Biological molecules - Nucleic acids/DNA/RNA/protein synthesis/protein structure

Question 1

what enzymes are involved in the semi-conseravtive replication?

Answer 1

DNA helicase - unzips DNA
DNA primase - primes DNA
DNA polymerase - attaches the new nucleotides in the okaski fragments to old strand
DNA ligase- sews the strand together

Question 2

what is the lagging and leading strand?

Answer 2

Lagging - As the DNA polymerase enzyme is unable to move continously in the 5’ to 3’ direction, it has to repeatedly start and stop again, resulting in the synthesise of short sections/fragments called okazaki fragments that are joined together later in enzyme-catalysed reactions using ligase

Leading - As DNA polymerase enzymes assembles new strands in the 5’ to 3’ direction (opposite direction to lagging), this new strand is syntheised in one continously growing length following the replictaion fork witout interruption.

Question 3

what does codon mean?

Answer 3

a sequence of 3 nucleotides (trinucleotide) that encodes a particular amino acid or terminates protein synthesis

Question 4

what is a gene?

Answer 4

a specific sequence of DNA bases which codes for a particular protein or functional RNA

Question 5

what are the bases for DNA.RNA and their named groups?

Answer 5

Purines: Adenin and Guanine
Both have 2 carbon rings
Pyrimidines: Cytosine and Thymine and Uracil
Has one carbon ring

The pairs for DNA: A-T and C-G
The paris for RNA: A-U and C-G

Question 6

what does an nucleotide consist of?

Answer 6

A deoxyribose sugar (pentose sugar) and nitrogenous base(ATCG) and phosphate

Question 7

what is semi-conservation replication?

Answer 7

Before a (parent) cell divides, it needs to copy the DNA contained in it
Doubling the DNA ensure that the 2 daughter cells produced will receive full copies of the parental DNA
The DNA is copied via a process known as semi-convervative replication
- This is because each new polynucleotide strand is from an original polynucleotide strand
- The new DNA molecule is semi-consevative from the origibla DNA strands

Question 8

what is DNA and how is it formed?

Answer 8

DNA=deoxyribose nucleic acid
-phosphodiester bond formed between nucleotides forming a sugar phosphate backbone
-hydrogen bonds hold togther the nitrogenous bases
-Adenine is complementary base pair with Thymine thrpugh 2 hydrogen bonds
-Guanine is complemenatry abse pair with cytosine through 3 hydrogen bonds

Question 9

what does RNA stand for?

Answer 9

ribonucleic acid

Question 10

what are the codon pairs and where do they start and end?

Answer 10

complementary pairs: A and U, C and G

The codon will code for the amino acid MET to start but end with STOP

Question 11

what are the differences between RNA and DNA? and what do they look like?

Answer 11

DNA’s ribose has no hydroxyl group (-OH) on carbon-2. The lack of oxygen results in a deoxy-ribose nucleic acid (DNA).
Oxygenated ribose results in ribo-nucleic acid (RNA)
-RNA is a single helix but DNA is a double helix
-RNA contains uracil instead of thymine
-ribose is oxygenated in RNA

Question 12

what is DNA made up of? (in terms of anti-parallel)

Answer 12

DNA is made up of 2 complementary polynucleotides and 2 strands are antiparallel.
One strands goes from5’ to 3’ and the opposite goes from 3’ to 5’.
The bonds that hold it all together are phosphodiester bonds.

Question 13

what are the forms of RNA? and what they?

Answer 13

messenger RNA (mRNA)
-only occurs in eukaryotic cells because it has a nucleus
-made in nucleus and travels to cytoplasm
-3 consecutive nucleotides makes a codon
transfer RNA (tRNA)
-bind to mRNA using its anticodons (complementary base pairs to the codon it binds to)

ribosomal RNA (rRNA)
-subunits of a ribosome
-rRNA catalyse peptide bonds

Question 14

what is the kiwi practical?

Answer 14

1)detergent & salt are added to the sample solution
-the detergent breaks down the lipid membrane, whilst the salt neutralise the charge in the DNAs phosphate backbone
2)The solution is heated to further break down the DNA
-the high heat denatures enzymes in the cells as well as breaking down the DNA further
3)Protease enzymes break down proteins bound to the DNA, through breaking peptide bond
4)ethanol helps the DNA to precipitate
-DNA is not soluble in alcohol
-As such, adding ethanol to the solution allows the DNA to precipitate on top of the solution

Question 15

whta is the marmur preparation?

