3 - Biological Molecules Flashcards
What makes up molecules?
Atoms
What are different types of atoms called?
Elements
What distinguishes different elements from one another?
the number of protons in their atomic nuclei
How many bonds can carbon make?
4
How many bonds can nitrogen make?
3
How many bonds can oxygen make?
2
How many bonds can hydrogen make?
1
What is methane’s formula?
CH4
What is ammonia’s formula?
NH3
What are ions in solutions called?
electrolyte
Cations
What is calcium necessary for?
Ca2+
- nerve impulse transmission
- muscle contraction
Cations
What is sodium necessary for?
Na+
- nerve impulse transmission
- kidney function
Cations
What is potassium necessary for?
K+
- nerve impulse transmission
- stomatal opening
Cations
What is hydrogen necessary for?
H+
- catalysis of reactions
- pH determination
Cations
What is ammonium necessary for?
NH4 +
- production of nitrate ions by bacteria
Anions
What are nitrate ions necessary for?
NO3 -
- nitrogen supply to plants for amino acid and protein fomration
Anions
What are hydrogen carbonate ions necessary for?
HC03 -
- maintenance of blood pH
Anions
What are chloride ions necessary for?
Cl-
- balance positive charge of sodium and potassium ions in cells
Anions
What are phosphate ions necessary for?
PO4 3-
- cell membrane formation
- bone formation
- nucleic acid and ATP formation
Anions
What are hydroxide ions for?
OH-
- catalysis of reactions
- pH determination
What elements are present in carbohydrates?
carbon, hydrogen and oxygen
What elements are present in lipids?
carbon, hydrogen and oxygen
What elements are present in proteins?
carbon, hydrogen, oxygen, nitrogen and sulfur
What elements are present in nucleic acids?
carbon, hydrogen, oxygen, nitrogen and phosphorus
What monomers make up carbohydrates?
sugars (saccharides)
What monomers make up proteins?
amino acids
Define polarity
The uneven distribution of charges
How is water a polar molecule?
- oxygen has a negative charge
- two hydrogen have two positive charges
- positive and negative regions of the molecule attract each other and form hydrogen bonds
Define a hydroxyl group (OH)
Organic molecules containing oxygen and hydrogen bonded together
Why is water’s bp unusual?
Very hugh
Why is water a liquid at room temp. despite being a small molecule?
due to hydrogen bonding between water molecules - takes a lot of energy to increase the temp
What is water’s density when it freezes?
Less dense as ice
What happens as water cools below 4°C?
hydrogen bonds fix the positions of polar molecules slightly further apart than normal
What is made when water cools below 4°C?
A giant, rigid, but open structure with every oxygen atom at the centre of a tetrahedral arrangement of hydrogen atoms
Why does water move as one mass?
Due to cohesion as molecules are attracted to one anofjer
Why is water attracted to other molecules?
Adhesion
What is a property of water from strong cohesion?
gives water a “skin” of surface tension
Why is water an efficient transport medium in living things?
cohesion between water molecules means that water and molecules stick together
What are the effects of adhesion and cohesion on water?
Capillary action - process by which water can rise up a narrow tube against the force of gravity
Why is water important for temperature?
Acts as a coolant so controls organisms temperature as it is a stable substance
Why is surface tension important on water?
Provides a habitat to support small insects such as pond skaters
What is the general formula for carbohydrates?
Cx(H2O)y
What is a single sugar unit called?
monosaccharide
Give examples of monosaccharides
glucose, fructose, ribose
What are two monosaccharides called?
disaccharide
Give examples of disaccharides
lactose, sucrose
What are more than two monosaccharides joined together called?
polysaccharide
Give examples of polysaccharides
glycogen, cellulose, starch
Formula of glucose
C6H12O6
In molecular structured diagrams, how are the carbon atoms numbered?
clockwise, beginning with the carbon to the right of the oxygen atom within the ring
What are the types of glucose and how do they vary?
Alpha and beta glucose vary in their position of the OH group on carbon 1
Properties of glucose
polar, soluble due to hydrogen bonds between hydroxyl group
What happens when 2 alpha glucose molecules are side by side?
two hydroxyl groups interact, breaking bonds and reforming them in different places = produces new molecules
What happens in a condensation reaction?
