Biological Chemistry

Question 1

What is the central dogma of biology?

Answer 1

A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein

Question 2

What does DNA stand for?

Answer 2

Deoxyribonucleic Acid

Question 3

What are nucleotides made up of?

Answer 3

phosphate group
sugar
base

Question 4

How are nucleotides linked together?

Answer 4

By phosphodiester bonds

Question 5

What is important about phosphate groups for structure and stability?

Answer 5

They are negatively charged

Question 6

How do RNA nucleotides differ to DNA ones?

Answer 6

• the ribose backbone is far less stable due to self-cleavage
• RNA uses Uracil instead of Thymine to pair with Adenine

Question 7

What can the R-group of amino acids be?

Answer 7

• hydrophobic and non-polar
• hydrophilic and polar

Question 8

What are proteins?

Answer 8

They are polymers of amino acids joined by a planar peptide bond

Question 9

What is the protein primary structure?

Answer 9

the linear sequence of amino acids in a peptide or protein

Question 10

What is the protein secondary structure?

Answer 10

comprised of regions stabilised by hydrogen bonds between atoms in the polypeptide backbone

Question 11

What are two protein secondary structures?

Answer 11

α-helices
β- strands

Question 12

How are α-helices stabilised?

Answer 12

by H-bonds between NH of residue i and C=O of residues i-4

Question 13

How are β- strands stabilised?

Answer 13

by H-bonds forming to parallel strands thus forming sheets

Question 14

How are the side chains arranged in α-helices?

Answer 14

they point away from the helical peptide backbone

Question 15

How are the side chains arranged in β- strands?

Answer 15

they stick above/ below the sheet

Question 16

What is a protein tertiary structure?

Answer 16

it is the 3D shape of a protein

Question 17

What is a protein quaternary structure?

Answer 17

the structure of proteins which are themselves composed of two or more smaller protein chains

Question 18

What is glycogen?

Answer 18

a polymer of glucose and it is the primary energy storage in animal cells

Question 19

What is cellulose?

Answer 19

a polymer of glucose and the main component of plant cell walls

Question 20

Metabolism defined

Answer 20

the set of biochemical reactions to make or break compounds (such as glucose, produced by plants, broken down by humans)

Question 21

What is glycolysis?

Answer 21

the catabolic process to break down glucose to produce Adenosine triphosphate (ATP)

Question 22

What is gluconeogenesis?

Answer 22

the β process to produce glucose from smaller metabolites (usually a small-molecule intermediate molecule)

Question 23

What makes up a lipid?

Answer 23

a strongly hydrophobic part (usually alkyl chains), and a highly polar or charged hydrophilic part

Question 24

What can lipids be classified as due to their charactersitics?

Answer 24

amphiphiles

Question 25

What are the most common lipids?

Answer 25

glycerophospholipids

Question 26

Double-chain lipids

Answer 26

they are not soluble in water so form lipid bilayers - the basic boundary for all cells

Question 27

What other lipids are key components of higher organisms’ cell membranes?

Answer 27

sphingolipids

Question 28

Prokaryotes defined

Answer 28

a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles

Question 29

Eukaryotes defined

Answer 29

organisms whose cells have a defined nucleus separated by a phospholipid bilayer containing the DNA

Question 30

Why are Archaea classified as the third domain of life?

Answer 30

they look like bacteria, but they’re genetically closer to Eukaryotes

Question 31

Gram positive bacteria

Answer 31

• they retain the violet Gram stain

Question 32

Gram negative bacteria

Answer 32

• they don’t retain the violet stain and go pink or red in colour

Question 33

What is the make-up of gram positive bacteria?

Answer 33

• they have a thick outer peptidoglycan layer
• inner phospholipid bilayer
• contain a lipid-glycan

Question 34

What is the make-up of gram negative bacteria?

Answer 34

• outer lipopolysaccharide (LPS) layer
• outer cell membrane (phospholipid bilayer)
• thin peptidoglycan in the periplasm
• inner cell membrane enclosing the cytoplasm

Question 35

What is the peptidoglycan?

Answer 35

It is made of two sugars:
- N-acetylmuramic acid (NAM)
- N-acetyl glucosamine (NAG)

They are cross-linked by a tetrapeptide.

Question 36

Endosymbiosis

Answer 36

the process where one type of cells is engulfed and then continues living within the predator

Question 37

What is the strongest evidence for endosymbiosis?

Answer 37

mitochondria and chloroplasts contain their own DNA distinct from nuclear DNA and more closely related to bacterial DNA

Question 38

What are the basic components of eukaryotic bilayers?

Answer 38

• glycerolphospholipids (GPL) with different head groups
• sphingolipids
• cholesterol

Question 39

The nucleus of a eukaryotic cell

Answer 39

• it is defined by the nuclear membrane bilayer membrane
• substances are controlled entering and leaving by the Nuclear Pore Complex
• the nucleus contains the DNA wrapped up in proteins (histone) to form chromatin

Question 40

The Mitochondria

Answer 40

It is the main producer of ATP and it has its own DNA

Question 41

What is the endoplasmic reticulum (ER)?

Answer 41

the sheet/ tube-like extensions of the nuclear envelope

Question 42

What is the role of endoplasmic reticulum?

Answer 42

• to provide different micro-environments to enable specific metabolic pathway that would not be possible in the cytosol
• it also functions as a transport system to bring the right protein (enzyme) to its designation within the eukaryotic cell

Question 43

Rough ER

Answer 43

located closer to nucleus and has many ribosomes (responsible for protein synthesis)

Question 44

Smooth ER

Answer 44

closer to the cell membrane and responsible for lipid and steroid synthesis

• for transport

Question 45

What is the golgi apparatus?

Answer 45

it helps process and package proteins into lipid vesicles to be secreted from the cell

• it contains the enzymes for glycosylation
• transport and secretion

Question 46

What are microbodies?

Answer 46

small vesicles with micro-environment to enable specific reactions

Question 47

What is a vacuole?

Answer 47

membrane-enclosed water-filled compartments

• storage of inorganic and organic compounds

Question 48

Describe the geometry of the peptide bond

Answer 48

it is planar due to the double bond character (cis and trans configuration)

Question 49

Shape of a bacillus

Answer 49

Rod shaped

Question 50

What is Plasmodium?

Answer 50

unicellular eukaryotes that are obligate parasites of vertebrates and insects

Question 51

Two key chemical differences between DNA and RNA?

Answer 51

• DNA contains deoxyribose which misses a OH group at the sugar phosphate backbone, RNA contains ribose.
• RNA uses Uracil instead of Thymine

Question 52

Reasons why RNA is less stable than DNA

Answer 52

• self-cleavage by forming a cyclic phosphodiester
• thymine is more photostable than uracil due to its additional methyl group
• cytosine easily de-aminates to produce Uracil, which in RNA leads to mutation
• RNA cannot form regular B-form RNA due to additional OH group. B-DNA is generally more stable as bases are protected by negatively charged backbone