(U1) Molecules Flashcards
Why is water a good solvent?
- Due to their polarity, water molecules are attracted to other polar molecules
- this allows them to form clusters around the solute and therefore dissolve them
What is a polar molecule?
Why is water a polar molecule?
- A molecule where individual atoms have slight, opposite charges due to uneven distribution of covalent bonds (electron slightly more attracted to one of the molecules)
- the oxygens have a slight -ve charge, hydrogens slight +ve
In what 3 ways is water used within the body?
- most of the reactions in cells take place in aqueous solutions (in water)
- water acts as a transport medium
- it has different effects on hydrophobic and hydrophilic molecules (e.g. fat won’t dissolve in water) - key for membrane structure
What are calcium ions used for by humans and plants? (4)
- helps produce calcium pectate for use in plant cell walls
- a component of bones and teeth
- key in blood clotting
- key in muscle contraction
What are Iron ions used for by humans and plants? (2)
- in the haem group of haemoglobin (oxygen carrier in RBCs)
- key constituent of electron carriers in respiration
What are magnesium ions used for in plants?
Helps make chlorophyll able to absorb light
What are potassium ions used for in humans?
Maintaining electrical gradients across neurones
What are nitrate ions used for by humans and plants?
A component of amino acids, nucleic acids and chlorophyll
What are phosphate ions used for by humans and plants? (2)
- helps form phospholipids for cell membranes
- component of bio molecules like ATP (adenosine triphosphate) and nucleic acids
What are Hydrogencarbonate ions used for by humans and plants?
Used as a natural buffer
What are buffers? (2)
Why are they needed?
- Chemicals or substances that resist changes to pH - meaning pH is maintained
- when small volumes of acid/alkali are added
- pH changes can result in enzyme denaturation, buffers prevent this and allow enzymes to operate at their optimum pH
Give 2 examples of buffers
- HCO3- ions
- blood proteins e.g. albumin
What are ions?
Charged particles
Name 7 inorganic ions
and
state their formula
- calcium - Ca2+
- iron - Fe2+
- magnesium - Mg2+
- potassium - K+
- nitrate - NO3-
- phosphate - PO43-
- hydrogen-carbonate - HCO3-
What are organic molecules?
Name 3 examples
- complex carbon containing molecules
- carbohydrates, proteins and lipids
What are monomers and polymers?
What is the name of the process used to form polymers?
and
what does it entail?
- mono - individual subunits
- poly - many subunits joined together
- polymerisation - adding monomers together to form polymers
What elements are contained in carbohydrates?
- carbon
- hydrogen
- oxygen
What is the ratio between the number of hydrogen and oxygen atoms in carbohydrates?
2 hydrogen : 1 oxygen
What are the 3 types of carbohydrates?
- monosaccharides
- disaccharides
- polysaccharides
What are monosaccharides?
Which 3 categories are biologically important?
- simple sugars with different categories depending on no. of carbons
- important ones:
- trioses (3 carbons),
- pentoses (5 carbons) and
- hexoses (6 carbon)
What are disaccharides? (2)
- Double sugars formed from 2 monosaccharide monomers
- which join through condensation reactions
What are polysaccharides? (2)
- Complex molecules consisting of many monosaccharide monomers
- bonded through condensation reactions
What is DNA Helicase
and
How does it work? (3)
- An enzyme
- breaks hydrogen bonds between complementary bases (ATCG),
- separating into 2 polynucleotide strands
What is DNA polymerase
and
How does it work?
- an enzyme
- joins mononucleotides together to form a new polynucleotide strand
Which 2 enzymes are used in DNA replication?
- DNA helicase
- DNA polymerase
Why is DNA replication referred to as being semi-conservative?
Each newly synthesized DNA molecule retains 1 parental strand and 1 newly synthesized strand
What are hydrogen bonds? (Biology)
How are they broken?
- Weak bonds between hydrogen and oxygen ions in water due to uneven distribution of covalent bonds
- broken by thermal energy
What are isomers?
Name 2 examples
- Compounds with the same chemical formula but slightly different structural formula
- a-glucose and ß-glucose
How do the structures of a-glucose and ß-glucose differ?
