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)
