Chapter 1: Biological Molecules Flashcards
1.1 Carbohydrates
Describe what separates monosaccharides, disaccharides, polysaccharides.
Monosaccharides are single units, disaccharides are double and polysaccharides consist of many units (similar to monomers compared to polymers).
1.1 Carbohydrates
What contains more energy carbohydrates or lipids
Lipids actually contain about twice as much energy per g than carbohydrates.
1.1 Carbohydrates
Describe the elements that make up carbohydrates
Carbohydrates are made of carbon, hydrogen and oxygen is varying ratios.
1.1 Carbohydrates
What are monosacharides?
They are crystals, soluble and sweet.
Monosaccharides are the monomers from which more complex structures are made eg: carbohydrates.
1.1 Carbohydrates
What are the three kinds of monosacharides?
Three kinds (depends on the number of carbon atoms)
3 C atoms – triose sugar
5 C atoms – pentose sugar
6 C atoms – hexose sugar (alpha glucose)
1.1 Carbohydrates
What is the difference between alpha glucose and beta glucose?
Both are hexose sugars.
The OH and H groups are flipped on 1C in the hexose sugar.
In beta glucose: The OH is on top.
In alpha glucose: The H is on the top
1.1 Carbohydrates
What are the three monosaccharides to know? Include diagram
glucose, fructose, galactose
1.1 Carbohydrates
What are the two pentose sugars and draw them?
Deoxyribose and ribose
1.1 Carbohydrates
What are the disaccharides that form when two of the three hexose monomers are combined?
- Sucrose (glucose + fructose)
- Lactose (glucose + galactose)
- Maltose (glucose+glucose)
1.1 Carbohydrates
How do monosacharides form disacharides?
Condensation reaction:
* Joins together biological monomers and forms a covalent bond between two non metal atoms.
* As part of this reaction a water molecule is released.
* Polymers can be formed this by joining lots of monomers together through many condensations reactions.
1.1 Carbohydrates
How can disaccharides or polysaccharides break?
- Breaks apart the covalent bonds formed during condensation reactions.
- As part of this reaction a water molecule is required/used.
- Polymers can be broken down through many hydrolysis reactions.
1.1 Carbohydrates
What is a glycosidic bond?
When two monosaccharides are joined by a single O.
1.1 Carbohydrates
Describe the uses of polysaccharides like starch?
- Starch (polysacharide)-energy storage molecule in plants.
- Starch is insoluble which means lots can be stored in cells as it doesn’t affect water potential.
- Glucose(makes up starch)-respiration
- Amylose and amylopectin(long chains of alpha glucose molecules)-excess of glucose produced from photosynthesis the glucose molecules are stored as either amylose or amylopectin.
1.1 Carbohydrates
Compare amylose and amylopectin
Amylose: Long unbranched chains, Compact and good for storage
Amylopectin: Branched chains, Higher surface area and Better for immediate energy needs
1.1 Carbohydrates
Describe glycogen and its relationship with glucose?
Energy storage molecule in animals.
Glucose is used for respiration, glycogen is a long branched chain of alpha glucose molecules.
Excess of glucose from the diet glucose molecules are stored as glycogen in the liver.
1.1 Carbohydrates
Describe cellulose
Major structural component of plant cell walls.
It is made of beta glucose molecules.
Because of the arrangement of the –OH on C1 alternating beta glucose monomers need to be flipped in order form the glycosidic bonds between monomers.
1.1 Carbohydrates
What is cellulose made of, and how does the structure of beta-glucose monomers affect its formation?
Cellulose is made of chains of beta-glucose monomers, which can be up to 10,000 monomers long and form straight chains. These are the most abundant polysaccharides. The different arrangement of beta-glucose monomers around C1 affects the way they form 1-4 glycosidic covalent bonds, leading to structural differences.
1.1 Carbohydrates
How do hydrogen bonds contribute to the structure and strength of cellulose?
- The arrangement of cellulose is highly specific, with an abundance of -OH groups that allow for multiple hydrogen bonds.
- 60-70 cellulose chains are cross-linked by hydrogen bonds to form microfibrils.