- a-glucose: the hydroxyl group connected to carbon 1 points downward (hydrogen points up)
- ß-glucose: the hydroxyl group points upward (hydrogen points down)
Which polysaccharide(s) contain a-glucose?
- starch
- glycogen
Which polysaccharide(s) contain ß-glucose?
Cellulose
What are the properties of disaccharides? (2)
- soluble in water
- sweet tasting
What are condensation reactions? (In amylose chains) (4)
- reversible reactions where the Hydroxyl group of the Carbon 1 on a monosaccharide
- and the hydrogen (from the hydroxyl group) of the carbon 4 on another
- are ejected as a water molecule
- leaving a 1-4 glycosidic bond
What is hydrolysis?
- When a water molecule is added to a disaccharide
- breaking the 1-4 glycosidic bond
- and separating it into monosaccharides
Name 2 disaccharides
and
state their monosaccharide components
- maltose - 2 a-glucose
- sucrose - 1 a-glucose and 1 fructose
How is the structure of fructose visibly different to glucose?
- Fructose has a pentagonal shape,
- whereas both forms of glucose are hexagonal
What are the properties of polysaccharides? (2)
- insoluble in water
- not sweet
What are the 2 forms of starch chains?
- Amylose
- amylopectin
How is amylose structured? (3)
- long chains of a-glucose with alpha 1-4 glycosidic bonds
- that form a helical structure held in place by hydrogen bonds
- chains are unbranched
How is amylopectin structured? (4)
- long chains of alpha 1-4 glycosidic bonds
- with branched ends
- formed by alpha 1-6 glycosidic bonds
- chains form helical shape held in place by hydrogen bonds
How is amylose different to amylopectin?
- Amylopectin is branched and contains 1-6 glycosidic bonds
- amylose does not
Why is starch a good storage molecule? (4)
- amylose and amylopectin are compact and dense with glucose
- insoluble / osmotically inert: doesn’t affect cell’s water relations
- large molecule, so doesn’t leave cell membrane
- amylopectin: branching creates terminal ends - easily hydrolysed especially in rapid enzymatic breakdown
Where is starch found? (Amylose and amylopectin)
And
In what form?
- Plant cytoplasm or chloroplasts
- starch grains
Where is cellulose found?
Plant cell walls
How is glycogen structured (3)
What is its function and where is it found?
- formed of chains of a-glucose
- has a-1-4 and a-1-6 glycosidic bonds
- meaning it is branched
- To store carbohydrates (for energy)
- Found as granules in mammalian liver and muscle cells
How does glycogen’s structure compare and contrast with amylopectin? (6)
Contrasts:
- glycogen is more branched and chains are shorter
- glycogen has no unbranched chains
- glycogen has proportionally more terminal ends, enabling faster hydrolysis
Comparisons:
- both compact and insoluble - don’t affect cell water relations
- both have a-1-4 and a-1-6 glycosidic bonds
- both are formed of a-glucose monomers
How is cellulose structured (5)
What is its function and where is it found?
- ß-glucose monomers form 1-4 glycosidic bonds
- every 2nd monomer is inverted
- forming long, straight chains
- nearby chains are hydrogen bonded together, forming a microfibril
- many microfibrils form a cellulose fibre
- Structural support for plants
- Plant cell walls
What effect does the flipping of alternate monomers in cellulose have on its structure? (2)
- Chains are very straight
- due to the -CH2OH groups alternating above and below the chain
Why do hydrogen bonds form between adjacent cellulose chains?
Oxygen and the -CH2OH are available on both sides of chains
What is the chemical formula of fructose?
C6H12O6
What is the chemical formula of glucose?
C6H12O6
What is the formula of Glycerol?
C3H8O3
What group do fatty acids belong to?
Carboxylic / organic acids
What elements do lipids contain?
Carbon, hydrogen and oxygen
Although lipids are hydrophobic, what solvents do they dissolve in?
Organic ones like ether and ethanol
What are the 2 main types of lipids
Where are they found?
- triglycerides - fats and oils
- phospholipids - cell membranes
How are triglycerides formed? What else is formed?
