Module 1 Flashcards
What are the properties of living organisms
Order
Energy Processing
Sensitivity or response to stimuli
Reproduction
Growth and Development
Regulation/Homeostasis
Adaptation
Evolution
What is order?
Life is cell based, with a complex organisation which all works together to form life
What is energy processing
Capture energy from sun or other sources and convert it into chemical energy in food or use chemical energy from food
What is sensitivity or response to stimuli
Responding to stimuli such as touch or sun (for plants)
What is reproduction
Transferring DNA (from parental to daughter cells)
What is regulation/homeostasis
The set of internal conditions maintained by living things despite a changing environment
What is adaptation
Allows organisms to survive better in their environment by changing their behaviours are features to adapt to environment
What is the main difference between a eukaryote and a prokaryote
Eukaryotes have a defined nucleus where the DNA is kept, whereas prokaryotes don’t have a defined nucleus
What is an important element for life?
Carbon.
Life is carbon based. Carbon can bond with itself and other elements in different ways
All major biopolymers have a carbon backbone
However, there are some other useful elements such as Hydrogen, Nitrogen, Oxygen, Phosphorous and Sulfur which are important to life
Describe the hydrophobicity and polarity of C
C is neutral and non-polar/hydrophobic
Describe the hydrophobicity/polarity of O, N, P and sometimes S
They make compounds polar/hydrophillic, partly (dipoles) or fully charged
What does polar mean
It is a molecule with a charge on one side of the molecule
What does hydrophillic mean
It means that a molecule ‘loves water’, and have a tendency to mix and dissolve in water
What does non-polar mean?
there are no positive or negative poles formed in the molecule. The charges are equally distributed across a molecule
What does hydrophobic mean?
It means that a molecule ‘hates water’, and thus doesn’t have a tendency to mix
I.e. oil
What are the main building blocks of life
Water, carbohydrates (sugars), lipids, amino acids and nucleic acids
Explain the importance of water as a building block of life
We are ~62% water. It is a good solvent of polar molecules
Water helps stabilise body temp (good evaporative cooling, buffers temp change as freezing water releases energy and melting water absorbs it)
Ice floats (layers of ice can insulate water underneath / floating platforms)
Explain the composition of carbohydrates/sugars
Composed of C, H, O with the general formula C(n) (H2O) (n), where n is the no. of carbon atoms
Lots of ‘O’ means a very polar molecule
What is the function of carbohydrates/sugars?
Sugar polymers play an important role in life.
Starch - storage
Chitin - protection
Cellulose - structure
Bacterial cell walls/surrounding coats
What are lipids, and what do they do
Lipids are fatty compounds that perform a variety of functions in your body. They consist of a vast set of molecules, such as fats, oils, waxes, steroids. However, they are poorly soluble in water, whereas they are normally soluble in organic solvents
They’re part of your cell membranes and help control what goes in and out of your cells. They help with moving and storing energy, absorbing vitamins and making hormones.
They can act as energy stores, signal molecules, protect and act as waterproofing, and also function as structures/barriers (i.e. phospholipids barriers)
What are saturated lipids vs unsaturated lipids
saturated = all single bonds
unsaturated = one or more double bonds
Explain what a nucleic acid is and what it does
Nucleic acids are normally made up of nucleotides. These contain a phosphate group (negatively charged), and a nucleobase (A,C,T,G,U)
Their function is for genetic information storage (DNA), protein synthesis (RNA), and has regulatory functions.
What are biopolymers
polymers are made up of the same repeating units. Biopolymers are unique as they contain information unlike normal polymers.
Examples include DNA, RNA and proteins
What is the conventions of direction/ends of proteins
Proteins have an N terminus and C terminus. the N terminus is an amino acid group (and is basic). The C terminus is a carbonyl group (and is acidic)
The N terminus is the start of the protein, whereas the C terminus is the end of the protein
So gaps in protein are filled with anything as long as it goes from N terminus to C terminus
What is the conventions of direction/ends of nucleic acids
Here, they have a 5’ (5 prime), and a 3’ (3 prime) end.