- These microfibrils are further bonded to form macrofibrils. Although individual hydrogen bonds are weak, their large number gives cellulose remarkable mechanical strength, comparable to steel.
- In cell walls, cellulose is embedded in a polysaccharide glue of pectin, adding additional strength.
1.1 Carbohydrates
How does the structure of plant cell walls contribute to their function?
- Cellulose provides plant cell walls with massive mechanical strength.
- Arrangement of macrofibrils allows water movement through, along, in, and out of cells. Strength of cellulose, cells cannot burst, enabling them to become turgid, which adds to their structural support.
- Shape and arrangement of cellulose cell walls allow for specialized cell functions, such as guard cells around stomata.
- Additionally, cell walls can be reinforced with substances like lignin, which aids in waterproofing.
1.2 Lipids
Draw the structure of glycerol
1.2 Lipids
Describe the structure of tryglycerides
1.2 Lipids
What are triglycerides?
- Used as energy storage in plants and animals.
- Energy is released when bonds are broken
- Long chains in the fatty acids means lots of energy can be stored in fats..
- Fats contain twice as much energy as carbohydrates.
- They are insoluble and do not dissolve.
1.2 Lipids
Outline the synthesis to form triglycerides.
3 fatty acid molecules + 1 glycerol molecule -> 1 triglyceride molecule +8H2O
1.2 Lipids
Describe the bonds in formation of triglycerides
The glycerol backbone joins with the three fatty acids by ester bond linkage.
1.2 lipids
Explain the difference between cis and trans double bonds in fatty acids.
Cis double bonds have both hydrogens on the same side of the hydrocarbon chain, causing a kink, while trans double bonds have hydrogens on opposite sides, resulting in a straighter chain.
1.2 lipids
Describe the impact of hydrogenation on fatty acids.
Hydrogenation converts unsaturated fats into trans fats, which have similar physical properties to saturated fats due to their straighter chain structure.
1.2 lipids
Where are cis fats usually found?
Cis fats are the typical form of unsaturated fat found in nature. Cis fats have a different shape, so the physical properties are different.
1.2 Lipids
Explain the characteristics of lipids: insulation
Lipids act as insulators in structures like the myelin sheath, speeding up impulse transmission, and in subcutaneous layers to reduce heat loss in mammals.
1.2 Lipids
What does the low density of lipids aid?
Lipids have a low density, which causes them to float on water, aiding in buoyancy.
Explain the characteristics of lipids: hydrophobic
Lipids also have a hydrophobic nature, therefore are very good as acting as waterproof layers (especially in cell membranes).
1.2 Lipids
Define hydrophilic and hydrophobic substances.
Hydrophilic substances are attracted to water and will dissolve in it, while hydrophobic substances are not attracted to water and will not dissolve.
1.2 Lipids
Cell membranes are made of…
phospholipids
1.2 Lipids
1.2 Lipids
What structure are phospholipids arranged in?
The phospholipids are arranged in a phospholipid bilayer
1.2 Lipids
Phospholipids are described as being (xxx) as they have both hydrophobic and hydrophilic properties.
amphipathic
1.2 Lipids
What are micelles?
When surrounded by water the phospholipid will form a liposome-enclosed structure so none of the lipid tails are in contact with water.
1.2 Lipids
What is the fluid mosaic model?
- The fluid mosaic model explains the structure of cell membranes, highlighting that they are composed of a phospholipid bilayer with proteins interspersed throughout.
- The phospholipids are not rigidly fixed; they can move laterally, providing fluidity. The proteins serve various functions, including transport, signaling, and structural support.
- This model emphasizes the dynamic nature of membranes, where components can shift and rearrange, contributing to the membrane’s functionality and adaptability.
1.3 Proteins
What is the structure of an amino acid?
An amino acid consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a variable R group (side chain) that determines the specific properties of the amino acid.
1.3 Proteins
How are amino acids linked together?
Linked by peptide bonds in a condensation reaction.
1.3 Proteins
What are the levels of protein structures?
primary, secondary, tertiary and quarternary
1.3 Proteins
What role do R groups play in protein structure?
