Biological Molecules & Flashcards
What is a protein? How many are there? What is the composition of proteins?
One or more polypeptides
There are 20 proteinogenic amino acids each with a different R group.
CHONS
How is a peptide bond formed?
In a condensation reaction between the hydroxyl group of a carbonyl group, and the hydrogen of an amine group.
Molecule of water formed
What are the 3 components of an amino acid?
1) amine group on left ( NH2 )
2) carbonyl group ( C—O C-OH )
3) R group ( variable side chain )
The R group determines how each amino acid differs and why their properties differ
What is a dipeptide? What is a polypeptide? How does a peptide bond look?
2 amino acids joined together by peptide bonds
This a polymer of amino acids, so chains of amino acids joined by amino acids
C - N double bond O H
What is the primary sequence? What is the effect of a change in amino acids?
This is the sequence of amino acids that makes up a polypeptide joined by peptide bonds. This is determined by the DNA of a cell. This is specific for each protein, so a change in amino acids cause a change in the primary structure.
What is the secondary structure? What bonding is present?
The initial folding and coiling of a polypeptide chain
This includes alpha helixes ( between double bond oxygen of carboxyl group and hydrogen of amino group ) and regions of beta pleats
Hydrogen bonding ( between the NH and C double bond o group between nitrogen and hydrogen ) - this forms the beta pleats
This can be broken by high temp or pH changes
What is the tertiary structure? What bonding exists?
The further coiling of the secondary structure which forms the overall 3D shape.
Bonding :
- disulphide bridges between sulfur atoms, more specifically - two cysteine R groups of amino acids
- hydrophobic and hydrophilic interactions ( between polar and non polar R groups )
- hydrogen bonding ( between R groups )
- ionic bonding ( between positively and negatively charged R groups )
What is the quaternary structure?
One or more polypeptide chain
Each polypeptide is a subunit
What is the difference in hydrogen bonding between the secondary and tertiary structure?
Secondary - between amine and carboxyl groups
Tertiary - between R groups
How do plants make amino acids? What does a lack of proteins mean?
Glucose is joined with nitrate ions
Stunted growth
How do we get our proteins?
This is by consumption in our diet. But, many essential amino acids are not needed by our body.
Compare fibrous and globular proteins
Fibrous proteins are :
- strong
- insoluble ( hydrophobic R groups )
- unreactive
Eg. Collagen, keratin etc
Also, long and flexible
Structural roles
Globular proteins :
- soluble ( due to hydrophilic amino acids on outside - hydrophilic R group folded on outside and hydrophobic R group regions folded inside)
- spherical
- compact
- 3D structure
- often complementary to another molecule and therefore specific
- metabolic roles
Eg. Haemoglobin, enzymes, hormones
Why are globular proteins easily transported?
They are soluble
What are thr tests for lipids, proteins and starch?
Lipids :
Ethanol and water
Cloudy white emulsion if present
Proteins :
Bieuret solution
Blue to lilac / purple
Starch :
Iodine
Yellow brown to blue black
How do temp and pH affect structures?
Can cause tertiary and quaternary structure to unravel and go back to primary and secondary
Explain the structure of collagen, and where do we find it?
It is STRONG.
Glycine molecule every third amino acid so polypeptide chains lie close together
Small R group to allow polypeptide chains to wrap tightly
3 polypeptide chains wrap to form a triple left handed helix
CrossLinks between adjacent molecules and hydrogen bonding between chains
Staggered ends so no weak spots
We find it in tendons ( connect muscle to bones ), skin, and ligaments ( bone to bone ). It is suited to this purpose as it has a high tensile strength, flexible, insoluble, does not stretch
Explain the structure of keratin. Where do we find it?
This is made up of 2 polypeptide chains coiled together
It has a high proportion of cysteine so it can form desulfide bridges, making it strong
In hair, nails, claws ( i.e delicate parts of the body )
Outer layer of skin has keratin so impermeable to water
Explain the structure of elastin. Where do we find it?
It has tropoelastin fibres coiled like a spring. It stretches when blood passes through and recoils when blood leaves. It also has cross links between adjacent molecules. It is made up of hydrophobic groups joined together.