Nucleic acid sequences are conventionally named from the 5’ end to the 3’ end
In this case, the 5’ is the start of the nucleic acid, and the 3’ is the end
What are the common features of nucleic acid polymers (DNA/RNA)/ what are the chemical components
Involves nucleotide building blocks (phosphate, sugar, base/nucleobases)
Common phosphate sugar backbone (sugars and phosphates are hydrophillic, and the phosphate is negatively charged)
5’ and 3’ ends
What are the common features of proteins/peptides?/ what are the chemical components?
Amino acid building blocks
Common peptide backbone (N-C-C)
Sidechains (R) of different amino acids are also different
Peptides if short have <50 amino acid residues, but long ones have >50 residues (but no strict definition
What is the difference between DNA and RNA
In RNA, the amino acid “thymine” doesn’t exist, instead there is only “uracil” (It becomes an A-U bond instead of an A-T bond in RNA compared to DNA)
Also, the chemical structure of RNA is that it has an OH at the bottom, whereas there is only an H at the bottom of DNA
DNA consists of two strands in a double helix, however, RNA only has one strand - both made up of nucleotides
Explain the properties of sugar phosphate backbone which is essential in nucleic acids
The backbone is composed of alternating sugar and phosphate groups, which form covalent phosphodiester bonds between the 3’ carbon of one sugar and the 5’ carbon of the next. This strong bond structure provides high stability, allowing nucleic acids to withstand various cellular conditions without breaking down easily.
The phosphate groups in the backbone carry a negative charge, which helps prevent the nucleic acids from folding into tight coils by repelling each other.
The backbone’s sugar and phosphate groups are hydrophilic (water-loving), making the exterior of the DNA double helix water-soluble. This property allows DNA to interact with the aqueous cellular environment and various proteins and enzymes.
Describe the repeating units in proteins
Proteins are made up of repeating units called amino acids, which connect in a linear chain to form a polypeptide. Each amino acid consists of two main parts: the backbone and the side chain (or R group). Together, these components give proteins their unique properties and functions.
The backbone of the protein has an amino group on the N terminus, which bonds to an alpha carbon (central carbon atom), which serves as a place for bonding to a side chain (R group). This also bonds to a carboxyl group (-COOH) at the end of the protein
How do peptide bonds forms?
Two amino acids react by condensation to form a dipeptide. This is energetically unfavourable, so it doesn’t happen spontaneously
Describe the sidechains in proteins (amino acids)
They have varied properties such as:
Size/shape, hydrophobicity, change, aromaticity, polarity, redox sensitivity, hydrogen bonding potential, flexibility
A small peptide combines various amino acid subgroups and thus combines many different properties such as the ones above. These all have different effects
Describe how the physical and chemical properties of proteins and nucleic acids can be exploited in
experimental situations
We can monitor the purity of DNA samples by checking ratios of absorbance values for likely contaminating molecules through A260 and A280
What can a A260:A280 ratio tell us
1.8-20 = pure dna
<1.8 = protein contamination
> 1.8 = RNA contamination
What can a A260:A230 ratio tell us?
> 1.8 = pure nucleic acid
<1.8 = Organic compounds
Is DNA a source of genetic information
Yes
What are the nucleobases used in DNA and RNA
DNA: Adenine (A), cytosine (C), guanine (G), Thymine (T)
RNA: Adenine (A), cytosine (C), guanine (G), Uracil (U)
What are the base pairings
A with T (DNA)
A with U (RNA)
C with G (DNA and RNA)
Is the number of A equal to something?
number of A is equal to number of T
Number of c is equal to number of G
Is A-T or C-G stronger?
