week 7 nucleic acids and protein synthesis

Question 1

DNA

Answer 1

deoxyribonucleic acid

Question 2

RNA

Answer 2

ribonucleic acid

Question 3

Common nucleotide structure?

Answer 3

1-3 phosphate groups
pentose (5 carbon) sugar
nitrogenous base (pyrimidine or purine)

Question 4

1 phosphate group

Answer 4

Monophosphate (AMP)

Question 5

2 phosphate groups

Answer 5

Diphosphate (ADP)

Question 6

3 phosphate groups

Answer 6

Triphosphate (ATP)

Question 7

Ribose (pentose sugar)

Answer 7

RNA only
2’ carbon hydroxyl group (OH)

Question 8

Deoxyribose (pentose sugar)

Answer 8

DNA only
2’ carbon (H)

Question 9

Purines

Answer 9

Adenine (A)
Guanine (G)

Question 10

Pyrimidines

Answer 10

Uracil (U) - in RNA only
Thymine (T) - in DNA only
Cytosine (C)

Question 11

Nucleoside

Answer 11

Nucleotide structure excluding the phosphate groups

Question 12

Nucleotide functions (as monomers)

Answer 12

-building blocks of nucleic acids (RNA and DNA)
-Energy carriers (cell energy currency), carrying high-energy bonds between phosphate groups
-Form coenzymes (essential for enzymatic activity)
-Intracellular signalling molecules

Question 13

Nucleic acid strand / backbone

Answer 13

In RNA/DNA, nucleotides are covalently linked to form a polynucleotide strand (backbone)

Question 14

Phosphodiester bonds

Answer 14

Linking 5’ phosphate of one nucleotide to the 3’ OH of the next, creating a 3’-to-5’ directionality

Question 15

Human cells

Answer 15

Nucleic acids of human cells have 5’ end and a 3’ end e.g., 5’-TCG-3’

Question 16

Prokaryotic cells

Answer 16

5’ and 3’ ends of DNA strands are linked to form circular DNA, which is also found in plasmids and mitochondrial DNA

Question 17

Hydrogen bonding between nucleotides

Answer 17

Two DNA strands are held together by hydrogen bonds between complementary base pairs in double - stranded nucleic acids

Question 18

Purine-pyrimidine pairing

Answer 18

A with T (DNA) -> 2 hydrogen bonds
A with U (RNA)
C with G -> 3 hydrogen bonds, more stable than AT pairs

Question 19

DNA double helix

Answer 19

The complementary base pairing cause the two DNA strands to twist around each other in helical manner -> stable DNA double helix
-Antiparallel (hains run in opposite directions)

Question 20

DNA in B-form

Answer 20

Has two helical grooves of different widths, providing binding sites for proteins/drugs

Question 21

Major

Answer 21

Wider

Question 22

Minor

Answer 22

Narrower

Question 23

RNA

Answer 23

Usually single stranded ssRNA in human cells
dsRNA (double stranded) is possible in nature - many viruses contain dsRNA chromosomes.
Immune cells recognise dsRNA as a viral signature, triggering antiviral responses

Question 24

DNA denaturation

Answer 24

Separation of the DNA double strands into single strands

Question 25

DNA renaturation

Answer 25

Restores DNA double helices (nucleotide pairs re-formed) When conditions are reversed, H bonds can be reformed

Question 26

Conditions for DNA denaturation

Answer 26

High temperatures (90-100 degrees C) break H bonds between complementary nucleotide pairs. Higher G-C content increases DNA stability and so more energy needed

Question 27

Gemome

Answer 27

Contains the genetic instructions guiding a cell's survival and function - Human genome has approx. 25,000 genes

Answer 28

DNA provides biological messages through the precise sequence of nucleotides

Question 29

Gene

Answer 29

-A DNA segment that encode specific, inheritable traits -Nucleotide sequence in genes determine the specific amino acid sequence of certain proteins through the genetic code (DNA > RNA > PROTEINS)

Question 30

Pharmacogenomics

Answer 30

Variations in individuals’ genes can influence the response to drugs

Question 31

Eukaryotic DNA

Answer 31

-Nuclear DNA (nucleus) -Mitochondrial DNA (mitochondria)