R groups determine the properties of amino acids, influencing the folding and final tertiary structure of proteins.
1.3 Proteins
What is the primary structure of a protein?
The chain/sequence of amino acids
1.3 Proteins
What is the secondary structure of a protein?
The secondary structure of proteins includes alpha helices OR beta pleated sheets, stabilized by hydrogen bonds.
1.3 Proteins
What is the tertiary structure of a protein?
The folding of a polypeptide chain into a compact, globular shape, involving various bond formations.
1.3 Proteins
What is the quarternary structure of a protein?
Quaternary structure involves the assembly of multiple polypeptide chains and may include the binding of prosthetic groups.
1.3 Proteins
What is the role of ionic bonds in proteins
Ionic bonds form between positively and negatively charged R groups of amino acids, contributing to the stability and overall shape of the protein.
1.3 Proteins
What is the role of hydrogen bonds in protein structure?
Hydrogen bonds form between polar R groups and are crucial in stabilizing secondary structures like alpha helices and beta pleated sheets in proteins.
1.3 Proteins
What is the role of disulfide bonds in protein structure?
Disulfide bonds form between the sulfur atoms of cysteine residues, providing additional stability and rigidity to the protein’s tertiary and quaternary structures.
1.3 Proteins
What are the differences between globular and fibrous proteins?
- Fibrous proteins are long coiled structures
- Globular proteins are highly soluble in water and are more spherical in shape
- Fibrous- structural/support
- Globular-functional
1.3 Proteins
How are the structures of collagen and hemoglobin related to their functions?
Collagen has a fibrous structure providing strength and support in connective tissues, while hemoglobin has a globular structure allowing it to efficiently transport oxygen in the blood.
1.4 DNA and Protein Synthesis
Know the structure of DNA.
DNA is composed of nucleotides, which include a phosphate group, a sugar (deoxyribose), and nitrogenous bases (adenine, thymine, cytosine, guanine). It has two sugar-phosphate backbones and base pairs held together by hydrogen bonds.
1.4 DNA and Protein Synthesis
Describe the process of DNA replication.
DNA replication is semi-conservative, involving the unwinding of the double helix by DNA helicase, followed by the synthesis of new strands by DNA polymerase, and the joining of Okazaki fragments by DNA ligase.
1.4 DNA and Protein Synthesis
Which neucleotides are purines and pyrimidines?
Pyrimidine (6+5 membered ring)- Adenine and Guanine
Purine (6 membered ring)- Cytosine, Uracil, Thymine
1.4 DNA and Protein Synthesis
Define a gene in the context of DNA.
A gene is a sequence of bases on a DNA molecule that codes for a specific sequence of amino acids in a polypeptide chain.
1.4 DNA and Protein Synthesis
What is the genome?
All your genetic information
1.4 DNA and Protein Synthesis
What is a chromosome?
The genes found in a nucleus (23 pairs/46 chromosomes)
1.4 DNA and Protein Synthesis
What is DNA?
Deoxyribonucleic acid, protein that makes up genes
1.4 DNA and Protein Synthesis
What is genotype and phenotype
Genotype is the alleles/bases that you have in your genome. While phenotype is the characteristic you have/how you look.
1.4 DNA and Protein Synthesis
Why are nitrogenous bases on the inside of the helix?
Nitrogenous bases MUST be on the inside of the helix as they are relatively hydrophobic and will face inwards.
1.4 DNA and Protein Synthesis
What is antiparallel?
One strand must run antiparallel (upside down compared to the other) and purines will always pair with pyrimidine bases in order to obtain the tight packaging required for DNA to be a COMPACT molecule.
1.4 DNA and Protein Synthesis
What are the steps required to make a copy of current DNA?
- The double helix is untwisted/uncoiled
- Hydrogen bonds between the bases are broken apart to ‘unzip’ the DNA and expose the bases this is done by DNA helicase
- Free DNA nucleotides are hydrogen bonded onto the exposed bases according to the base pairing rules (A-T and C-G) by DNA polymerase.
- Covalent bonds are formed between the phosphate of one nucleotide and the sugar of the next to seal the backbone.