Answer 15

we can extract and purify the nucleic acids from the DNA of different biological samples through a precipitation reaction
-breaking (lysing) the cell and disrupting the nuclear membranes to release DNA
-using enzymes to denature and remove proteins (histones) associated with DNA
-precipitating the DNA using an organic solvent (eg. ethanol)

Question 16

what is the process of semi-conservative replication?

Answer 16

1)helicase unwinds the helical DNA structure
2)SSB (single stranded binding) proteins bind to the DNA strands to keep them separate
3)Topoisomerase keeps the DNA from further uncoiling
4)primase makes RNA primers on both the leading (3’ to 5’) and lagging (5’ to 3’) strands
5)DNA polymerase builds the new strands in the 5’ to 3’ direction. This means the ‘old’ strand was in 3’ to 5’ direction
6)As the DNA further unwinds the helicase, the lagging strand is built in okazaki fragments
7)the okazaki fragments are glued together using ligase
8)the leading and lagging strands build a new strand, to compliment the original old DNA strands
9) this is DNA replication as a semi-conservative replication

Question 17

what does ATP and ADP stand for?

Answer 17

ATP - adeosine tri-phosphate
high energy store
3 phosphates
ADP - adeosine di-phosphate
medium energy store
2 phosphates

Question 18

what are the similarities and differences between ATP and ADP?

Answer 18

ATP and ADP is structured in a similar fashion to nucleotides, except with multiple phosphate group
ATP and ADP are sometimes referred as phosphorylated nucleotides
ATP and ADP both play important roles in energy metabolism within cells, due to the multiple phosphate groups
ATP is the primary energy current of the cell - while ADP is a precursor to ATP and canbe converted back into ATP when energy needed
ATP has 3 phosphate (last 2 phosphates are joined by an anhydride bond which is broken to release energy, meaning it becomes ADP) and ADP has 2 phospates

Question 19

what is the process of protein synthesis?

Answer 19

1) RNA polymerase separates the DNA strands at the promoter (initiation)
2) complementary nucleotides are built, making a chain that grows 5’ to 3’ (elongation)
3) sequences called terminators signals that RNA transcript is complete
4) introns are spliced from the mRNA leaving just the extrons (codons)
5) mRNA travels out of the nulceus thrpugh the nuclear pores into cytoplam
6) mRNA attaches itslef to a rRNA, inbetween in 2 subunits ready for translation
7) tRNA have complementary anticodons which form hhyrdorgen bond with start codon (AUG) on the mRNA attaching methioine
8) A second complementary tRNA (bringing 2nd amino acid)bonds with the next codon forming a peptide bond between amino acid
9) the 1st tRNA (now without an amino acid) is released from rRNA
10) rRNA moves along the mRNA in a 5’ to 3’ direction forming a polypeptide chain
11) This movemnet of mRNA, tRNA and rRNA continues until a stop codon is detected on the mRNA
12) A protein is formed

Question 20

what does transcription mean?

Answer 20

The process by which the information in the strand of DNA is copied into new molecules of messenger RNA (mRNA)

Question 21

what does translation mean?

Answer 21

the process by which the sequence of nucleotides in mRNA is read by the ribosomes and is trnslated into the sequence of amino acids in a polypeptide chain.
Its the synthesis of protein under the instructions of mRNA

Question 22

Process of transcription:
1) what is initiation?

Answer 22

RNA polymerase binds to a sequence of DNA, called the promotor found near the beginning of a gene.
Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription.

Question 23

Process of transcription:
2)what is elongation?

Answer 23

One strand of DNA, the template strand, as a template for RNA polymerase.
Polymerase builds an RNA molecule out of complemnetary nucleotides, making a chain that grows from 5’ to 3’

Question 24

Process of transcription:
3) what is termination?

Answer 24

sequence called terminators signals that the RNA transcript is complete.
Once they are transcribed they cause the transcript to be released from RNA polymerase

Question 25

what is introns and extrons?

Answer 25

introns: intruding sequence (regulate and stablise transciption)
extrons: expressing sequence (used to code for proteins)

Question 26

what is splicing?