- 2 hydrogen atoms and 2 oxygen atoms are removed from glucose monomers and join to form water
- bond forms between carbons 1 and 4 on glucose for example, joining molecules
- ## covalent bond called glycosidic bond forms between two glucose
Define a condensation reaction
when a water molecule is formed as one of the products of the reaction
Give examples of hexose monosaccharides
fructose, galactose, glucose
What forms the disaccharide lactose (milk)?
galactose and glucose
What forms the disaccharide sucrose (cane sugar)?
fructose and glucose
What is ribose present in?
ribose is sugar in RNA nucleotides and deoxyribose is the sugar in DNA nucleotides
What are pentose monosaccharides?
sugars containing 5 carbon atoms
What is starch?
Glucose made by plants is stored as starch as it isa chemical energy store
Name a polysaccharide in starch
amylose
How is amylose formed?
by alpha glucose molecules joined together only by 1-4 glycosidic bonds
What makes amylose more compact and less soluble than glucose?
angle of 1-4 glycosidic bond means long chain of glucose twists to form a helix, which is stabilised by hydrogen bonding
Which starch polysaccharide is made by 1-4 glycosidic bonds between alpha glucose molecules, but formed by condensation reactions?
Amylopectin
Where are the condensation reactions on amylopectin and how does this affect it?
between carbon 1 and carbon 6 on two glucose molecules, meaning it has a branched structure
What is the animals and fungi equivalent to starch?
glycogen
How is glycogen’s branching imporant in its storage?
it can be coiled very compactly, meaning less sace is needed to store it
What are the key properties of amylopectin and glycogen?
insoluble, branched and compact
Why does the branching glycogen help?
means there are many free ends where glucose molecules can be added or removed, speeding up the process of storing or releasing glucose
How is starch/glycogen released for respiration?
in a hydrolysis reaction, requring the addition of water molecules
What catalyses hydrolysis reactions?
enzymes
Can beta glucose molecules join in the same way as alpha glucose?
No, the only way that beta glucose molecules can join together and form a polymer is if alternate beta glucose molecules are turned upside down
What is a straight chain molecule of beta glucose called, and what are its properties?
cellulose - it is unable to coil or form branches
How are microfibrils formed?
when cellulose molecules make hydrogen bonds with each other
What happens when microfibrils join together?
macrofibrils are formed, which combine to produce fibres
Why is cellulose imporant to our diet?
it is hard to break down, and forms fibre necessary for healthy digestive system
What is the chemical test for sugar?
Benedict’s reagent, an alkaline solution of copper(II) sulfate
How is a Benedict’s reagent test carried out?
- place sample in a boiling tube (grind it up or blend in water if its a solid)
- add an equal volume of Benedict’s reagent
- heat the mixture gently in boiling water bath for 5 mins
How will reducing sugars react in Benedict’s reagent?
will react with copper ions, resulting in the addition of electrons to the blue Cu2+ ions, reducing them to brick red
What is the result of a reducing sugar test?
a brick-red precipitate is formed - the higher the conc. of reducing sugar, the less blue Cu2+ ions left
What is the most common non-reducing sugar
Sucrose
What is the test for non-reducing sugars
- first boil sugar with dilute HCL
- this will give it a positive result when then mixed with benedicts
- this is because the sugar has been hydrolysed by the acid to its monosaccharides
What is the test for starch?
Iodine test - add a few drops of iodine dissolved in potassium iodide solution
What is the result for the iodine test for starch?
yellow/brown to purple/black
Why are manufactured reagent strips good?
the concentration of the sugar can be determined using the colour-coded chart
What are biosensors?
use biological components to determine the presence and conc. of molecules such as glucose
How does a colorimeter work?
quantitatively measures the absorbance, or transmission of light by a coloured solution
more conc a solution = more light it will absorb
What are the building blocks of proteins?
Amino acids
What does every amino acid possess in its structure?
An amino group and a carboxylic acid group
How many naturally occurring amino acids are there?
20
What bond is formed when amino acids join together?
Peptide bond
What is formed when two amino acids bond during a condensation reaction?
A dipeptide molecule
What enzymes catalyse the condensation reaction of amino acids to form peptides?
Peptidyl transferase found in ribosomes
What enzyme catalysed the hydrolysis reaction, turning peptides back into amino acids?