- Because DNA runs antiparallel synthesis occurs in 2 directions. The Leading strand is made TOWARDS the fork as it opens. The lagging strand is made running AWAY from the fork.
- Replications occurs as (okazaki) fragments on the lagging strand as it waits for more bases to be exposed at the fork.
1.4 DNA and Protein Synthesis
What is the process of semiconservative replication?
When the replicaiton process occurs and the two new DNA molecules are formed.
Each is an exact replica of the original DNA molecule because of the base pairing rules.
This process is known as semi-conservative replication.
Each new DNA molecule consists of one conserved strand plus one newly built strand
DNA replication occurs in the direction of 5 to 3. this is because DNA polymerase can only add nucleotides to the 3’ end of a primer.
1.4 DNA and Protein synthesis
In what direction does DNA replication occur?
5 to 3 direction
1.4 DNA and Protein Synthesis
What does coding, noncoding, sense and antisense strand mean?
Coding – contains the genes to form proteins
Non coding – complimentary
Sense strand – same as the non coding strand
Antisense strand – same as the coding strand
1.4 DNA and Protein Synthesis
mRNA is synthesised in the direction of xxx ON THE mRNA molecule.
Which means the xxx strand must be synthesised in the direction xxx.
mRNA is synthesised in the direction of 5 to 3 ON THE mRNA molecule.
Which means the DNA antisense/template/coding strand must be synthesised in the direction 3 to 5.
1.4 DNA and Protein Synthesis
How does RNA differ from DNA?
t contains the base URACIL instead of THYMINE
It contains a RIBOSE sugar instead of a DEOXYRIBOSE sugar.
It is usually single stranded.
It has three different forms (tRNA, mRNA and rRNA)
1.4 DNA and Protein Synthesis
What are the rules of RNA base pairing
- A ALWAYS bonds to U (ONLY in RNA)
- G ALWAYS bonds to C (in both RNA and DNA)
- These base pairs are COMPLIMENTARY
- Therefore a purine is always opposite a pyrimidine.
- Between A and U there are 2 Hydrogen bonds.
- Between G and C there are 3 Hydrogen bonds.
1.4 DNA and Protein Synthesis
Outline the process of DNA transcription
- DNA helicase unzips DNA at the beginning of the gene by breaking H bonds.
- Leaving the bases exposed.
- RNA polymerase binds to DNA at a specific sequence of nucleotides called the promoter (start).
- Only one of the unwound DNA strands (template strand) acts as a template for the RNA synthesis.
- RNA polymerase adds free nucleotides from the cytoplasm to the exposed DNA template strand bases.
- RNA polymerase can only add nucleotides to the 3’ end of the strand so like DNA, RNA must be synthesized in the 5’ to 3’ direction.
- RNA polymerase moves along the DNA joining bases to form an mRNA strand. ON THE RNA T’S ARE REPLACED BY U’S
- RNA polymerase continues this until it reaches the terminator, a specific sequence of nucleotides that signals the end of transcription.
- Transcription stops and mRNA polymerase and the new mRNA transcript are released from DNA.
- mRNA leaves the nucleus
- The DNA double helix zips back up (DNA ligase)
1.4 DNA and Protein Synthesis
What are the forms of RNA
- tRNA – carries AA’s to the ribosomes where they are bonded together to form polypeptides eg: enzymes/proteins etc.
- rRNA – found in the ribosomes, reads mRNA
- mRNA – is made as a complimentary strand to the DNA, therefore acts as a coding strand as a copy of the original DNA molecule.
1.4 DNA and Protein Synthesis
Describe the binding sites on a ribosome
Ribosomes have three binding sites for tRNA molecules, but only two can bind. The binding sites are the E (exit site), P (peptidyl site) and A (aminoacyl site).
Also a binding site for mRNA
1.4 DNA and Protein Synthesis
What is the genetic code?
The genetic code consists of triplets of nucleotides (codons) that specify amino acids, including start and stop codons, and is characterized by its degenerate and non-overlapping nature.
Triplet Code: The genetic code is made up of triplets of nucleotides called codons.Each codon specifies a particular amino acid.
