Topic 1

describe monosaccharide

simple sugar monomers
All monosaccharides are reducing sugars, and will show a result for benedict's test.
They have a general formula (CH2O)n

Types of monosaccharides and general properties

Triose sugars (n\=3): important in mitochondria (found in respiration and photosynthesis)
Pentose sugars (n\=5) important in nucleic acids (ribose and deoxyribose)
hexose sugars n\=6 generally sweet in taste (glucose galactose and fructose)

examples of monosaccharides

Hexose: fructose, galactose and glucose
pentose: ribose

Draw alpha glucose (isomer of glucose)

(check notes, same as beta but first oh is down)

Draw beta glucose

check notes (up down up down pooh bear)

Draw ribose

Molecular formmula C5H10O5
check notes

Describe what is meant by a disaccharide

two monosaccharides joined together by a glycosidic bond in a condensation reaction
The reaction involves the formation of a molecule of water (H2O)

types of glycosidic bond

1,4 and 1,6

examples of disaccharides

sucrose, lactose, maltose

Sucrose

alpha glucose + fructose, it is stored in plants

main transport sugar in plants

lactose

alpha glucose + galactose
its the main carbohydrate in milk

maltose

alpha glucose + alpha glucose
found in germinating seeds
(digestion of starch by amylase)

describe what is meant by a polysaccharide

Are formed from many monosaccharide units joined by glycosidic bonds by a condensation reaction

Properties of polysaccharides

Form very compact molecules, therefore can be stored in cells
Glycosydic bonds are easily broken, allowing for monosaccharides to be released rapidly
Not very soluble, therefore they will not affect water potential or osmosis

subsections of polysaccharides

oligosaccharides: 3-10 sugars
more is a true polysaccharide

Explain the structure of starch

Is a combination of two polysaccharides, amylose (30/20%) and amylopectin (70/80%)

Amylose: unbranched chain (of 200-500 glucose) molecules joined by 1,4 glycosidic bonds (it is coiled good for storage)

Amylopectin: branched chain made of glucose joined by 1,4 and 1,6 glycosidic bonds. (branches can be easily broken off)

coils up into a helix held together by hydrogen bonds.

Explain the structure of gycogen

1. animal storage polysaccharide
2. It is formed by alpha glucose molecules joined by 1,4 and 1,6 glycosidic bonds.

(has more 1,6 bonds than starch so it is hydrolised faster and energy is released more rapidly)

Explain the structure of cellulose

only found in plants it is the main component of cell wall

Chain of beta glucose monomers joined by 1,4 glycosidic bonds.

Every other beta glucose must be reversed (draw)

hydrogen bonds may form between the oxygen on one chain and the hydrogen on the other (polar)

cellulose molecules form straight chains that are linked together by hydrogen bonds between the chains to form cellulose microfibrils.

structure of cellulose in cell walls.

1.Cellulose is a {polymer / polysaccharide} of β glucose
2. Joined by 1-4 glycosidic bonds
3. Every other glucose is inverted ;
4. cellulose molecules are arranged in parallel as microfibrils
6. Held togehter by hydrogen bonds
7. { matrix / hemicelluloses /pectin / )

Starch vs cellulose

1. cellulose is made of β glucose and starch is made of
α glucose
2. 1,6 glycosidic bonds only in starch ;
3. starch made of amylose and amylopectin ;
4. cellulose is linear / starch is {branched / helical )

What is a lipid

(CHOP)

Describe the formation of a triglyceride

Glycerol (3c molecule with three OH) combines with three fatty acids
through a condensation reaction
to form a triglyceride

the ester bond forms between the carboxyl group of the fatty acid and the hydroxyl group of glycerol

Draw glycerol + describe

draw glycerol

3-carbon molecule with three alcohol (OH) groups.

draw a fatty acid + describe

draw a fatty acid

long molecules
nonpolar hydrocarbon chain
polar carboxyl acid group at one end
formula R-COOH.

How do fatty acids differ?