C and G have 3 hydrogen bonds between them –> stronger binding
Compared to A and T/U which have 2 hydrogen bonds between them –> weaker binding
Thus, the G/C base pairing is stronger than the A/T(U) base pairing in nucleic acids
Describe the double helical structure of DNA
Strands run in opposite directions. Negative phosphates repel each other –> DNA spreads out
Major and minor grooves are present
Right handed double helix (twists clockwise when viewed from the top)
DNA has a right-handed double-helix shape, with two strands twisted around each other. The structure consists of a sugar-phosphate backbone on the outside and complementary base pairs (A-T and G-C) on the inside, held together by hydrogen bonds. The twisting creates major and minor grooves, which allow proteins to interact with the DNA for processes like gene regulation. This stable yet flexible structure is crucial for DNA’s role in storing genetic information.
What is the difference between major and minor grooves
Major Groove: This groove is wider and deeper, occurring where the backbones of the two DNA strands are further apart. It exposes a larger portion of the nitrogenous bases.
Minor Groove: This groove is narrower and shallower, occurring where the backbones are closer together. It exposes less of the nitrogenous bases.
Distinguish DNA from RNA in terms of structure and stability
DNA has a H at the bottom, whilst RNA has an OH at the bottom. DNA lacks an O which is present in RNA
DNA is also double stranded, whilst RNA is single stranded
DNA has A,C,T,G whilst RNA has A,C,U,G
RNA is less stable than DNA (because it has an OH group, which makes for more chemistry happening at OH, making it more susceptible to degradation/breakdown )
What is the central dogma of molecular biology
The central dogma of molecular biology is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.
We can’t go direct from DNA to protein - it has to go through RNA
We also can’t go back from protein to RNA
What are the key components of the central dogma?
The genome (the DNA)
The transcriptome (the RNA)
The proteome (the protein)
How does information flow between DNA, RNA and proteins?
The DNA undergoes transcription into RNA, and that in turn undergoes translation to form proteins (which are amino acids)
What is the genome
The genome is the complete set of genetic material in an organism, encompassing all of its DNA, including coding regions (genes) and non-coding sequences.
What is the transcriptome
The transcriptome refers to the complete set of RNA transcripts produced from the genome at a specific time or under specific conditions.
It includes all types of RNA, such as messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and non-coding RNAs (like microRNAs).
The transcriptome reflects gene expression, indicating which genes are actively transcribed into RNA in a given cell type, tissue, or developmental stage, thereby providing insight into the functional state of the cell.
What is the proteome
The proteome is the entire set of proteins that are expressed and modified in a particular cell, tissue, or organism at a given time.
It encompasses not only the proteins encoded by the genes in the genome but also variations due to post-translational modifications (e.g., phosphorylation, glycosylation) that affect protein function and activity.
Ultimately, it is all proteins expressed from the transcriptome, including their modifications
For example, they include ion channels, receptors, antibodies, enzymes etc
What is the difference in size and construction between bacterial and eukaryotic genomes?
Most bacteria (and prokaryotes) have circular chromosomes. They also tend to be relatively small. They are singular, circular chromosomes
However, eukaryotes have big genomes (multiple, linear chromosomes, condensed into chromatin and wrapped around histone proteins)
Describe features of the human genome
Eukaryotic and linear
Encodes ~20 000 proteins
6 billion base pairs
22 pairs of chromosomes (plus sex chromosomes)
What does mRNA do?
It is the messenger for making proteins.
It often makes multiple copies, and is designed to be used then degraded. It allows for cytosine deanimation to uracil
Degradation via the ribose
OK to be less stable than DNA. mRNA production rates vary
What are proteins
They are determined by a specific amino acid sequences which determines structure, and also the function
Proteins make up 50% of cell by dry weight, and give the cell its shape by forming receptors, enzymes, hormones, growth factors etc.
What is the universal genetic code
The universal genetic code is the set of rules by which genetic information encoded in DNA (or RNA) is translated into proteins. It defines how sequences of three nucleotide bases, called codons, correspond to specific amino acids or signal the termination of protein synthesis.