Start and Stop Codons: There are specific codons that signal the start (AUG) and stop (UAA, UAG, UGA) of protein synthesis.
Degeneracy: The genetic code is degenerate, meaning that multiple codons can code for the same amino acid.
Non-overlapping: Codons are read in a sequential manner without overlapping.
1.4 DNA and Protein Synthesis
Describe tRNA activating enzymes
Each tRNA is recognized by a tRNA activating enzyme, which attaches using ATP
Each tRNA has a slightly different base sequence and causes some variability in structure.
Active sites are specific to both amino acid and correct tRNA.
Once the amino acid and tRNA are bound to the enzyme the enzyme is activated by a bond forming between the enzyme and an AMP molecule (ATP minus a phosphate).
Then the AA is covalently bonded to tRNA, energy from this bond is later used to form peptide bonds between amino acids in the polypeptide chain.
1.4 DNA and Protein Synthesis
How does termination occur in protein synthesis?
The process of elongation continues (in the direction of 5 to 3) until a stop codon is reached. This releases the polypeptide when it moves to the golgi apparatus.
1.4 DNA and Protein Synthesis
What are the possible base alterations that result in mutation?
Addition, deletion, duplication and inversion
1.4 DNA and Protein Synthesis
When does a frame shift occur?
After an insertion or deletion the following DNA will move (either towards or away from the mutations), this movement/shift is called a frame shift.
1.4 DNA and Protein Synthesis
Describe the mutation causing sickle cell anemia and the disease itself
SCA is an autosomal recessive disease caused by a point mutation in the hemoglobin beta gene (HBB). This is a substitution mutation.
What shape is the tRNA and why?
The tRNA is clover shaped, determined by hydrogen bonding
1.5 Enzymes
An enzyme is a ____ protein
Globular
1.5 Enzymes
What are the key characteristics of an enzyme?
- Globular proteins
- Water soluble
- Act as biological catalysts (speed up reactions without being used up themselves)
- Highly specific
- Have an ‘active site’
- Activitiy is usually affected by pH and temperature
1.5 Enzymes
What is the primary structure of an enzyme?
Their primary structure is the initial chain of AA’s.
1.5 Enzymes
What is secondary structure of an enzyme?
The secondary structure is the initial folding.
1.5 Enzymes
What is tertiary structure of an enzyme?
Tertiary structure is its functional shape with hydrophobic groups in the middle and hydrophilic groups surrounding them on the outside.
1.5 Enzymes
Draw a diagram for enzyme action
1.5 Enzymes
What is lock and theory model?
The enzymes specifically shaped active site will only allow one kind of substrate to fit in.
The substrate has to have a complimentary shape to the active site therefore can fit in.
1.5 Enzymes
What is the induced fit hypothesis?
Once in the active site the substrate is broken down, this process is aided by the ‘induced-fit hypothesis’. This suggests that the enzyme active site is malleable to fit the shape of the substrate. The enzyme will change shape slightly to hold the substrate in place, this change puts stress on the substrate further speeding up the process
1.5 Enzymes
Draw the enzyme action activation energy curve
1.5 Enzymes
Why does pH affect enzyme action?
A hydrogen (H+) ion carries a positive charge so is attracted to negative charges. And likewise repelled by positive charges.
Hydrogen and ionic bonds are responsible for maintaining the tertiary structure and repulsion or attraction may alter tertiary structure.
Some ‘R’ groups are slightly charged and therefore will be attracted/repelled by the presence of H+ ions.
1.5 Enzymes
The intial rate is always…
…the highest.Maximum number of active sites available when compared to number of substrates.
1.5 Enzymes
Draw the three types of enzyme Inhibtion
1.5 Enzymes
Describe competitive inhibition
**The inhibitor competes with the substrate for the active site of the enzyme. **
Inhibitor is structurally similar to the substrate, binding to the active site. When the inhibitor binds, substrate cant bind, decreasing RoR
The presence of a competitive inhibitor can be overcome by increasing the concentration of the substrate. As more substrate molecules are available, they are more likely to outcompete the inhibitor
1.5 Enzymes
Describe non competitive inhibition
**In non-competitive inhibition, the inhibitor binds to a different site on the enzyme, not the active site. This other site is called the allosteric site.