We find this in connective tissue and places like blood vessels, cartilage, walls of bladder and alveoli etc
What is the structure of haemoglobin? Describe the structure.
Haemoglobin has 4 polypeptide chains. Each polypeptide chain has a haem group, Fe 2+, which has a high affinity for oxygen - it can hold 4 oxygen molecules. It is a conjugated protein, so a protein with a prosthetic group ( non protein group ).
What molecules make enzymes?
Golgi apparatus, RER, lysosomes, ribosomes
What does Q10 mean? What is the formula for Q10?
The increase in ROR when temp is increased by 10 degrees. Rate of reaction at T+10 degrees / rate of reaction at T degrees
What is an enzyme?
Biological catalysts that increase the ROR by providing an alternative pathway with a lower AE. It is not used up.
Globular proteins with a specific tertiary structure to what it binds to
Active site of enzyme is complementary to the substrate
How are enzymes biological catalysts?
The substrate binds to the enzyme, lowering the activation energy. More substrates exceed the AE barrier so increased ROR
How does temp affect enzyme action?
Increase in temp means :
- enzymes and substrate have MORE KINETIC ENERGY
- move around more quickly and randomly
- more successful collisions between enzyme and substrate
- more ESC formed
Increased initial rate of reaction
An increase in temp can affect the bonds in the tertiary structure. It puts a strain on, and then breaks the hydrogen and ionic bonds. There is a change in tertiary structure so there is a change in the active site. This prevents the substrate binding to the enzyme, so the enzyme denatures. Less product formed. Causes a linear decrease in graph after optimum temp reached
Why are enzymes soluble in water?
They are globular proteins with hydrophilic amino acids on the surface
What is the impact of controlling the factors affecting enzyme action? What are the four factors?
Homeostasis should be maintained. This means enzymes can work at their optimum and function properly for the survival of organisms
These are
- pH
- enzyme conc
- substrate conc
- temp
What is an intracellular enzyme?
This is an enzyme that acts and functions inside the cell. For eg, catalase converts the harmful hydrogen peroxide to water and oxygen
What is an extracellular enzyme?
They are secreted by cells and catalyse reactions outside of cells. Examples of this are amylase which turns starch into maltose. It is secreted in the pancreas and released in the s.i. Also, trypsin turns proteins to peptides.
What is a key feature of enzymes?
It has a high turnover number so can catalyse substrates quickly
What type of pathways do enzymes control?
Metabolic pathways
Anabolic = building up reactions
Catabolic = breaking down reactions
Explain the lock and key theory
Active site of enzyme is complementary to the substrate
The substrate fits into the active site of the enzyme. This forms an ESC due to strains on the bonds. These are held together by amino acids on the surface of the enzyme. The product is a different shape to the enzymes active site, so it can no longer bind. This means it leaves the active site to catalyse another reaction. It remains UNCHANGED
Explain the induced fit theory
When the substrate binds to the active site of the enzyme, it affects and strains the bonds holding the tertiary structure. Therefore, the shape of the active site changes to accommodate to the substrate. It moulds itself around the substrate and is held together by oppositely charged groups. It also weakens the bonds in substrates, lowering the AE.
How does pH affect enzyme action?
An increase in H+ ions interferes and alters the with hydrogen and ionic bonds in the tertiary structure. Changes the charges on r groups. This changes the tertiary structure, changing the shape of the active site. This means the substrate can no longer fit into the active site as the enzyme is no longer complementary. This denatures the enzyme.
Or if more or less, less ESC complexes formed
The conc of H+ ions can give the best shape.
Use the phrase H+ ions
How does substrate conc affect enzyme action?
When the substrate conc is higher, there is a greater chance of substrate entering active site and hence collisions between the enzyme and the substrate. More ESC formed so higher rate of reaction.
However, once all the active sites are occupied, increasing substrate concentration no longer has an effect on the rate of reaction. This means enzyme conc is now the limiting factor.
How does enzyme conc affect enzyme action?
Increase enzyme conc = more active sites available
Greater chance of enzyme and substrate colliding, increased frequency of successful collisions, more ESC complexes formed, increased rate of reaction.