Ultimately, the universal genetic code features triplets (of bases) to form a codon. It is also non-overlapping (meaning that we read genetic code in triplets - three nucleobases at once)
Some amino acids can also have more than one code (there is some redundancy in the code)
The genetic code is degenerate or redundant, and is universal (used by all life forms)
What is the required codon for a protein to ‘start’
You need AUG codon, which goes on to form a MET amino acid. There is only one codon which can ‘start’ the formation of the protein
However, AUG can encode Met even in the middle of a protein sequence
What is a reading frame
A reading frame in a nucleic acid sequence refers to the way nucleotides are grouped into consecutive, non-overlapping triplets (codons) for translation into a protein. Each reading frame starts from a specific nucleotide and determines how the sequence is read and interpreted during protein synthesis.
In summary, a reading frame is a specific grouping of nucleotides into codons that dictates the amino acid sequence during translation. Selecting the correct reading frame is essential for accurate protein synthesis.
How do you select the right reading frame?
You want to try and identify the start codon (which is typically AUG), and then after that, the codon reads in triplets, so you want to keep following the triplet codons until you find a stop codon. This is normally how you identify the correct reading frame
The initial amino acids of the reading frame might not necessarily have to be a set of 3, because it all depends on what enables AUG to be found (have to look at booklet to understand)
What is the open reading frame
It is the region from the start to the stop codon of a gene. However, the STOP codon doesn’t encode an amino acid
What are the different types of mutations
Point
Silent
Nonsense
Insertion
Deletion
Missense
Frameshift
Duplication
What is a point mutation
Mistake in the DNA code, one of the DNA base pairs is changed
What is a silent mutation
A mutation of the protein coding region that has no effect on the protein sequence
What is a nonsense mutation
Single change in DNA code produces a stop codon, prematurely terminating protein synthesis
What is an insertion mutation
Addition of one or more nucleotide base pairs into the DNA sequence
What is a deletion mutation
A piece of DNA is removed from the sequence
What is a missense mutation
A single amino acid has been changed
What is a frameshift mutation
Insertion or deletion mutation results in change to a gene’s reading frame
What is a duplication mutation
Incorrect copying leads to repeated sequences
What is the general mechanism for copying DNA to DNA before cell division - replication?
1) Initiation (where/when/how to start)
2) Chain elongation (forming long polymers)
3) Termination (where/when to stop)
Note: there is an “origin” of replication for initiation (i.e. the spot where we start copying DNA)
Also, note that it involves a template for base pairing, and the newly synthesised strand is complementary to template strand.
The whole process uses a DNA polymerase (enzyme). We need a primer (short piece of DNA/RNA to start)
What is a DNA polymerase - what is its function
Makes a DNA copy from a DNA template. Needs a primer to start.
proof reads the last nucleotide added –> has exonuclease activity to remove mismatched nucleotide –> decreased rates of something wrong happening
How can helical DNA be unwound?
Pulling long heical strands apart causes supercoiling. To address this, the topoisomerase enzymes cut strands, allowing it to unwind and stick back together, and ultimately reduce supercoiling. In cells topiosmerase only unwinds small sections of DNA at a time
What are some problems associated with replication?
DNA is a double-helix with strands tightly wound around each other, making it challenging to separate for replication.
As helicase unwinds the DNA, it causes supercoiling and tension further along the DNA molecule, which could impede replication.
DNA polymerase, the enzyme that synthesizes new DNA strands, can only add nucleotides to an existing strand and requires a 3’-OH group to initiate synthesis.
DNA strands are anti-parallel, meaning one strand runs 5’ to 3’ (leading strand), while the other runs 3’ to 5’ (lagging strand). DNA polymerase can only synthesize in the 5’ to 3’ direction, creating challenges for the lagging strand.
Mistakes in replication could lead to mutations, affecting the integrity of the genetic information.
What was the strategy used to overcome the problem of ‘ DNA is a double-helix with strands tightly wound around each other, making it challenging to separate for replication.’
