M2, C3 Biological Molecules Flashcards
what are all living things primarily made of
carbon
hydrogen
oxygen
nitrogen
phosphorus and sulphur are also important
whats a covalent bond
when two atoms share a pair of electrons. present in the outer orbitals of the atoms
what are the bonding rules for carbon, nitrogen, oxygen and hydrogen?
carbon - 4 bonds
nitrogen - 3 bonds
oxygen - 2 bonds
hydrogen - 1 bond
whats the displayed formula for:
a) carbon dioxide
b) hydrogen
c) water
a) O=C=O
b) H-H
c) H-O-H
what’s a cation
when an atom or molecule loses one or more electrons and it gets a net positive charge
what’s an anion
when an atom or molecule gains electrons and it gets a net negative charge
what are ions in solutions called
electrolytes
what is an ionic bond
when an atom loses or gains electrons
forms positive or negative ions
held together because of the attraction of opposite charges
what are the uses of calcium ions?
nerve impulse transmission
muscle contraction
what are the uses of sodium ions?
nerve impulse transmission
kidney function
what are the uses of potassium ions?
nerve impulse transmission
stomatal opening
what are the uses of hydrogen ions?
catalysis of reactions
pH determination
what are the uses of ammonium ions?
production of nitrate ions by bacteria
what are the uses of nitrate ions?
nitrogen supply to plants for amino acid and protein formation
what are the uses of hydrogen carbonate ions?
maintenance of blood pH
what are the uses of chloride ions?
balance positive charge of sodium and potassium ions in cells
what are the uses of phosphate ions?
cell membrane formation
nucleic acid and ATP formation
bone formation
what are the uses of hydroxide ions?
catalysis of reactions
pH determination
define polymer
long chain molecules made by linking monomers.
give examples of monomers
glucose, amino acid, nucleotide
give examples of polymers
glycogen, protein, DNA, starch
what does it mean saying a water molecule is polar
the oxygen atom is slightly more negative and the hydrogen atoms are slightly more positive
this means it forms hydrogen bonds
what are the 9 properties of water
universal solvent liquid at room temp specific capacity latent heat of vaporisation latent heat of fusion density capillarity surface tension wetness
what does the universal solvent property in water mean
water can dissolve many substances
enables many chemical reactions to occur in the cell cytoplasm. And enables substances to be transported eg. xylem
what does the liquid at room temp property in water mean
provides a liquid environment both within cells and for aquatic organisms
what does the specific heat capacity property in water mean
water has a high specific heat capacity so it needs lots of energy to increase the temperature - the energy is needed to break the hydrogen bonds
water resists temperature changes, providing a more stable environment within cells and aquatic organisms
what does the latent heat of vaporisation and latent heat of fusion property in water mean
needs lots of heat to turn water into a gas and needs a large lack of heat for water to freeze
evaporation of water from the surface of organisms eg. sweating/transpiration - can provide a significant cooling effect
water within cells and aquatic habitats is slow to freeze providing a more stable environment
what does the density property in water mean
water is less dense as a solid than a liquid
when a water freezes each molecule forms hydrogen bonds with four others. this creates a lattice that holds molecules further apart than a liquid.
Ice therefore floats on water, enabling aquatic organisms to survive in water underneath the ice of frozen lakes and ponds
what does the capillarity property in water mean
water can move up a narrow tube against gravity by capillarity/capillary action
helps plants move water from their roots to their shoots
adhesion/surface tension/cohesion
what does the surface tension property in water mean
at a water-air interface, water molecules form hydrogen bonds with other water molecules but not with air. This uneven distribution results in surface tension.
causes surface of water to form a ‘skin’ which can support aquatic plants and insects
define cohesion and adhesion
cohesion - water molecules stick together because they form hydrogen bonds with each other
adhesion - water can stick to other polar substances and this is the reason why water is wet
what is hydrogen bonding in water
the negative charge of an oxygen atom of one molecule attracts the positive charge of the hydrogen on other molecules
what makes up carbohydrates
carbon
oxygen
hydrogen
what is a monosaccharide and give some examples
a single sugar unit
eg. glucose, fructose and ribose
what is a disaccharide and give examples
when two monosaccharides join together
eg, lactose and sucrose
what is a polysaccharide and give examples
when more than two monosaccharides join together
eg. glycogen, cellulose and starch
what is the formula is glucose and what type of monosaccharide is it?