What bonds are formed?
What is formed in the reverse of this, and what is this called?
- Condensation reactions between 1 glycerol and 3 fatty acid molecules + 3 molecules of water liberated
- ester bonds
- 1 glycerol and 3 fatty acids reformed - Hydrolysis (by adding 3 molecules of water)
Where do condensation reactions occur in triglycerides?
What is this process also known as?
- Between:
- The (-OH) group of glycerol and
- the (-COOH) group of fatty acids
- Esterfication
What are the differences between saturated and unsaturated fatty acids? (2)
- saturated consist of chains of single carbon bonds and hydrogen - unsaturated have at least 1 C=C double bond
- unsaturated aren’t as straight structurally
What is the name of an unsaturated fatty acid with 1 C=C bond?
Monosaturated fatty acids
What is the name of an unsaturated fatty acid with more than 1 C=C bond?
Polyunsaturated fatty acids
How are phospholipids formed?
- condensation reactions between 1 glycerol molecule and 2 fatty acid molecules
- as well as a phosphate group - replaces a fatty acid in a triglyceride
What are the properties of phospholipids? (4)
- fatty acid molecules are hydrophobic
- phosphate makes the glycerol hydrophilic and soluble in water
- they are polar - key in their role in cell membranes
- cell membranes contain the steroid cholesterol, located among hydrocarbon chains
What are the functions of triglycerides? (3)
- energy store - release more energy per unit mass than carbs
- insulation (thermally) e.g. as adipose tissue
- protection of body organs
What type of lipid are fats and oils?
What are the differences between both generally? (2)
- Triglycerides
- fats are solid at room temp, oils are liquid
- fats are usually animal products - oils are made by plants
What elements are contained in a protein molecule?
- carbon
- hydrogen
- oxygen
- nitrogen
- sometimes sulphur
How many amino acids are in 1 protein?
20
What is a protein’s shape determined by? (2)
- It’s sequence of amino acids
- and the bonds / attractions between their R-groups
How does each amino acid differ?
Each has a different R group
What is the R group of glycine?
-H
What is the R group of alanine?
-CH3 (methyl group)
What is the R group of cysteine?
-CH3 -SH
What reaction is responsible for linking amino acids?
What bonds are produced?
What is the inverse reaction called?
- Condensation
- peptide bonds
- hydrolysis
What is a pair of bonded amino acids called?
A dipeptide
What is a polypeptide?
Many amino acids joined together
What are the 4 levels of structure in a protein?
- primary
- secondary
- tertiary
- quaternary
What is a primary structure caused by? (protein)
The sequence of amino acids in a polypeptide chain
What is a secondary structure caused by? (protein)
What shapes can they be?
- hydrogen bonds between (-C=O)- and (-NH)+
- a-helix (held by hydrogen bonds) or ß-pleated sheets - more rigid and less flexible (due to hydrogen bonds)
What bonds/attractions can be present between R-groups in a tertiary structure? (protein)
What are their properties?
(4)
- hydrogen bonds - weak and easily broken
- ionic bonds - strong but weak with pH changes
- disulfide bonds / bridges - very strong covalent bonds
+ hydrophobic interactions between amino acids and hydrophobic R-groups - R-groups tend to be surrounded by other parts of the polypeptide
How are tertiary protein structures formed broadly? (3)
- further folding
- creating a 3d shape
- due to a range of bonds between R-groups of amino acids in the chain
bonds covered in another card
What do quaternary protein structures consist of? (2)
What are the 2 types?
- 2 or more polypeptides
- with some containing prosthetic groups - conjugated proteins
- Globular and fibrous
What are prosthetic groups?
What are proteins containing prosthetic groups called?
- Non-protein components of proteins e.g. the haem group of haemoglobin (which contains iron)
- conjugated proteins
Name 3 conjugated proteins
Include what type of protein they are.
Any 3 from:
Globular:
- haemoglobin
- glycoprotein
- enzymes
- insulin
Fibrous:
- collagen
- actin
- keratin
Etc.