Proteases
What are R groups in proteins?
A variable group
How can amino acids be neutral molecules?
When the amino acids possesses one acid (carboxylic acid) and one basic group (amino group)
How can amino acids be acidic molecules?
When the R group is a carboxylic acid group. It thus has 2 acidic and 1 basic group
How can amino acids be basic molecules?
When the R group is an amino group. It thus has 2 basic groups and 1 acidic hroup
Name the two sulphur-containing amino acids
Sulfur is in the R-group
Cysteine and Methionine
Define hydrogen bonds in proteins
Formed between R-groups; easily broken but numerous
Define disulphide bonds in proteins
Formed between sulfur-containing amino acids; strong bonds important in structural proteins (eg.skin/hair)
What are long, thin proteins called that are insoluble and structural?
Fibrous
What are proteins rolled into a ball, that are soluble and important in metabolism called?
Globular
Protein Structure
What is the primary structure?
Is the number, type, order and sequence of amino acids that make up this linear chain together with peptide bonds
Protein Structure
Define the general secondary structure
The arrangement in space of the atoms that form the backbone or linear chain of the protein
Protein Structure
What is the alpha helix secondary structure?
- Amino acid chain coils into a right handed helix
- hydrogen bonds form between oxygen and hydrogen atoms that have been brought into close proximity
- hydrogen bonds stabilise structure
Protein Structure
What is the beta-pleased secondary structure?
- amino acid folds back upon itself lots forming anti-parallel chains
- oxygen and hydrogen atoms brought into close proximity form hydrogen bonds
- hydrogen bonds stabilise structure
Which proteins display tertiary structure?
Globular proteins
Protein Structure
What is the tertiary structure?
Folding of a protein into its final shape
Once the secondary structures have formed, the molecule bends and folds into a 3D globular shape
Define ionic bonds in proteins
Stronger than hydrogen bonds and fork between oppositely charged R-groups
Define hydrolysis
The type of reaction that occurs when water is added to break a bond in a molecule
Define hydrophilic
The phosphate group of a phospholipid that readily attracts water molecules
Define hydrophobic
Substances that can’t become part of water’s hydrogen-bonded structure will not dissolve
Protein Structure
When is quaternary structure shown?
A level of structure displayed by proteins that consist of more than one polypeptide chain
Give an example of a protein with quaternary structure?
Haemoglobin
- consists of 4 polypeptide chains that are held together by weak forces
In haemoglobin, what does each polypeptide chain contain?
an iron containing a haem group that binds to molecules of oxygen
What happens with hydrophobic R groups in proteins?
Tend to cluster towards the interior of the protein mowlcule
Name a protein that has tertiary structures & where is it found?
Myoglobin is found in muscle cells
Give examples of biological processes requiring energy
Muscle contraction, cell division, the transmission of nerve impulses, memory formation
Cell require energy for what 3 main types of activity
- synthesis
- transport
- movement
How is energy supplied inside cells in a way it can be used?
Adenosine triphosphate (ATP)
What composed an ATP molecule?
A nitrogenous base, a pentose sugar and 3 phosphate groups - it is a nucleotide
What is the base and the sugar in ATP?
Base = adenine
Sugar = ribose
What is ATP known as?
Universal energy currency
How much energy is released to break the bond holding the last phosphate group in ATP?
Small amount of energy as the bond is weak
How much energy is released when the free phosphate in ATP undergoes other reactions involving bond formation?
A large amount of energy
Overall, how much more energy is released than used in ATP?
30.6 kJ / mol
Why is the removal of the phosphate group in ATP a hydrolysis reaction?
As water is a reactant
Where does the hydrolysis of ATP happen?
In association with energy-requiring reactions - reactions are said to be “coupled” as they happen simultaneously
What are the products of the hydrolysis of ATP?
Adenosine diphosphate (ADP) + a phosphate ion + energy
Why is ATP not a good long-term energy source, and what is a better source?
The phosphate bonds are too unstable. A better source would be fats and carbs
What is phosphorylation?
Reattaching a phosphate group to an ADO molecule to create ATP. It is a condensation reaction as water is removed
Why is ATP a good immediate energy source?
The inter conversion of ATP and ADP is rapid and constant in living cells
What are the properties of ATP?