Helicase Enzyme: Helicase unwinds the DNA at the replication fork by breaking the hydrogen bonds between the two strands, creating two single-stranded templates for replication.
What was the strategy used to overcome the problem of ‘ As helicase unwinds the DNA, it causes supercoiling and tension further along the DNA molecule, which could impede replication.
.’
The use of topoisomerase: Topoisomerases relieve the supercoiling tension by temporarily breaking one or both DNA strands, allowing the DNA to relax, and then rejoining the broken ends. In this way, topoisomerases prevent DNA tangling and damage during replication.
What was the strategy used to overcome the problem of ‘ DNA polymerase, the enzyme that synthesizes new DNA strands, can only add nucleotides to an existing strand and requires a 3’-OH group to initiate synthesis.’
Primase Enzyme: Primase synthesizes a short RNA primer with a free 3’-OH group to serve as a starting point for DNA polymerase. This primer is later replaced with DNA.
What was the strategy used to overcome the problem of ‘DNA strands are anti-parallel, meaning one strand runs 5’ to 3’ (leading strand), while the other runs 3’ to 5’ (lagging strand). DNA polymerase can only synthesize in the 5’ to 3’ direction, creating challenges for the lagging strand.’
Leading Strand Synthesis: The leading strand is synthesized continuously in the same direction as the replication fork.
Lagging Strand Synthesis: The lagging strand is synthesized discontinuously in short fragments known as Okazaki fragments. Each fragment requires its own RNA primer. DNA polymerase synthesizes these fragments in the 5’ to 3’ direction, moving away from the replication fork.
Joining Okazaki Fragments: Once the fragments are synthesized, DNA polymerase I removes the RNA primers and replaces them with DNA. DNA ligase then joins the fragments together by forming phosphodiester bonds, creating a continuous strand.
What was the strategy used to overcome the problem of ‘ Mistakes in replication could lead to mutations, affecting the integrity of the genetic information.’
Proofreading by DNA Polymerase: DNA polymerases have a proofreading ability. They can detect mismatched nucleotides and remove them using their 3’ to 5’ exonuclease activity before continuing DNA synthesis, which enhances the fidelity of replication.
Describe the functions of DNA helicase
Helps unwind the DNA double helix
Describe the functions of DNA topisomerase/gyrase
Helps reduce supercoiling by temporarily breaking one or both DNA strands, allowing the DNA to relax, and then rejoining the broken ends. In this way, topoisomerases prevent DNA tangling and damage during replication.
Describe the function of Single stranded binding proteins
Coat single stranded DNA to keep strands apart / stop small segments of basic pairing / protect DNA
Describe the function of DNA polymerase
Lay down the DNA which is complementary to the template
DNA polymerase III = the main one laying down the DNA
DNA polymerase I = the one which removes RNA primers and replace it with DNA
How many replication forks are there ?
2
How many strands are copied at a replication fork
A lagging and leading strand (2 strands)
Thus, it would have 4 total replications occurring
Explain the process of Leading Strand replication
The gyrase/topoisomerase goes ahead on the dna and releases supercoiling, followed by the helicase which pulls the DNA strand apart. A primaseis placed at the start of the leading strand, which places down an RNA primer.
DNA polymerase 3 then synthesises DNA from that RNA primer, and continues extending. As helicase unwinds the strand continues to be copied.
This is all occurring simultaneosuly to lagging strand replication
Here, the replication is going towards the replication fork
Explain the process of the lagging strand replication
A primase also places down a complementary RNA primer to the lagging strand. However, instead of DNA synthesis going towards the helicase, here the DNA synthesis is going away from the replicaiton fork (because it has to be a 5’ to 3’ dna synthesis)
The primase also places other RNA primers as the helicase unwinds the DNA. This leadas to a couple RNA primers next to the lagging strand. The DNA polymerase III makes lots of small fragments of DNA between the RNA primers. These are called OKAZAKI FRAGMENTS because they aren’t joined to primases yet
DNA polymerase I comes and removes the RNA primers and fills them in with DNA
DNA ligase joins the DNA fragments to make the lagging strand complete
How are the ends joined in circular chromosomal DNA
1) DNA polymerase 3 reaches the RNA primer
2) DNA polymerase 1 removes RNA primer and replaces it with DNA
3) DNA ligase joins the ends of the DNA
4) completed strand
What is the very basic mechanism of transcription (DNA to RNA)
RNA polymerase makes an RNA copy from a DNA template. Doesn’t need a primer to start
What are features of RNA polymerase
Doesn’t need a primer to start
Limited proofreading - increased chances of error
What are the unique problems associated with transcription?