C6H12O6
hexose monosaccharide
how do you label carbons on a molecular structure diagram
start from the carbon on the right and go clockwise
what is different in the structure between alpha and beta glucose
the OH (hydroxyl) group in carbon 1 is in opposite directions in alpha glucose the OH is on the bottom whereas beta glucose has the OH on top on carbon 1
why are glucose molecules polar and soluble in water
this is due to the hydrogen bonds that form between hydroxyl groups and water molecules
what is a condensation reaction between glucose
when 2 alpha glucose molecules are next to each other, 2 hydroxyl groups interact.
two hydrogen atoms and an oxygen atom are removed from glucose monomers and join to form a water molecule. A bond forms between carbon 1 and carbon 4 (a 1-4 glycosidic bond)
glucose + glucose = (a)
(bi) + (bii) = lactose
glucose + (c) = sucrose
a) maltose
b) glucose + galactose
c) fructose
what is amylose
formed by alpha glucose 1-4 glycosidic bonds
helix
much less soluble
in starch
what is amylopectin
the other starch polysaccharide
formed by alpha glucose 1-4 glycosidic bonds and alpha glucose 1-6 glycosidic bonds
branched
what is glycogen
storage molecule to starch
forms more branches than amylopectin which means it is more compact - good for storage
alpha glucose 1-4 and 1-6 glycosidic bonds
how is glucose released for respiration
by a hydrolysis reaction
(opposite of condensation)
addition of water
catalysed by enzymes
how is cellulose formed
beta glucose 1-4 glycosidic bonds
every other beta glucose molecules flips upside down so the hydoxyl groups can bond
this means it is unable to coil or make branches so cellulose is a straight chain
in cellulose, what are microfibrils?
what are macrofibrils?
what are fibres?
cellulose molecules make hydrogen bonds with each other forming microfibrils
these microfibrils join together forming macrofibrils
macrofibrils join to form fibres
the fibres are strong and insoluble and are used to make cell walls
how do you test for reducing sugars?
Benedict’s Test:
Place sample to be tested in a boiling tube
Add an equal volume of Benedict’s reagent
Heat mixture gently in a boiling water bath for 5 minutes
what do the results show for reducing sugars
high concentration - red medium - orange low - yellow very low - green none - blue
why do reducing sugars make benedict’s reagent turn red
They react with the copper ions in the reagent and the blue copper ions ( Cu2+) gain an electron making Cu+ which is red when heated.
The more reducing sugars the more darker red will form because more copper ions can react with the reducing sugars.
what do you do if you test for reducing sugars and the solution remains blue?
example: sucrose
once you get a negative result you get another sample of the solution and boil with dilute hydrochloric acid. If the sample is sucrose then the solution will split into glucose and fructose and when you do the Benedicts test again it will turn red because they are reducing sugars. if it still is blue then the sample isn’t sucrose (could be water)
how do you test for starch
iodine test
add a few drops of iodine to the sample and it will turn purple/black if starch is present
it remains yellow/brown if the test is negative
what are triglycerides
made of one glycerol molecule with 3 fatty acids
these bond through their hydroxyl groups therefore they produce water molecules
what is the bonding of triglycerides called?
how would they unbond?
esterification
three water molecules need to be supplied to cause the reverse reaction (hydrolysis)
because there are 3 ester bonds between each of the 3 fatty acids and glycerol
what does it mean if fatty acids are saturated?
they have no double bonds present between carbon atoms
why are unsaturated fatty acids liquid at room temperature?
give examples
double bonds causes the molecule to bend and can’t pack together to form a solid
oils
what are phospholipids
modified triglycerides
contains phosphorus along with carbon, hydrogen and oxygen
phosphate ions in the cytoplasm which are negatively charged so is soluble in water
what is the structure of phospholipids
one of the fatty acid chains in triglycerides is replaced with a phosphate group
hydrophobic - hydrophilic structure
head is hydrophilic and tails are hydrophobic which makes a surfactant (surface active agent)
what are sterols
complex alcohol molecules based on four carbon ring structure with a hydroxyl group at one end
hydrophobic - hydrophilic structure
name an important example of a sterol and its role
cholesterol
made in intestine and liver
form cell membranes - stabilises them and regulates their fluidity by keeping them at low temps
makes vitamin D, steroid hormones and bile
helps waterproof the skin
what are some roles of lipids
- membrane formation and creation of hydrophobic barriers
- hormone production
- electrical insulation necessary for impulse transmission
- waterproofing eg. birds feathers and plant leaves
what are some roles triglycerides?