**
Inhibitor binds to the allosteric site, causing a conformational change in the enzyme. This change can either reduce the enzyme’s ability to bind to the substrate or lower the catalytic activity
- this MAY permenantly alter the enzymes shape making it inactive
Cant be overcome by increasing concentration of substrates
1.5 Enzymes
Describe uncompetitive inhibition
In uncompetitive inhibition, the inhibitor binds to a site on the enzyme that is only available after the enzyme has bound to the substrate, forming the enzyme-substrate complex. This site is different from the active site and does not exist in the free enzyme alone. This is also called ‘end product inhibition’.
Effect on Enzyme-Substrate Complex:
- Inhibitor binds to enzyme-substrate complex, preventing product release.
- “Locks” substrate in enzyme, reducing reaction rate.
Effect on Enzyme Activity:
- Decreases both Vmax (maximum reaction rate) and Km (apparent affinity).
- Lower enzyme-substrate complex concentration reduces product formation.
- Vmax and Km decrease proportionally, keeping the Km/Vmax ratio constant.
Kinetics of Uncompetitive Inhibition:
- Decrease in Vmax: Fewer active enzyme-substrate complexes available, lowering reaction rate.
Decrease in Km: Lower effective enzyme-substrate complex concentration increases substrate affinity.
1.6 Inorganic ions
What is the role of nitrate ions
Makes DNA and amino acids
Nitrification results in stores of nitrates in the soil that plants can absorb via their roots and assimilate into useful products (DNA and amino acids).
If plants are unable to obtain sufficient amounts of nitrogen then they will develop deficiency symptoms. Cannot absorb nitrogen directly as it is inert
1.6 Inorganic ions
What is the role of calcium ions
To form calcium pectate in the middle lamella
Bind with pectins to form a rigid structure. They also play a role in regulating enzyme activity, signaling pathways, and membrane permeability.
1.6 Inorganic ions
What is the role of magnesium ions
Magnesium ions are essential for plants as they are the central atom in chlorophyll, crucial for photosynthesis.
1.6 Inorganic ions
What is the role of phosphate ions
Phosphate ions are vital for plants as they are key components of ATP, the molecule that stores and transfers energy for cellular processes. They are also crucial for nucleic acid synthesis, forming part of DNA and RNA, and play a role in cell membrane structure, signaling, and root development.
1.7 Water
Draw a molecule of water
2 hydrogens 1 oxygen with 2 lone pairs on oxygen giving it a positive charge.
1.7 Water
Draw the hydrogen bonding of water to other water molecules
dotted line from hydrogen with sigma+ to oxygen sigma -
1.7 Water
Why is water a good solvent?
Because water is dipolar it allows chemicals to dissolve readily and easily, this makes it an ideal transport medium.
1.7 Water
What is the temperature at which water is most dense?
At 4°C, water’s dipole properties allow hydrogen bonds to form a more efficient arrangement, maximizing molecular packing. Below this temperature, water molecules form an open hexagonal structure due to hydrogen bonding, reducing density. Thus, water reaches its maximum density at 4°C before expanding upon freezing.
1.7 Water
Why does water have surface tension?
Water’s dipole nature leads to strong hydrogen bonding between molecules at the surface, creating a cohesive “film” that resists external forces. This cohesive force, due to the alignment of water molecules, results in surface tension, allowing small objects to float and insects to walk on water.
1.7 Water
Discuss waters high specific heat capacity?
Water’s dipole nature creates strong hydrogen bonds between molecules, requiring significant energy to break. This extensive hydrogen bonding means that water can absorb a lot of heat energy before its temperature rises, resulting in a high specific heat capacity. This property stabilizes temperatures in living organisms and environments.
1.7 Water
Discuss the incompressible nature of water
Incompressibility means that water does not significantly change in volume when a force is applied to it. This property is crucial for:
Structural support: Water in cells and tissues provides structural support and shape to organisms.
Buoyancy: The incompressibility of water allows aquatic organisms to float and move more easily.