Where to start? (initiation)
How are they made? (elongation)
Where to stop? (termination
How to switch on/off/upregulate?
How does initiation process work
Transcription begins at specific DNA sequences called promoters, located upstream of the gene. In eukaryotes, the promoter often includes a TATA box.
This TATA bbox is easy to melt, and it is the promoter region where RNA polymerase must bind to transcribe the gene
RNA polymerase associates with DNA bound transcription factor (s) which are proteins capable of recognising a specific base sequence - in this case it is the TATA box. They are able to help facilitate the binding of RNA polymerase to the single stranded DNA. The DNA is “melted” in the local region
How does the elongation process work
Using the DNA template strand, RNA polymerase adds complementary RNA nucleotides (adenine, uracil, cytosine, and guanine) in the 5’ to 3’ direction, building an RNA strand.
RNA polymerase moves along the DNA, continuously synthesizing RNA as it unwinds and rewinds sections of the DNA, allowing only a small region to remain open at a time. This small region is called the transcription bubble (in here, the two strands of DNA are separated - one is a template strand and the other isn’t )
This ultimately continues
How does the termination process work?
Transcription stops when RNA polymerase encounters a specific termination sequence in the DNA.
For example a G/C rich region , followed by an A/T rich sequences can form a ds hairpin structure, causing transcription to pause and the RNA polymerase to dissociate and the RNA be released
OR
a Rho protein binds, and uses helicase activity to travel up to and dissociate the DNA/RNA hybrid complex (physically pull or force apart the protein nucleic acid complex) - the RNA dissociates from DNA template
How can transcription be regulated?
Repression
Accelerator
How can transcription be repressed?
A protein repressor binds. This blocks the binding of the sigma factor / transcription factor –> no RNA polymerase binding –> no transcription and thus no gene expression
How can transcription be accelerated?
Sigma factor / transcription factor doesn’t bind strongly/often. However, a transcriptional activator (a protein) can bind at a specific DNA sequence and alter the structure of the promoter so that transcription factor can now bind more frequently –> accelerates transcription
How are repressors and activators modulated?
Often modulated by small molecule binding (often metabolites)
What are the unique problems associated with converting information as a nucleic acid sequence to an amino acid sequence
Need to somehow convert a sequence of nucleotides (A,C,T,G,U) to a sequence of amino acids –> need to adopt a different chemistry - we can’t rely on base pairing to do this.
We also need to have a correct order of amino acids
Peptide bonds formation is very thermodynamically unfavourable
What are the 3 types of RNA
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
What are aa-tRNA synthases?
WOrk with tRNA, and they essentially make sure the right amino acids is attached to the tRNA
These recognise amino acid, anticodon and other parts of tRNA. Attaches correct amino acid to its matched tRNA
They also give ijt the energy to overcome the unfavourable thermodynamics associated with forming a peptide bond
Ultimately the synthetases allows the tRNA to transform into an aa-trna to be used
What does the mRNA do
Contains template for protein synthesis / information about which amino acids to be added in which order (i.e. the RNA strand which was produced)
What does the tRNA do
Matches the correct amino acid to the template
There are different tRNAs for each amino acid/ codon combination
Decodes mRNA sequence to protein
What does the rRNA do
Combines with proteins to form the machinery for protein synthesis / catalyses peptide bond formation
What is a ribosome and how does it work
It consits of small and large subunits, and enzymes
The A-site accepts income tRNA, and the amino acid is deposited in the P-site, before the remainder of the tRNA is moved to the E-site to exit
What are the 3 stages of protein synthesis in the ribosome
Initiation
Elongation
Termination
Explain the process of Initiation
Small subunit of ribosome binds mRNA and Met-tRNA. This initiates everything, and the large subunit of ribosome binds
Explain the process of elongatin
The tRNA comes in guided by anticodon/codon matching. Activated amino acids are positioned next to each other. Since they are ‘activated’, they can use the energy stored in the aa-trna bond.