where are they found?
stored under the skin and around vital organs
- thermal insulation to reduce heat loss
- cushioning to protect vital organs like heart and kidneys
- bouyancy for aquatic animals (they can float)
what does a double bond in a fatty acid lead to?
a kink in the chain causing the lipid to be more liquid
what type of triglycerides to plants contain and do animals contain?
plants - unsaturated triglycerides which normally occur as oils
animals - saturated triglycerides which are normally solid fats
what is the structure of an amino acid
amine group - nitrogen and 2 hydrogen
carboxyl group - O = C - OH
C - H in the middle
An R group which results in different amino acids
how many amino acids do we have
20
9 are essential
6 are conditionally essential (growing children)
5 are non-essential
what is a peptide bond
formed between 2 amino acids and water is formed
resulting compound is a dipeptide
how do amino acids bond
the amine group of one amino acid bonds with the carboxyl group of another amino acid
the hydroxyl of the carboxyliuc group bonds with the hydrogen of the amine group
water is formed
what is a polypeptide
when many amino acids join together
it is catalysed by peptidyl transferase
what do different R groups mean
they interact with each other and form complex structures called proteins
different shapes mean different functions
what is thin layer chromatography
It separates individual components in a mixture.
Stationary phase - thin layer of silica gel is applied to a rigid surface. Amino acids are added to one end of the gel. It’s then submerged in organic solvent
Mobile phase - the organic solvent moves through silica gel
Different amino acids move a different paces so you know which ones a present in the mixture
What is Rf and what is the calculation
retention value
distance travelled by component / distance travelled by solvent
what is the primary structure of protein
sequence in which the amino acids are joined. directed by structure carried in DNA
only bonds involved are peptide bonds
what is the secondary structure of protein
the oxygen, hydrogen and nitrogen atoms of the amino acid interact
Hydrogen bonds may form within the amino acid chain pulling it into a coil shape called an alpha helix
The chains can also lie parallel forming sheet-like structures. This is called beta pleated sheet
what is the tertiary structure of protein
folding of a protein into its final shape
includes sections of secondary structure
brings R groups closer together so they interact:
-hydrophobic/hydrophilic reactions
-hydrogen bonds formed
-ionic bonds
-disulphide bond which are covalent
what is the quaternary structure of protein
association of two or more individual proteins called subunits.
protein subunits can be identical or different
eg. insulin has different subunits
haemoglobin has 4 subunits (2 sets of 2)
how do you break down peptides
protease catalyses the reverse reaction - turning peptides back to amino acids
a water molecule is used so its a hydrolysis reaction
what is the biuret test
like the benedict’s test
peptide bonds form a violet colour
no peptide bonds means solution remains blue
what are globular proteins
Compact, water soluble and roughly spherical.
Form when proteins fold into their tertiary structure
The hydrophilic R groups are on the outside of the protein, hence are soluble in water.
what is insulin
a globular protein
hormone involved in regulating blood glucose concentration
transported in bloodstream so need to be soluble
what are conjugated proteins
globular proteins that contain a non-protein component called a prosthetic group
lipids and carbs can combine with proteins forming lipoproteins or glycoproteins
metal ions and molecules derived from vitamins also form prosthetic groups
Haem groups are examples of prosthetic groups
what is catalase
an enzyme
increase reaction rates
a quaternary protein containing 4 haem prosthetic groups
Fe2+ allows catalase to interact with hydrogen peroxide and speed up its breakdown
what are fibrous proteins
long, insoluble molecules
limited range of amino acids usually with small R groups
amino acids sequence is in primary structure and is repetitive
what is keratin
group of fibrous proteins present in hair, skin and nails
large proportion of cysteine
many strong disulphide bonds
strong, inflexible and insoluble
what is elastin
fibrous protein found in elastic fibres
in walls of blood vessels and in alveoli
what is collagen
fibrous protein
connective tissue found in skin, tendons, ligaments and the nervous system
made up of three polypeptides wound together in long rope-like structures
has flexibility
what do nucleotides contain
phosphate group
nitrogenous base
pentose sugar
what are some difference between DNA and RNA
- RNA is single stranded but DNA is double stranded
- The sugar in RNA is ribose but in DNA it is deoxyribose
- The base uracil and thymine differ so the bases in RNA are A,U,C,G but in DNA it is A,T,C,G
- DNA is longer - has millions of nucleotides but RNA only has thousands
- Only one type of DNA but 3 types of RNA
What are pyrimidines?