- small = moves easily in/out of cells
- soluble
- easily regenerated
- releases energy in small quantities
- contains bonds between phosphates with intermediate energy = large enough to be useful but not so large that energy is wasted
What will affect how amino acids and proteins ionise?
The hydrogen ion concentration (pH)
What type of ions are most amino acids?
Cations
Define an Iso-electric point (IEP)
the pH at which the amino acids or proteins carry no net charge
What state are different lipids at room temperature?
Fats = solid
Oils = liquid
What are macromolecules?
Large, complex molecules which are not built from repeating units or monomers
Eg. Lipids
Are lipids polar molecules?
No as the electrons in the outer orbitals that form the bonds are more evenly distributed than in polar molecules
What makes up a triglyceride?
One glycerol molecules and 3 fatty acids
Which group does glycerol beli to?
Alcohols
Which group do fatty acids being to?
Carboxylic acids
How does esterification (condensation) occur in lipids?
Hydroxyl groups interact, producing 3 waters and ester bonds between fatty acids and glycerol
What is it called when a fatty acid chain has no double bonds with carbon atoms, and is full of hydrogen?
Saturated
What is it called when a fatty acid has double bonds between some of the carbon atoms?
Unsaturated
What is it called if a fatty acid has only 1 double bonds
Monounsaturated
What is it called when a fatty acid has 2 or more double bonds?
Polyunsaturated
What does the presence of double bonds in fatty acids cause?
The molecule can’t link or bend, so they can’t pack closely together = why they are liquid at room temp
What lipids do plants contain?
Unsaturated triglycerides (healthy oils)
What can excess saturated fats in a diet lead to?
Coronary heart disease / obesity
What are phospholipids?
modified trig. and contain phosphorus, carbon, hydrogen, and oxygen
Where can you find organic phosphate ions in a cell?
In the cytoplasm
Why are phosphate ions soluble in water?
the have extra electrons and so are negatively charged
Why are phosphate ions soluble in water?
the have extra electrons and so are negatively charged
How is a phospholipid structurally formed?
One of the fatty acid chains in a trig. is replaced with a phosphate group
What is the non-polar end (tail) of a phospholipid and what does this mean?
Tail = fatty acids chain
Repelled by water = hydrophobic
Mix readily with fat
What is the charged end (head) of a phospholipid and what does this mean?
Charged head = phosphate group
Interacts with water = hydrophilic
How do phospholipids interact with water due to their hydrophobic/hydrophilic structure?
Form a layer on surface of water with the phosphate heads, with the fatty acids tail sticking out of the water
What are phospholipids called because of their reaction with water?
Surface active agents / surfactants
How is a phospholipid bilayer formed in water?
Two-layered sheer formation (bilayer) with hydrophobic tails pointing towards centre of sheet, protected from water by hydrophilic heads
How are phospholipids important in playing a key role in forming cell membranes?
Able to separate an aqueous environment in which cells usually exist from the aqueous cystol within cells
It is thought this is how first cells were formed
What are the biological roles of lipids due to their non-polar nature?
- membrane formation + creation of hydrophobic barriers
- hormone production
- electrical insulation = impulse transmission
- waterproofing (birds’ feathers/leaves)
What is the role of triglycerides stores under the skin and around vital organs?
- thermal insulation
- cushioning to protect vital organs
- buoyancy for aquatic animals
What is manufactured using cholesterol?
Vitamin D, steroid hormones, bile
Where does the body manufacture the sterol Cholesterol?
primarily in the liver and intestines
What is the role of cholesterol?
Formation of cell membranes, becoming positioned between the phospholipids with the hydroxyl group at the periphery of the membrane
Why is cholesterol important in cell membranes?
Adds stability and regulates their fluidity by keeping membrane fluid at low temps
What is the structure of sterols aka steroid alcohols?
Complex alcohol molecules, based on a 4 carbon ring structure with a OH group at one end
How are sterols similar to phospholipids?
Dual hydrophilic/hydrophobic
Hydroxyl group in sterols is polar = hydrophilic and rest of molecule is hydrophobic
What is the test for lipids?
Emulsion test
- Mix sample with ethanol
- Mix solution with water
- White emulsion forms = lipids are present
What is food synergy?
Nutrients do not work in isolation but as part of the combined effect of a whole range of nutrients
Define cohesion
Water is attracted to water
Define adhesion
Water is attracted to other substances
What 3 components are in a nucleotide?