1. carbon chain length
2. degree of saturation
(can be monosaturated or polysaturated)

properties of saturated and unsaturated fatty acids

between unsaturated fatty acids intermolecular forces will be weaker so unsaturated lipids will have a low melting point and will be liquid at room temperature. Saturated fatty acids will be solid

Types of lipids

oils (liquid) and fats (solid)

LIst all properties of lipids

store more energy per gram than carbohydrates
Are waterproofing
Are good insulators (thermal blubber and electrical mielin )
Have a very low density
Are insoluble (non polar covalent bonds)

What are phospholipids

In a phospholipids one of the fatty acids will be a phosphate containing group instead.
(draw) amphipatic
They form through esterification reactions

Describe the formation of a monolayer

A monolayer may form between air and water.

hydrophobic fatty acid tails will point away from the water and towards the ai
and the polar head will point towards the water.

describe the formation of a bilayer

Bilayers often form in cells,
The basis of the cell membrane
waterbased solutions on either side of the membrane
Hydrophobic tails will turn away, protected by the polar head

What are proteins

Poteins are polymers/ macromolecules made from monomer amino acids. They are joined by peptide bonds formed in condensation reactions

Draw and describe the basic structure of an amino acid

central atom bonded to amino group (NH2), a carboxyl group (COOH) a hydrogen and R group
Draw

1. a hydrogen atom
2. a basic amino group (NH2 )
3. an acidic carboxyl group (COOH )
4. "R" group (or side chain)

Draw amino acid

draw

Why do properties vary between amino acids

The r group varies between amino acid molecules
it affects how amino acids bond and will affect its properties and polarity
It may contain sulfur or selenium

Illustrate and describe formation of peptide bonds between amino acids

hydroxyl from the carboxyl group of one of the amino acids will react with hydrogen in the amino group of another amino acid to form a water molecule and a peptide bond

Draw formation of peptide bonds

dipeptide

Two amino acids bonded together

polypeptide

many amino acids bonded together

Bonds in proteins

Aside from peptide, many different bonds can form depending in the r group of the amino acid

hydrogen bonds in amino acids

small negative charge on carboxyl group weakly attracted to positive charge on hydrogens in amino group

disulphide bonds

Form between to cytesine molecules that are close together in a polypeptide

ionic bonds

form between strongly oppositely charged r groups, also known as salt bridges. (uncommon)

What is the primary structure of a protein?

linear sequence of amino acids
determine the rest of the protein structure.

What is the secondary structure of a protein?

The repeating pattern in the structure of the amino acids of a polypeptide chain, it can be alpha helix or beta pleated

a-helix

The polypeptide chain is wound round to form a helix.
held together by hydrogen bonds
Hydrogen bonds

B pleated sheet

polypeptide chain zig-zags forming a sheet of antiparallel strands.

Held together by hydrogen bonds.

What is the tertiary structure of a protein?

three dimensional folding of a polypeptide chain due to interactions between side chains of amino acids.
Bonds can be
ionic
hydrogen
disulphide
hydrophilic and hydrophobic interactions

What is the quaternary structure of a protein?

the three dimensional arrangement of two or more tertiary polypeptide

types of protein with quaternary structure

fibrous (structural role) and globular(physiological role)

Properties of fibrous proteins

-structural role (bones tendons or walls of arteries)
long parallel polypeptide chains, not folded into complex 3D structures like globular proteins.
occasional cross linkage which increase tensile strength (rope)
insoluble (hydrophobic r group)
strong
little to no tertiary or quaternary structure

Properties of globular proteins

physiological role (haemoglobin enzymes, insulin immunoglibin)
hydrophobic r groups point inwards and hydrophilic point outwards, making it soluble
Form a spherical shape

Collagen

fibrous protein
found in bones, tendons, ligaments and skin

Describe the structure of DNA

1.Consists of two polynucleotide chains arranged in a double helix structure
2.DNA is antiparallel
3.two sugar-phosphate backbones (nucleotides bonded through phosphodiester bonds)
4.Hydrogen bonds between complementary base pairs

Draw sugar phosphate backbone

draw

Structure of nucleotide

A phosphate group: negatively charged
A pentose sugar
A nitrogenous base

Bases in DNA

Adenine, Thymine, Guanine, Cytosine

Bases in RNA

adenine, guanine, cytosine, uracil

Purine

Two carbon ring
adenine and guanine
pair with pyramidine
(pure angels have two wings)

Pyramidine

one carbon ring
cytosine, thymine, uracil
pair with purine

How many hydrogen bonds between base pairings

A and T form a double hydrogen bond
Guanine and cytosine form a triple hydrogen bond

semi-conservative replication

Model is semi-conservative replication
each new DNA molecule contains one new strand and one old strand.