What are purines?
Pyrimidines are the smaller bases which contain single carbon ring structures - T and C
Purines are the larger bases which contain double carbon ring structures - A and G
In DNA what bases pair with each other and how many bonds are there?
How does RNA differ?
T and A bond with 2 hydrogen bonds
C and G bond with 3 hydrogen bonds
Same with RNA but the T is replaced with U
what are the bonds between nucleotides called?
phosphodiester bonds
how do the bonds form between the nucleotides
condensation reaction
carbon 5 on the phosphate end from the five prime end bonds with carbon 3 on the hydroxyl group at the three prime end
what is the double helix in the DNA
bases form hydrogen bonds with each other and are parallel to each other
the two parallel strands are arranged so that they run in opposite directions so are antiparallel
what does it mean if there are more C-G bonds?
there is a higher melting and boiling point
If there was 16% of A
How much T, C and G will there be?
A = T so T = 16%
100-(16+16) = 68
C=G so half 68
68/2 = 34
T = 16% C = 34% G = 34%
what are the three types on RNA
mRNA - messenger
tRNA - transfer
rRNA - ribosomal (component of ribosomes)
what are DNA and RNA
nucleic acids
what are the steps in dna replication
1) DNA unwinds and unzips. This is catalysed by the enzyme DNA helicase.
2) Produces 2 strands: antisense and sense
3) Free DNA nucleotides in the nucleus bind to both the sense and antisense strand by complementary base pairing, forming hydrogen bonds
4) DNA polymerase catalyses the reaction to form the sugar-phosphate backbone
what is the basic process of protein synthesis
1) transcription of the gene in the nucleus - mRNA strand formed
2) Processing of mRNA (spliced)
3) Translation of mRNA in a ribosome - polypeptide chain formed
4) modification of the protein
what is the detailed process of transcription
In the nucleus
1) The gene unwinds and unzips which is catalysed by the enzyme DNA helicase.
2) Only the antisense strand is used for complementary base pairing with RNA nucleotides (A,U,C,G). Catalysed by the enzyme RNA polymerase.
3) A new molecule of mRNA is formed.
4) This detaches and leaves the nuclear pore.
what is the detailed process of translation
1) mRNA leaves the nucleus and attaches to a ribosome.
2) The first codon of the mRNA is read
3) A tRNA molecule has an anticodon attached which matches the codon.
4) Attached also to the tRNA is the specific amino acid
5) The ribosome then moves along and reads the next codon.
6) The two adjacent amino acids join together by a peptide bond.
7) This is repeated all the way along the mRNA until the stop codon is reached
8) A polypeptide is formed which is the primary structure of a protein
what are the roles of mRNA, tRNA and rRNA in protein synthesis?
mRNA - copies gene from DNA and takes copy to the ribosome
tRNA - brings amino acid to ribosome
rRNA - forms the ribosome
what is the DNA code wheel?
shows how the genetic code is degenerate
different combinations of bases can code for the same amino acid
you start from the centre and work outwards to find the amino acids
there are 20 amino acids
what are the 3 main groups in which we need energy for
synthesis
transport
movement
what is ATP made of?
adenine base
3 phosphate groups
ribose
what is formed when you hydrolyse ATP
ATP + water ->
ADP
+inorganic phosphate
+30.5 kJ of energy
what are the properties of ATP
stores and releases only a small manageable amount of energy
soluble
easily broken down
can transfer its phosphate group into other molecules
no energy wasted
easily transported around cell
easy release of energy
immediate supply of energy always at hand
why is DNA replication described as semi-conservative?
(new molecule consists of) one old strand and one new strand
what are the similarities between DNA replication and transcription
- both use DNA helicase to unwind and unzip the DNA
- both involve complementary base pairing
- both involve breaking of hydrogen bonds between the DNA strands
what are the differences between DNA replication and transcription
- DNA replication involves DNA polymerase, whereas transcription is RNA polymerase
- The whole DNA molecule unzips in DNA replication but in transcription, only the gene unzips
- In DNA replication both strands (sense and antisense) are copied whereas in transcription, it’s only the antisense that acts as a template and the nucleotides bind to
- The products of DNA replication are 2 DNA molecules but transcription makes 1 single stranded mRNA molecule