What are prions? (2)
- A type of protein
- found in the mammalian nervous system and some other animals
What is the notation for:
- Normal
- Disease causing
Prions?
- normal = PrP / PrPc
- disease causing = PrPsc
Structurally, how do disease causing prions differ from normal prions? (2)
- disease causing = missfolded
- disease causing = greater proportion of ß-pleated sheets than a-helices
Why does the presence of a disease causing prion pose a threat? (4)
- causes a chain reaction where other normal prions become progressively missfolded
- this increases no. of disease causing prions
- if at a threshold level, neurodegenerative disorders can emerge in nervous tissue
- this can lead to death
What are the 2 key features of disease causing prions?
- can replicate
- are infectious
How long can prions be incubated for?
5 to 20 years
Name 3 ways diseases caused by prions can arise.
- normal prions spontaneously adopt the PrPsc form
- mutations in DNA bases coding for prion proteins —> disease-causing form can be passed to offspring
- eating contaminated food with diseased prions
Name 3 prion diseases
and
What animals they are found in
- scraple in sheep
- Bovine Spongiform Encephalopathy (BSE) - ‘mad cow disease’
- variant Creutzfeldt-Jakob disease (vCJD) - in humans - acquired usually by eating beef with BSE
What’s the subunit of a nucleic acid?
A nucleotide
What are the components of a nucleotide?
- phosphate
- a Pentose sugar
- a base
What are the bases found in DNA?
Include how they pair
- Adenine
- Guanine
- Cytosine
- Thymine
- AT and CG
What are the bases found in RNA?
Include how they pair
- Adenine
- Cytosine
- Uracil
- Guanine
- They don’t (single strand)
Why are strands of DNA described as being anti parallel?
2 strands run in opposite directions
What bonds are there between phosphates and pentose sugars in nucleic acids?
Phosphodiester links
What are the differences between DNA and RNA? (4)
- DNA contains deoxyribose sugar, RNA contains ribose sugar
- subunits of DNA are deoxyribonucleotides, subunits of RNA are ribonucleotides
- DNA is longer and double stranded, RNA is shorter and single stranded
- DNA contains thymine, RNA contains Uracil instead
What are the 3 types of RNA?
- mRNA - messenger RNA
- tRNA - transfer RNA
- rRNA - ribosomal RNA
What are the roles of the 3 types of RNA?
- rRNA: component of ribosomes
- tRNA: carries amino acids to ribosomes where protein synthesis takes place
- mRNA: carries code from DNA in the nucleus to a ribosome where protein synthesis takes place
What is the function of DNA? (2)
- Acts as the genetic code for amino acid synthesis
- according to base triplets
What are the ends of a polynucleotide strand called?
Why are they called this?
- 5’ ends and 3’ ends
- 5’ ends are closest to the 5th carbon of a sugar
- 3’ ends are closest to the 3rd carbon of a sugar
What is a gene?
A sequence of DNA that codes for a polypeptide
Outline the process of semiconservative replication (4)
- DNA helicase breaks hydrogen bonds between complementary bases to reveal 2 polynucleotide strands
- DNA polymerase moves along each strand and acts as a template for the synthesis of a new strand
- DNA polymerase catalyses the joining of free deoxyribonucleotides to each original strand - new complementary strands form
- process continues along entire length of DNA molecule
Outline the Meselson Stahl experiment (4)
- cultured E. coli using 15N
- 15N incorporated into the bases of the DNA in all the bacteria over time; bacteria with 14N died and were replaced
- bacteria were transferred to a medium with 14N
- bacteria extracted and analysed using a centrifuge at intervals:
- While growing before 15N
- While growing in 15N
- 1st gen after transfer to 14N
- 2nd gen after transfer to 14N
Explain the results of the Meselson Stahl experiment (3)
What trend would results follow after a further gen?
- gen 0: all DNA at bottom of centrifuge tube - 15N bases
- gen 1: DNA in middle - 1 strand 15N bases, 1 strand 14N bases —> medium mass
- gen 2: half DNA = medium mass with 15N and 14N bases, other half only DNA with 14N bases (top)
- More DNA with 14N bases, less mixed DNA