When all active sites occupied, increasing enzyme conc no longer has an effect on the rate of reaction. Substrate conc becomes the limiting factor
Extremes of pH and temp causes the conc of enzymes to reduce
What controls should we consider when carrying out the enzyme practical?
- Volume and conc of enzyme solution
- Volume and conc of substrate solution
- Controlling of temp ( use a thermostatic water bath )
- Control of pH ( buffer solution controls pH )
What is coenzymes and cofactors? Give examples.
Coenzymes are large organic molecules which transfer reactants between enzymes. Example of coenzyme is NAD. A cofactor is an inorganic ion that increase the activity of an enzyme and allow the enzyme to catalyse reactions. Examples of Cl- in amylase.
What is an competitive inhibitors? How does this affect rate of reaction?
This has a similar structure to the substrate and competes with substrate. This binds to the active site. This prevents the substrate binding to the enzyme. This reduces frequency of successful collisions, so there was ESC formed. This reduces the rate of reaction temporarily
How do we reduce the effect of a competitive inhibitor?
This is by increasing the substrate conc.
What affects the rate of inhibition?
The conc of inhibitors and substrates
What is a non competitive inhibitor? What is the effect on the rate of reaction?
The substrate binds to the allosteric site. This alters the tertiary structure of the enzyme, which changes the active site. This means the substrate can no longer fit into the active site of the enzyme. Reduced rate of reaction
What is a prosthetic group?
A non protein group permanently bound.
For eg, zn2+ in carbonic anahydrase
What is the key difference between inhibitors?
Competitive = binds temporarily
Non competitive = binds permanently
What does DNA and RNA stand for? What is its composition?
RNA - ribonucleic acid
DNA - deoxyribonucleic acid
CHOPS
What does DNA do?
Codes for sequences of amino acids which determine the final 3D structure of the protein
What is the monomer of DNA? Describe the structure of a DNA nucleotide, and how does this differ to a RNA nucleotide?
Nucleotides
Phosphate group attached to deoxyribose sugar ( ribose sugar ) attached to a nitrogenous base
DNA has a deoxyribose sugar, but RNA has a ribose sugar
What are polynucleotides, and how are they formed?
Polymers of nucleotides
They are formed via a condensation reaction between the deoxyribose sugar and phosphate group forming a phosphodiester bond and therefore, forms a sugar phosphate backbone. The bases stick out of the chain. These are strong covalent bonds, and ensure the genetic code is not damaged and passed onto other cells.
What are phosphorylated nucleotides? Give examples
ADP and ATP
More than one phosphate group
ADP ( 2 P )
ATP ( 3 P )
Where does the phosphodiester bond form specifically?
Between H on the carbon 3 of deoxyribose sugar, and hydroxyl group on phosphate group
Describe the structure of DNA, and how this links to function
2 polynucleotide strands running in opposite directions, twist to form a double helix
Sugar phosphate backbone ( therefore, STABLE )
2 anti parallel strands running in opposite directions ( one strand can act as a template )
Sugar phosphate backbone
DNA is long so can carry lots of genetic info
Bases pair up with one pyramidine to one purine ( if only one base is known, it can only pair with one another base )
Complementary base pairing between AT and CG ( allow identical copies to be made )
Weak hydrogen bonds so it can be easily unzipped
How many hydrogen bonds are formed in complementary base pairing?
AT = 2
CG = 3
Why is complementary base pairing necessary?
- allow the reforming of hydrogen bonds
- DNA replication without error
- reduces occurrence of mutations
Compare RNA and DNA
RNA
- found in cytoplasm and nucleus
- single stranded and shorter
- ribose sugar
- thymine replaced with uracil ( AU, CG )
DNA
- found in chromosomes of nucleus
- double stranded, longer
- deoxyribose sugar
- no difference
What are the functions of the three types of RNA?
rRNA - makes up the ribosome as a part of structure
tRNA - brings specific amino acids to the ribosomes
mRNA - carries genetic information from the nucleus to the ribosomes for protein synthesis, instructions for the primary structure
What are the pyramidines and purines? Why do they pair?
They pair due to different sizes
Pyramidine ( single carbon ring structure ) - CT
Purine ( double carbon ring structure ) - AG
How is DNA arranged in mitochondria and chloroplasts?