Answer 26

many eukaryotic pre-mRNAs undergo splicing before it can be sued in translation.
In this process, parts of the pre-mRNA (called introns) are chopped out, and the remaining pieces (called extrons) are stuck back together.

Question 27

what is the way to remember protein synthesis?

Answer 27

M essenger RNA (goes to ….)
R ibosomes (read sequence to ….)

C odons (recognised by ….)
A nticodons (found on ….)
T ransfer RNA (which carries ….)

A mino acid (which join via ….)
P eptide bonds (to form ….)
P olypeptides

Question 28

what is the primary structure of protein?

Answer 28

chain of amino acids
unique sequence
joined together by peptide bonds in polypeptide chain

Question 29

what is the secondary structure of protein?

Answer 29

only relates to hydrogen bonds forming between the amino acid + carboxyl group
Alpha-helix shape:
-occurs whe hydrogen bond forms every 4th peptide bond (between the oxygen carboxyl group + hydrogen of the amine group)
Beta-pleated sheet:
-shape forms when protein folds so that 2 parts of polypeptide chains are parallel to each other, enabling hydrogen bonds to form between parallel peptide bonds

Question 30

what is the tertiary structure for protein?

Answer 30

3D shape
-formed because of the bonds between the R groups
-they adopt supercoiled shape (fibrous protein or more spherical shape / globular protein)
-when these coil and pleat themselves start to fold, along with areas of straight chain of amino acids

Additional bonds:
hydrogen (between R groups)
disulphide (occurs between cysteine amino acid)
ionic (occur between charged R groups)
weak hydrophobic interactions (between non-polar R groups)

Question 31

what is the quaternary stucture for protein?

Answer 31

occurs in protein that have more than 1 polypeptide chain working together as a functional macromolecule e.g.haemoglobin
Each polypeptide chain in the quaternary structure is referred to as subunits of the protein

Question 32

what is globular protein?
+ examples

Answer 32

Tend to roll up inot any spherical shape (almost spherical). Any hydrophobic R groups turned towards teh centre of the molecules. Hydrophilic groups are on the outside:
-makes protein soluble (water molecule cluster easily around them)
-often have specific shapes (take up roles like enzymes, hormones like insulin, haemoglobin)

examples:
haemoglobin
insulin
pepsin

Question 33

Explain/Expand how the examples are globular protein.

Answer 33

Haemoglobin:
made of 4 polypeptides (2 alpha globin chains and 2 beta globin chains)
each filled with 1 haem molecule (contains iron ions) which are held by bonds.
interactions between polypeptides give its specific shape
protein associated with haem group with iron ions is called conjugated protein
FUNCTION=carry oxygen from lungs to tissu, oxygen binds to iron in haem group - turns purple red colour to red colour
Insulin:
2 polypeptide chain. The A chain begins section of alpha helix and the B chain ends with the section of beta pleat, and folds to tertairy structure joined by disulfide links. Amino acids with hydrophilic R groups on the outsdie (soluble in water).
Insulin binds to glycoprotein receptors on muscle and fat cells (increases uptake of glucose from blood and increases rate of consumption of glucose
Pepsin:
enzyme that digest protein in stomach
amde of a single polypeptide
chain of amino acids folded into a tertairy structure
can be stabel in acidic places like tghe stomach
tertiary structure held by hydrogen bonds and 2 disulfide bridges

Question 34

what is Fibrous protein?
+ examples

Answer 34

have regular, repetitive sequences of amino acids and usually soluble in water
These features enable them to form fibres - tend to have structural function:
Collagen
Keratin
Elastin

Question 35

Explain/Expand how the examples are Fibrous Protein.

Answer 35

Collagen:
provides mechanical strength
-Artery walls: layers of collagen prevent arteries bursting when theres high blood pressure
-Tendons: connects muscle to bone (made of collagen)
-Bone: made form collagen and reinforced with calcium phosphate
-cartilage and connective tissue
Keratin:
rich in cysteine so lots of disulfide bridges form between polypeptide chains and hydrogen bonds make them stronger
forms where body needs to be hard and strong (fingernails/hair/claws/horns)
mechancial protection and impermeable barrier
Elastin:
cross-linking and coiling structure=strong and extensible
found in living things - where they need stretch/adapt to their shape
e.g. skin
around our lungs- inflate and deflate
blood vessels stretch and recoil as blood pumped through them