Peptidyl transferase in ribosome catalyses peptide bond formation using energy stored in the aa-trna bond. Te first tRNA is then released, and the ribosome moves along to the next codon on mRNA etc
Explain the process of termination
When stop codon is reached, no tRNA matches - a release factor (protein) binds. Fromm here, peptidyl transferase from ribosome adds water instead of an amino acid –> releases the polypeptide
What are two problems associated with protein synthesis
Unfavourable thermodynamics of peptide bond formation
Requirement for order
How is the problem with unfavourable thermodynamics addressed
Cells use a class of enzymes called aminoacyl-tRNA synthetases to couple each amino acid to its corresponding transfer RNA (tRNA) molecule, a process that requires ATP.
Energetically Favorable: This reaction creates an aminoacyl-tRNA complex, an “activated” form of the amino acid that can readily participate in peptide bond formation on the ribosome.
How is the requirement for order addressed
tRNA and mRNA Matching: Each amino acid is added to the growing polypeptide chain according to the mRNA sequence. The ribosome reads mRNA codons, and the corresponding aminoacyl-tRNA with the matching anticodon is selected.
What is a primary protein structure
It consists of the amino acid sequence of a protein - the very basic form of an amino acid
What is a secondary protein
Describes the local structures (e.g. Alpha helix, and beta sheet)
It has backbone-backbone hydrogen bonding interactions which are important for it structure
Sidechains also help hold structure together
What is a tertiary protein structure
Overall 3D arrangement of a polypeptide chain (i.e. combining secondary structures)
Held together by a lot of different interactions / bonds such as hydrogen bonds, iconic/electrostatic and polar interactions
Hydrophobic interaactions here, and it is a driving force for protein folding (force which groups nonpolar segments of molecules and polar sements of molecules together)
ph, solvents and temp are really important for maintaining structure here
What is a quarternary protein
Organisation of subunits (many but not all proteins have multiple subunits) (i.e. multiple polypeptide chains)
WHat are alpha helices?
They are the basic right handed helixes. They have their sidechains pointing outwards of the helix
What are beta sheets
These are expressed as arrows which points in direction of protein chains (i.e. from N to C )
They have their sidechains pointing above and below, ultimately creating a tangle of sidechains within the beta sheet. (compared to alpha helix, this is more chaotic in terms of sidechains)
Protein folding
information encoded in amino acid sequence
Burial of hydrophobic surfaces/sidechains in aqueous solvent
collapse of protein chain / formation of secondary structure
Firming up tertiary structre by interactions between different parts of protein
Not much extra space in protein after folding
Protein folding is crucial because it determines a protein’s three-dimensional shape, which directly impacts its function. Proteins must fold into specific shapes to perform their roles correctly within a cell, as their structure enables interactions with other molecules
Appreciate that the protein sequence defines the protein fold and function, and that
protein molecules are held together by the combination of many bonds
Demonstrate how 3D protein structure is related to function using the example of the
alpha helix in DNA binding proteins.
What is energy
Capacity to do work
What is potential energy
Potential energy is a form of stored energy which has the potential to be turned into other types of energy like kinetic energy
What is kinetic energy
Kinetic energy is the energy an object possesses due to its motion. Any object that is moving, regardless of direction, has kinetic energy because of its velocity and mass.