- a pentose monosaccharide
- a phosphate group
- a nitrogenous base
How does a condensation reaction occur in a nucleotide?
phosphate group at carbon 5 of sugar forms a covalent bond with the hydroxyl group at the third carbon of an adjacent nucleotide
What bond forms between nucleotides?
a phosphodiester bond
What are pyrimidines?
1 nitrogen-containing ring
What are purines?
2 nitrogen-containing rings
Which bases are pyrimidines?
Thymine and Cytosine
Which bases are purines?
Adenine and Guanine
What bonds are between bases?
Hydrogen bonds
What are DNA strands said to be?
Anti-parallel
How many hydrogen bonds do C and G form?
3 hydrogen bonds
Why is there a constant distance between the DNA backbones?
The complementary base pairing means that a small pyrimidine base always binds to a larger purine base
What carries the genetic info of an organism?
The sequence of bases along a strand in the form of a code
Why is DNA unable to leave the nucleus?
Each chromosome is a very long molecule which can’t be transported through nucleic pores
How is DNA changed to be able to leave the nucleus?
short section of the long DNA corresponding to a single gene is transcribed into a mRNA
How is RNA different to DNA?
RNA has ribose, DNA has deoxyribose
RNA has uracil, DNA has thymine
What happens to RNA after protein synthesis?
The RNA molecules are degraded in the cytoplasm. The phosphodiester bonds are hydrolysed and the RNA nucleotides are released and reused
Globular protein properties
Compact, water soluble, spherical
How do globular proteins form?
When proteins fold into 3Y in a way that the hydrophobic R groups are kept away from the aq environment
Where are the hydrophilic R groups on globular proteins and what does this mean?
On the outside of the protein = soluble
What type of protein is insulin?
A globular hormone - alpha helix -
Why is it important hormones are globular?
Transported in the bloodstream so need to be soluble, and hormones must fit into specific receptors on cell-surface membranes, so must be precise shapes
Why is it important hormones are globular?
Transported in the bloodstream so need to be soluble, and hormones must fit into specific receptors on cell-surface membranes, so must be precise shapes
What are conjugated proteins?
Globular proteins that contain a non-protein component called a prosthetic group
What are proteins that don’t have prosthetic groups called?
Simple proteins
What is an example of a prosthetic group in conjugated proteins?
Haem groups - contain iron 2+
What is haemoglobin’s structure?
4Y made from 4 polypeptides, two alpha and two beta units
What enables haemoglobin to transport oxygen around the body?
Each subunit contains a haem group, with the iron ions present in it are able to combine reversible with O2 (associate/dissociate)
What is Catalase’s structure?
4Y conjugated protein containing 4 haem groups
How does the presence of iron 2+ in Catalase’s haem group help it’s function?
Allows catalase to interact with hydrogen peroxide and speed up its breakdown
What is hydrogen peroxide (that is broken down by catalase)?
A common byproduct of metabolism but is damaging to cells if allowed to accumulate
What are fibrous proteins properties?
Long, insoluble molecules that are not folded into complex 3D shapes
Why are fibrous proteins insoluble?
Due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structure
Where is keratin found?
In hair, skin and nails
What sulfur-containing amino acid does keratin contain?
Cysteine
What does the presence of cysteine in keratin result in?
Many strong disulphide bonds (bridges) forming strong, inflexible and insoluble materials
What is the unpleasant smell when hair/skin is burnt?
Large quantities of sulfur in keratin
Give examples of fibrous proteins?
Keratin, elastin and collagen
What does the degree of disulphide bonds determine in keratin?
The flexibility
What makes hair more flexible than nails?
Contains fewer disulfide bonds making it more flexible
Where are elastic fibres containing elastin found?
In the walls of blood vessels and in the alveoli of the lunhs
What is elastin’s structure?
4Y made from stretchy molecules called tropoelastin - gives flexibility
Where is collagen found?
Skin, tendons, ligaments and the nervous system
What is tropoelastin?
Wiggly fibres that straighten when stretched
How is collagen used artificially?
Cosmetics - in lip fillers
Collagen is in a number of different forms, but all are made from…?
3 polypeptides wound together in a long, strong, rope-like structure with covalent bonds
Collagen has a lot of what amino acid every 3rd a.a.?