Replication process (overview)

1. hydrogen bonds are broken between complementary bases.
Catalyzed by DNA helicase
unraveling of the DNA double helix


2. One of the strands is used as the template.
free nucleotides attach to the bases on the original strands by complementary base pairing.

3.
DNA polymerase joins new adjacent nucleotides to each other by phosphodiester bonds, forming the sugar-phosphate backbone.(condensation)

4. hydrogen bonds form between complementary base pairs
A new DNA molecule automatically winds up into a double helix

DNA replication is said to be semi-conservative each new DNA molecule contains one "new" strand and one "old" strand.

Replication additional info

1. Helicase opens up the DNA at the replication fork.

2. Primase makes an RNA primer that provides a 3' end for DNA polymerase

3. DNA double helix is anti-paralle so one strand runs in the 5' to 3' direction the other runs in the 3' to 5' direction.
DNA polymerases can only make DNA in the 5' to 3' direction

4. 5' to 3' is made continuously it is called the leading strand
5.Lagging strand 3' to 5' is made of okazaki fragments which must then be joined by ligase

The Meselson-Stahl Experiment

gene

Is a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain.

RNA

1.RNA is made of ribose nucleotides instead of deoxyribose nucleotides
2.RNA has the base uracil instead of thymine
3.RNA is single stranded
4.RNA is shorter than DNA

tRNA

Draw
folds up by complementary base pairing to form a looped clover-leaf structure.

At one end of the molecule there is the amino acid attachement site, aa binds to base sequence ACC

anticodon.

rRNA

rRNA together with proteins forms ribosomes(site of mRNA translation and protein synthesis.)

Ribosomes are assembled in the nucleolus and exported into the cytoplasm.

Ribosomes free in the cytoplasm make proteins for use in the cell, while those attached to the RER make proteins for export.

Transcription

Initiation: RNA polymerase binds to promoter region of DNA
It breaks the hydrogen bonds causing the molecule to open up

Elongation: The polynucleotide strands will be seperate
1. RNA polymerase will synthesise mRNA using free nucleotides.
2. The ribose nucleotides attach themselves to the bases on the DNA by complementary base pairing
3. The new nucleotides are joined by phosphodiester bonds by the enzyme RNA polymerase.

termination:
mRNA separates from template when a terminatior sequence is reached.
Hydrogen bonds between strands of DNA reform, returns to original shape

What stfrands are used in transcripiton

3' to 5' is the template strand (antisense)
The strand produced will be 5' to 3' (sense strand)
(read up write down)

mRNA splicing

Process that removes introns from pre-mRNAs and joins exons together.

introns do not code for proteins
exons code for proteins

The initial mRNA that is transcribed is called pre-mRNA. Pre-mRNA is an exact copy of the gene on the DNA, so it contains exons and introns.

The introns in the mRNA are cut out
The exons are joined together by enzymes in a process called splicing.

Translation

Initiation
1. A ribosome attaches to the mRNA at start codon (AUG). The ribosome encloses two codons.

2. The anticodon of the first tRNA molecule also attaches to the first mRNA codon by complemtentary base pairing (amino acid attached (met-tRNA))

Elongation

1. tRNA molecule binds to the mRNA via its anticodon.
Hydrogen bonds form between the anticodon of the tRNA and the codon of the mRNA.
2.A second tRNA molecule attaches to the next codon of the mRNA and the two amino acids form a peptidede bond.
3. The ribosome moves along so that a new amino acid-tRNA can attach.

4.A third tRNA molecule joins and the first one leaves the ribosome.
5. The polypeptide chain elongates one amino acid at a time, and peels away from the ribosome, folding up into a protein as it goes.