What is entropy
Measure of disorder in a system
What is classified as a favourable reaction
A favourable reaction will typically be exergonic - releasing energy
What is classified as an unfavourable reaction
An unfavourable reaction will typically require energy input (endergonic) - absorbing energy
What is equilibrium
It is when the rate of the forward reaction is equal to the rate of the reverse reaction, without the concentrations of the products and reactants necessarily having to be the same
All chemical equations attempt to reach equilibrium
How does equilibrium link to cells
In living cells, reactions will never reach equilibrium. This is because new substrates are added, and products are used up which all ruin equilibrium
How does equilibrium relate to energy
Equilibrium shifts to favour the reaction which utilises the least energy (?!)
what is thermodynamics
Thermodynamics is the study of energy changes and the direction in which energy flows in a system. It deals with the relationship between heat, work, temperature, and energy in a system, and it helps predict whether a process or reaction is energetically favorable.
Law of thermodynamics
what is kinetics
Kinetics is the study of the rate at which a reaction occurs and the factors that affect that rate. It focuses on how quickly or slowly a reaction proceeds and the mechanisms involved in the process, such as the steps through which reactants are converted into products.
I.e. Activation energy, catalysts, reaction rates
Explain the difference between thermodynamic and kinetic properties of a reaction
Kinetics focus on pathway from reactants to products. Ultimately decides how fast a reaction will take. (Activation barriers)
Meanwhile, thermodynamics deals with eenergetics and equilibrium of reactions, ultimately indicating direction and final state of reaction
Thermodynamic properties focus on the overall energy change and stability of the reactants and products., Kinetic properties describe the rate of the reaction and the mechanism (pathway) by which it occurs.
How can enzymes act as a catalyst
Assist in lowering the energy barrier - they are biological catalysts. This results in the reaction rattes being sped up
Explain the effect of enzymes on the concentrations of substrates and products of a reaction
Enzymes have no effect on the end concentrations, however it just allows the reaction to proceed faster
What are 3 ways to explain enzyme binding
Lock and key model
Induced fit model
Selection model
What is the lock and key model
Substrate molecule fits directly into the active site
What is the induced fit model
Substrate induces a shape change for optimal substrate binding and activity
What is the selection model
The selection model for enzyme function, sometimes referred to as conformational selection, proposes that enzymes exist in multiple conformations (shapes) even before they bind to a substrate. In this model, the enzyme “selects” the appropriate conformation that best fits the substrate when the substrate is present, rather than needing to change shape after binding.
How are enzymes named
Typically have an “ase” ending
Naming system is based on their activity and what they assist in doing
What are characteristics of enzymes
Biological catalysts
Mostly proteins (some RNAs are enzymes)
Highly varied in terms of function, size and ability to be regulated
Arent used up in a reaction
Highly specific for a substrate
Can be regulated
Mutations in enzyme can and will cause disease
How are enzymes regulated
They have evolved to work best at specific temps and PH
Many require an additional chemical component (cofactor) for optimal activity
It could be inhibited by a compound that binds to the active site and prevents substrate binding OR binds outside the active site and stops the motion of enzymes required for activities
Explain enzymatic pathways
ENzymes can accelerate pathways for metabolism, synthesis of cellular materials, communication (signals) etc
Mutations that decrease activity / change specificity / increase activity or alter regulation can cause disease
These are all necessary enzymatic pathways for living organisms
Describe enzyme location
Partly regulated by compartmentalisation - can be found inside or outside cells, in particular cellular compartments
Enzymes in the wrong place can be a sign of a problem or cause a problem
Describe how a secondary reaction can drive equilibrium and provide energy for an unfavourable interaction
A secondary reaction can drive equilibrium and provide energy for an unfavorable reaction by coupling it with a favorable reaction. This coupling allows the combined reactions to proceed by effectively “paying” the energy cost of the unfavorable reaction with the energy released by the favorable one. This principle is commonly seen in biochemical reactions and is essential for cellular processes that would otherwise be energetically impossible.