Question 32

Nuclear DNA

Answer 32

DNA molecules are packaged with histones into chromatin

Question 33

Nucleosomes

Answer 33

Chromatin units

Question 34

Eukaryotic Chromosomes

Answer 34

Linear DNA stored in the nucleus, usually in the form of chromatin. In dividing cells (after DNA duplication) chromatin is further condensed to the X shaped chromosomes

Question 35

Karyotype

Answer 35

Representation of an individuals set of chromosomes

Question 36

Human Chromosomes

Answer 36

Number, size of chromosomes is species-specific

Question 37

Somatic cells

Answer 37

Human (somatic) cells have 46 chromosomes, 23 pairs -> in 22 pairs of homologous autosomal and a pair of sex chromosomes (XX/XY )

Question 38

Gametes

Answer 38

(sperm and egg cells) have one set of 23 chromosomes (haploid cells)

Question 39

Red blood cells

Answer 39

No DNA

Question 40

DNA replication

Answer 40

DNA replication is the process by which DNA makes a copy of itself, before cell divisions -Each chromosome will result in 2 identical DNA -Copied DNA is segregated into daughter cells -Occurs in the nucleus during the S phase of interphase

Question 41

Mutations in DNA replication

Answer 41

DNA replicates rapidly and precisely to avoid errors (mutations) -minimises mutations that can lead to disease -Mutations in microorganisms can lead drug resistance

Question 42

SEMI-conservative process

Answer 42

DNA replication is a SEMI-conservative process, It produces two copies of DNA, each containing one original strand and one new one

Question 43

4 steps of DNA replication

Answer 43

1. Replication Fork Formation 2. Initiation 3. Polymerase elongation 4. Termination

Question 44

1. Replication fork formation

Answer 44

-DNA replication starts at a sequences called origin of replication (rich in A - T) -At each, DNA is denatured by initiator proteins -Helicase enzymes unwind/unzip the DNA double strands bidirectionally by breaking H- bonds, creating two Y-shaped replication forks

Question 45

2. Initiation

Answer 45

-DNA polymerase requires an RNA primer, created by primase enzyme, to initiate synthesis -DNA polymerase attaches to the 3' end of the primer and synthesises a new DNA strand in the 5’->3' direction, using the parental strand as a template -DNA polymerase forms phosphodiester bonds between nucleotides, extending the new DNA strands -The process requires deoxynucleotide triphosphates (dNTPs) to drive the reaction

Question 46

3. Polymerase elongation

Answer 46

-The replication fork is asymmetrical (antiparallel strands) -Replication of leading strand is continuous, same direction as the growing replication fork -Replication of the lagging strand is discontinuous ▪ It requires many RNA primers ▪ Synthesis in short DNA fragments (Okazaki fragments), each initiated by a new RNA primer

Question 47

4. Termination

Answer 47

-A nuclease degrades RNA primers -The gaps are filled by DNA polymerase -The enzyme DNA ligase joins adjacent Okazaki fragments -> DNA Replication is complete

Question 48

Proofreading activity of DNA polymerase

Answer 48

DNA polymerase introduces approx. 1 error/1010 nucleotide copied -DNA polymerase has proofreading activity to check & correct base-pairing errors ▪ When a mismatch occurs, DNA polymerase removes the incorrect nucleotide and replaces it with the correct one. -Any uncorrected mistakes, can be fixed by many DNA repair mechanisms available in human cells ▪ Inactivation of DNA repair pathways is common in tumours

Question 49

DNA polymerase summary

Answer 49

-A complex of polymerases -Incorporates nucleotides to the growing DNA strands by forming phosphodiester bonds -One nucleotide at a time (triphosphate form)

Question 50

Helicase summary

Answer 50

-Unwinds parental double helix

Question 51

Ligase summary

Answer 51

-Joins Okazaki fragments and seals other breaks in sugar-phosphate backbone

Question 52

Other important enzymes

Answer 52

Primase -> Synthesise RNA primers for DNA polymerase to start the polymerisation process DNA Topoisomerase -> Unravel twists in DNA that occur as a result of DNA replication