Glyceine
How do the 3 polypeptides in collagen form a beta-pleated structure?
Forms a triple helix - 3 fibres twisted together are staggered at their ends to avoid weak points
How many strands do DNA and RNA have?
DNA = 2
RNA = 1
DNA + RNA summary of use
DNA = stores generic blueprint - stable
RNA = transfers genetic info for decoding
What are the 2 covalent bonds called between 2 nucleotides in a condensation reaction?
phosphodiester linkage
What did Watson and Crick notice as a copying mechanism?
Specific pairings of bases
What happens to the hydrogen bonds connecting the DNA strands before replication? Okay
They are unzipped = H bonds break
What is semi-conservative replication?
- one original strand acts as a template
- one strand is newly synthesised
- hence semi-conservative
What is the original DNA strand in replication called?
The template for the creation of a new double stranded molecule
When does semi-conservative replication happen?
During interphase
What determines the direction of replication?
The two strands run in anti-parallel directions (5prime and 3prime)
What enzyme is used for unzipping DNA strands?
Helicase
What does primase do?
Catalyses the formation of a primer from RNA nucleotides
What is the role of a primer in DNA replication?
Marks the starting point for the construction of the new DNA strand
DNA replication
What does helicase do?
Unwinds the double helix and separate the two polynucleotide strands that run anti parallel by unzipping the strand
DNA replication
What happens once the DNA strands are unzipped?
Two strands acts as templates for activated free nucleotides to align opposite their complementary base partner
DNA replication
What does DNA polymerase do?
Synthesises the new strands from 2 parental template strands by catalysing the formation of phosphodiester bonds between the aligned nucleotides
DNA replication
What is the leading strand?
The strand that is unzipped from the 3’ direction can be continuously replicated as the strands unzip
DNA replication
What is the lagging strand?
The other strand unzipped from 5’ end undergoes discontinuous replication
DNA replication
Why does the lagging strand undergo discontinuous replication?
Because DNA polymerase has to wait until a section of the strand has unzipped and then work backwards along the strand
DNA replication
What does discontinuous replication result in?
Sections of DNA called Okazaki fragments which then have to be joined with DNA ligase
DNA replication
How does DNA ligase join okazaki fragments together?
By covalently joining the sugar-phosphate backbones together with a phosphodiester bond
DNA replication
Where does DNA polymerase attach to the DNA strand?
Attaches to the 3’ hydroxyl end and covalently joins the free nucleotides togeher
What is a mutation?
Replication errors that occur randomly and spontaneously when an incorrect sequence of nucleotides and bases aren’t matched
What is genetic code?
The DNA blueprint that must code for a sequence of amino acids, to fold into complex structures and form proteins as the foundations of living things
Where is a simple triplet code found?
The code in the base sequences of DNA along the chain of nucleotides that make 2 strands
What is a codon
A sequence of 3 bases in a simple triplet code
Each codon codes for an amino acid
What is a gene?
A section of DNA that contains the complete sequence of bases (codons) to code for an entire protein
What does it mean if genetic code is universal?
All organisms use the same code
Why are there 64 different base triplets or codons possible?
4 bases
4 X 4 X 4 = 64
How many stop codons are there and what do they do?
3 stop codons that do not code for any amino acids and signal the end of a sequence
What does a start codon do?
Signals the start of a sequence that codes for a protein
What does a start codon in the middle of a gene do?
It codes for the amino acid methionine
What does having a single codon to signal the start of a sequence ensure?
That the triplets of bases (codons) are read ‘in frame’ = DNA base sequence is read from base 1, not base 2 or 3 = genetic code isn’t overlapping
What is degenerate code?
When many amino acids can be coded for by more than one codon
Why does degenerate code exist?
As there are only 20 different amino acids that regularly occur, but a lot more codons
Remember the genetic code is a triplet code!
3 bases =
= 1 codon
One codon codes for one amino acid
Where does protein synthesis occur in eukaryotes?
In the cytoplasm at ribosomes
Define transcription
For a gene to produce a protein, the DNA within the gene must first be copied into RNA
Define translation
The process by which a cell makes proteins using the genetic information carried in a messenger RNA
Although transcription results in a different polynucleotide it has many similarities with dna replication…:.
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