Short and not bound to histone proteins
What 3 words are used to describe the genetic code? Explain them
1) non overlapping
Read in a fixed point in groups of 3 bases
2) degenerate
More than one triplet of bases can code for the same amino acid
3) universal
Nearly all triplets of bases code for the same amino acid
What is a gene?
A sequence/ section of DNA that codes for one or more polypeptides
What is a mutation?
Change in the DNA base sequence means there is a change in the sequence of amino acids
This means the protein will fold differently, lose its function and denature
Occur randomly and spontaneously
Outline the process of DNA replication
DNA helix unwinds due to helicase enzymes - this breaks hydrogen bonds between complementary base pairs. It also unzips due to the gyrase enzyme. The helicase enzymes break the hydrogen bonds between complementary base pairs. This leaves 2 separate polynucleotide strands with exposed bases. This process uses ATP. Each DNA strands acts as a template to the complementary strand. Now, the free floating, activated DNA nucleotides line up by complementary base pairing. A & T pair and form 2 hydrogen bonds, C and G pair and form 3 hydrogen bonds. This is catalysed by DNA polymerase which catalyses the joining of the nucleotides, forming phosphodiester bonds. New strands are formed on the 2 old strands, and these twist to form the double helix. Semi conservative replication has taken place - a new DNA molecule is formed. It has one old strand containing parental DNA, and one new strand containing new DNA. The activated nucleotides lose 2 phosphate groups in the formation of a phosphodiester bond to provide energy for the reaction.
What is semi conservative replication?
When a new DNA molecule is formed containing one old strand from original DNA and one new strand newly synthesised. The original strand acts as a template for the complementary strand.
What is an activated nucleotide?
3 phosphate groups but normal nucleotide has one
Where does transcription take place, and why does it occur?
In the nucleus
DNA molecule is too large to leave the nucleus, so DNA strand is copied into the mRNA strand. This is much shorter and the generic code can be carried to the ribosomes for protein synthesis.
Where does protein synthesis take place?
In the ribosomes ( more specifically, on )
Outline the process of DNA transcription
In the nucleus, the DNA is copied into mRNA. The DNA helix unwinds due to helicase enzymes. Then, the DNA strand ( one as it is single stranded ) acts as a template to the complementary strand. Now free, activated mRNA nucleotides line up by complementary base pairing to the template strand. They form hydrogen bonds ( AT = 2, etc … ). The RNA nucleotides join to the nucleotides by RNA polymerase. Once the mRNA strand is synthesised, this leaves through pores in the nucleus to the ribosomes for protein synthesis.
What are introns?
Non coding parts of DNA, sequences of bases that do not code for amino acid. These are spliced out by the protein splicesome and leave the exons, the coding regions, before it goes to the ribosomes.
Outline the process of translation
The mRNA leaves through pores in the nucleus and moves to the ribosomes. The mRNA binds to the ribosome at the start codon. Then, the tRNA binds to the mRNA. This tRNA has a complementary anticodons to the start codon. This is held together by hydrogen bonds. The tRNA molecule carries specific amino acids. The ribosomes move along the mRNA molecule for more tRNA molecules to attach. Peptide bonds form between adjacent amino acids and ATP is required, catalysed by enzyme peptidyl transferase. This continues until the ribosome reaches the stop codon at the end of the mRNA molecule. This forms a polypeptide processed and modified by the Golgi apparatus.
What is the codon and anticodon?
Codon - triplet of bases on mRNA molecule
Anticodon - triplet of bases on tRNA molecule
Complementary to each other
What is the purpose of a start codon at the start of a sequence?
Ensure triplet of bases are read in frame so not overlapping
How many bases code for an amino acid? What is the maximum number of base combos?
3
4 to the power of 3 = 64
What are the remaining uses of bases not needed?
- as start or stop codons
- several codons can code for one amino acid
Why is an mRNA molecule shorter than a DNA molecule?
- it only copies one section of DNA
- DNA comprises many genes
What are things researchers should consider for seeing how genes control development?
