
- Temperature
- Light quality
What kinds of light does chlorophyll absorb best?
Blue followed by Red.
What kind of light does chlorophyll reflect?
Green light
Photosynthesis is most efficient in ….
Blue and red light
Main products of light dependent phase
ATP and NADPH
General understanding (TASC definition) of light and dark stages
Water is broken down, oxygen is emitted, then carbon dioxide is reduced and only glucose is produced.
Chemosynthesis.
The process by which some organisms, like bacteria, produce energy by using chemical reactions instead of sunlight, often using substances like hydrogen sulfide or methane.
Endosymbiosis
One living thing becomes incorporated into another (e.g. cyanobacteria into plant like organism, which later became cells with chloroplasts)
Cyanobacteria
- Prokaryotic micro-organisms.
- Cyanobacteria photosynthesise like plants and have similar requirements for sunlight, nutrients and carbon dioxide to grow and produce oxygen.
Glycolysis net yield of ATP
During glycolysis, a net gain of two ATP molecules are produced per glucose molecule, as four ATP molecules are produced in total, but two are used up in the initial steps of the process.
1 gene = ?
1 polypeptide
Genophore
Bacterial Chromosome (non-linear).
Silent mutation (mRNA)
Change in code that has no effect (e.g. third base change in threonine).
Initiation (transcription)
A section of DNA upstream from the gene called a PROMOTOR allows an enzyme called RNA polymerase to attach to the DNA at the “transcription bubble” (where the DNA has puffed open exposing the region to be transcribed). The start DNA triplet TAC is converted to AUG - the start codon - Transcription has begun.
T or F: Prokaryotes do not have introns
True
Gene expression
The process by which the information encoded in a gene is turned into a function. This mostly occurs via the transcription of RNA molecules that code for proteins or non-coding RNA molecules that serve other functions.
Gene Regulation
The process of controlling when, where, and how much a gene is expressed.It is a complex process that helps organisms respond to environmental changes.
Transcriptional Control
Regulates how much and whether a gene is transcribed into mRNA
Translational Control
Regulates how much and whether mRNA is translated into protein
Post-translational Control
Regulates whether a protein is active or inactive, and whether it is stable or degraded
Epigenetic Regulation
Modifies genes without changing the DNA or RNA sequence
Termination (translation)
- A stop codon on the mRNA (UAA, UAG or UGA) indicates that the synthesis process is concluded.
- When a ribosome matches a stop codon it releases from the mRNA, the polypeptide is also released and we have successfully gone from DNA to a protein.
Elongation (protein synthesis)
Elongation in Protein Synthesis is the stage of translation where amino acids are sequentially added to the growing polypeptide chain. It involves three main steps:
- Codon Recognition – A charged tRNA carrying an amino acid binds to the ribosome’s A site, matching its anticodon with the mRNA codon.
- Peptide Bond Formation – The ribosome catalyses a peptide bond between the new amino acid and the existing chain, transferring the chain to the tRNA in the A site.
- Translocation – The ribosome moves along the mRNA, shifting the tRNA from the A site to the P site, while the empty tRNA exits from the E site.