Termination: continues until a stop codon is reached:
ribosome falls apart
finished protein released

mutation definition

any change in the DNA sequence

Classification of mutations

Mutations can be hereditary or acquired

Gene mutations or chromosomal mutations

If gene mutation: substitution deletion or insertion

If substitution: silent missense non sense

substitution mutations

Mutation in which a single base is replaced/miscopied

can be
Silent: codon codes for the same amino acid ( genetic code degenerate) so no effect
Missense: Amino acid changes
Nonsense: premature stop codon created (incomplete + disfunctional protein)

Deletion and insertion mutations

Deletion and insertion mutations are frame shift mutations

Affects all of the codons
the protein is completely wrong and nonfunctional.

Hereditary mutations

Mutations passed from parents to the offspring via gametes

Acquired mutations

can be spontaneous

or induced
by a mutagen like
chemicals (in ciggarettes)
radiation (UV)
or infectious agents (HPV)

Sickle cell disease

haemoglobin is a protein made of four polypeptide chains.

It is caused by a point mutation in the gene for one of these chains

changes the shape of the whole haemoglobin molecule
causes them to link/stick together to form long rigid chains
1. less flexible than normal cells so can block capillaries and arterioles(cell death and sever pain. )

2. also destroyed faster than they can be made,so not enough oxygen can be carried in the blood

Nature of the genetic code

triplets called codons code for amino acids
with the exception of start and stop codons

Nature
degenerate: more than one codon can code for the same aminoacid
non-overlapping: each codon is only read once, and codons do not share bases
Not all the genome codes for proteins.

Types of inhibitor

reversible and irreversible
when a reversible inhibitor is removed from the enzyme, the enzyme will function normally.
An irreversible inhibitor will permanently change the structure of the enzyme permanently(can never be reversed.)

Types of reversible inhibitors

competitive and non competitive

Competitive: Inhibitor molecule is similar in shape to the substrate, it binds to the active site of the enzyme blocking it and preventing the substrate from binding to it

Non-competitive: the inhibitor molecule will bind to the allosteric site not the active site.

Describe the induced fit hypothesis

Similar to the lock and key method, the substrate will bind to the active site of the enzyme however the active site will slightly change in shape to accomodate the substrate, hence achieving optimum fit

How to measure the rate of reaction

When comparing the rate of reactions you must always measure the initial rate of reaction, because conditions are optimum

To calculate the effect of temperature on the rate of reaction

Use the temperature coefficient
Q10\=rate of reaction at (x+10 degrees celsius)/ rate of reaction at x degrees celsius

Effect of temperature on the enzyme activity (rate of reaction)

The greater the temperature the greater the rate of reaction, up until the optimum temperature is reached. From then on the increase in temperature will cause for the bonds that hold the tertiary and quaternary structures in place to break hence causing the enzyme to denature

Effect of PH on the enzyme activity (rate of reaction)

PH will affect the interactions between the r groups of proteins, the closer the PH to the optimum PH the greater the rate of reaction. If the PH is significantly greater the enzyme will denature

Effect of substrate concentration on enzyme activity (rate of reaction)

The greater the amount of substrate molecules the greater the rate of reaction up until all of the enzymes become saturated, then it will remain constant unless the number of enzymes is increased

Effects of substrate concentration on rate of reaction with inhibitors

Competitive: The greater the amount of substrates the less likely that inhibitor molecules will bind to the active site of enzymes, eventually the rate of reaction can become the same with and without inhibitors
It does not affect non competitive inhibition

describe end product inhibition

When a reaction is inhibited by one of the products of the metabolic chain (like in ATP in respiration)

Draw competitive, non competitive and normal enzyme

draw

List the most important ions in plants

nitrate (NO3-)
Phosphate (PO4 3-)
calcium (Ca2+)
Magnesium (Mg2+)

Role of nitrate in plants

It is needed for the formation of amino acids
Needed in nucleic acids (DNA/ RNA)

Role of phosphate ions in plants

To make ATP and ADP

Role of calcium ions in plants

Needed to form calcium pectate for the middle lamella

Role of magnesium ions in plants

Needed to produce clorophyll

Describe nitrate deficiency in plants

It will cause yellowing/ leaves will turn pale (lack of chlorophyll)
stunted growth (photosynthesis reduced+ lack of amino acids and dna)

Describe phosphate deficiency in plants

Older leaves may become purple, stunted growth

Describe magnesium deficiency in plants

Stunted growth and yellowing leaves