- if cheap
- readily available
Describe the structure of ATP
Adenosine triphosphate
Phosphorylated nucleotide made up of :
- adenine
- ribose sugar
- 3 phosphate groups
CHONP
High energy bonds between phosphate groups
What are the properties of ATP?
- Small, can move in and out of cells
- Water soluble
- bonds between phosphates with intermediate energy - can be used for cellular reactions but not so large that energy is wasted as heat
Why is ATP known as the universal energy currency?
It is present in all cells of all living organisms. It releases energy in small and manageable quantities
How is ATP formed?
ADP and a phosphate ion in a phosphorylation reaction
Why is energy necessary?
- synthesis
- transport
- movement
Why is ATP not a long term energy store? Give an example of a long term energy store
The phosphate bonds are unstable so cells do not store large amounts of it.
Fats as they are stable molecules so they have uses like insulation
What properties do inorganic ions have?
They are soluble so they can be transported
What is the role of phosphate ions?
Attaches to other molecules to make phosphate groups
- used to make phospholipid bilayer and make it hydrophilic
- used to make ATP ( phosphate bonds store energy )
- make nucleotides ( allow formation of polynucleotides )
How is energy stored in ATP?
Stored in high energy bonds between phosphates
Give an example of a protein and function of protein
Heamoglobin - transport
Insulin - hormone
Antibodies - defence against the body
Catalase - enzyme
Why is oxygen uptake a measure of metabolic rate?
Oxygen is used in respiration which is a metabolic process.
How are ester bonds formed?
Hydroxyl group of a glycerol molecule and carboxyl group of a fatty acid
Uses of triglycerides
Insulation
Buoyancy
Protection
Energy storage
Why do triglycerides store more energy?
Due to the C-H bonds of the hydrocarbon chains
Outline the properties of water that make it an ideal habitat for amphibians
Good solvent due to high specific heat capacity, making a thermally stable environment
High density because ice is less dense than water
What is the role of sodium ions
Regulate water potential
Co transport of glucose and amino acids
What is the role of hydrogen ions
Regulate pH
Why are solvents important for survival?
Medium for chemical reaction
Transport of substances
Dilutes toxic substances
Outline the key properties of water
High latent heat of vaporisation
Evaporation is a cooling mechanism
For example, mammals cool when they sweat
High density
Organisms can flow
Ice is less dense than water
High specific capacity so stable temp for aquatic organisms
This is due to the hydrogen bonds between water molecules - energy needed to break hydrogen bonds
Effective solvent
Meanings of this
High surface tension
Eg allows pond walkers to walk on surface
Ice floats because ice is less dense than water ( as lattice is spread out )
Ice can provide habitats for organisms
Ice can act as an insulating layer as water beneath ice is insulated, so organisms do not freeze
High cohesion ( holds water molecules together ) and adhesion ( water molecules stick to surface )
Transport of water up xylem and transpiration stream
Transparent so
Underwater organisms can see
Light can pass through water
Underwater photosynthesis occurs
Explain how water can contribute to the survival of organisms
ice, is less dense than water / floats ✓
ice, provides habitat for some species / AW ✓
(floating) ice insulates (water below) ✓
(aquatic) animals / gametes / spores, can move
Good solvent so
oxygen / nutrients / resources / AW, can circulate
water is similar density to living organisms
organisms can float
Composition of carbohydrates and lipids
CHO
CHO
What is a disaccharide?
Sugar formed from 2 monosaccharides joined by a glycosidic bond
Maltose, sucrose, lactose
What is a polysaccharide?
A polymer made from many monosaccharides joined by glycosidic bonds in a condensation reaction
Compare the similarities and differences in functions of carbs and lipids
Both :
Store of energy
Source of energy
However, carbs have structural importance - eg cellulose in cell wall of plant cell
However, lipids act as insulating layers ( thermal insulation under skin of mammals and electrical insulation around nerve cells )
Lipids are used in phospholipids
Composition of proteins
CHONS
What are the functions of proteins?
Can act as carrier molecules, antibodies, enzymes, hormones
Structural importance eg collagen in bone and keratin in hair
Cell growth and cell repair
What is the composition of nucleic acids? What is the function?
CHONP
Carries the genetic code in all living organisms
Control cellular processes eg protein synthesis
What is the components of maltose?
2 alpha glucose
What is the components of sucrose?
Alpha glucose and fructose
What is the components of lactose?
Alpha glucose and galactose
What is the difference between alpha and beta glucose?
Different alignment of H and OH
Alpha, H on top
Beta, OH on top
What is the energy storage in plants and animals?
Starch
Glycogen
How are carbohydrates used as a source of energy
Polymers of glucose
Glucose can be used as a substrate in respiration to release energy
Why do mammals store glycogen instead of glucose?
Insoluble - no effect on water potential
Highly branched so lots of ends to add or remove glucose / release monomers in animals
Can be broken down rapidly to release glucose when needed
Compact so can store large amounts of energy and lots can be stored in small spaces
Metabolically inactive
Explain how the structure of glycogen differs from that of amylopectin to make it better suited as an energy store in animals
glycogen (compared to amylopectin) more branched ✓
more coiled ✓
(so is) more compact / less space needed (for storage) ✓
(branching gives) many / more, free ends ✓
where glucose can be added or removed ✓
(so) speeds up glucose, release / hydrolysis ✓
Explain how the structure of galactose allows it to be used as a respiratory substrate.
Bonds contain energy
These can be broken by respiratory enzymes
Solouble so can move within cell and OH groups can form hydrogen bonds with water
Suggest and explain why lactose is unable to cross membranes.
Too big so cannot pass through gaps in phospholipids
Large ( like glucose which is also polar polar so cannot pass through hydrophobic core )
Require carrier proteins to diffuse through plasma membrane due to the hydrophobic core
State two other structural similarities between lactose and maltose.
They’re both POLYMERS OF GLCUOSE IDIOT
so share same features
Two 6 membered rings
1-4 glycosidic bonds
One oxygen atoms
Differences between lactose and maltose
Lactose
- one monomer is glucose and galactose
- beta galactose
- B glycosidic bond
Monomer
- both monomers of glucose
- alpha glucose
- A glycosidic bond
Describe the structure of cellulose ( polysaccharide ) & properties
Main component of cell wall
Unbranched chains of beta glucose joined by 1-4 glycosidic bonds
Microfibrils are long threads made of cellulose chains joined by hydrogen bonds
High tensile strength allows to withstand turgor pressure
Strengthens cell wall
Keeps it rigid
Structure and properties of glycogen
How glucose is stored in mammals
Structure :
- alpha glucose
- 1,4 and 1,6 glycosidic bonds
Properties :
Insoluble - no effect on water potential
Highly branched so lots of ends to add or remove glucose / release monomers in animals
Can be broken down rapidly to release glucose when needed
Compact so can store large amounts of energy and lots can be stored in small spaces
Metabolically inactive
What 2 polysaccharides make up starch in plants?
Amylose and amylopectin
Describe the structure of amylose
Unbranched molecule
1,4 glycosidic bond therefore
Coiled and compact molecule
Describe the structure of amylopectin
Not coiled
Branched molecule
1,4 and 1,6 glycosidic bonds
Why are lipids good energy storage molecules?
Fats have carbon-hydrogen bonds so they are energy rich / containmore energy per molecule
Compact - More energy stored in less space
Fats are insoluble
Do not affect water potential of cell
Fatty acids are long carbon chains
Can be broken down to release two carbon / acetyl groups (which enter Krebs cycle)
Animal fats saturated / harder
Have a role in protection / insulation as well as energy storage
Where are saturated and unsaturated lipids found?
Saturated lipids = animal fats
Unsaturated lipids = plants
Structure of a triglyceride
Glycerol molecule and 3 fatty acids
Ester bonds
What are the uses of phosphate ions?
Form component of ATP and DNA
What is the role of iron ions
Component of haemoglobin
What are reducing agents? Give examples of reducing sugars and non reducing sugars
Act as reducing agents ( i.e donating electrons to other molecules )
Monosaccharides ( glucose and fructose )
Some disaccharides ( lactose and maltose )
Non reducing = sucrose
What is a reducing sugar?
Sugar that can donate electrons to other molecules
Eg glucose and fructose
Eg some disaccharides - lactose and maltose
