W2L1 - Proteins & enzymes; tree of life; prokaryotes

Question 1

What are the building blocks and structure of proteins (2)

Answer 1

• Amino acids (20 in total)
• Each amino acid has four groups bonded to a central carbon atom
  
  • R Group (Gives uniqueness)
  • Amine (H2N)
  • Proton (H)
  • Acid (COOH)

Question 2

What are the different properties of R Groups (4)

Answer 2

• Some are polar but uncharged (hydrophilic - likes water)
• Some are charged (hydrophilic - likes water)
• Some are non-polar (hydrophobic - hates water)
• Some form rings

Question 3

How are proteins formed (2)

Answer 3

• Linear chain of amino acids joined by peptide bonds
  
  • Called polypeptides
• Variable lengths and order of amino acids gives almost infinite possibilities

Question 4

Number of genes to amino acids (3)

Answer 4

• Genetic code (4-letter alphabet)
• Genetic code is divided into 3-letters words,, total of 64 possible 3-letter words
• From 64 possible 3-letter words, can form 20 different amino acids

Question 5

What is the first amino acid put into proteins

Answer 5

Methionine, across all species

Question 6

Infinite number of possible proteins. What are some properties?

• How many building blocks
• How are they assembled
• What are the lengths
• What is the longest and shortest protein
• Shape

Answer 6

Properties of protein.

• 20 different amino acids (letters of protein alphabet)
• Assembled in any order (not random, dictated by genetic code; always start with M)
• Different lengths
  
  • Longest is titin - 34,540
  • Shortest is insulin - 51
• Each has a unique shape, crunched up into a 3-dimensional shape (every conceivable shape and size)

Question 7

What is the role of the ribosome (2)

Answer 7

Ribosome

• Synthesis of proteins (translation) using information (program) from the gene.
• Messenger RNA is the intermediate

Question 8

Why does protein have a 3-D shape (2)

Answer 8

• When it comes out of the ribosome, it goes into an aquarius environment
• The hydrophobic entities stick together and sheltered by hydrophilic entities, leading to a 3D shape

Question 9

What are some properties of ribosome? (3)

Properties, function, size

Answer 9

• All cells have ribosomes
  
  • Small machines composed of numerous proteins and several RNAs (Chicken and Egg)
• Site of translation
  
  • Take mRNA sequence and ‘translate’ it to protein sequence
• Bacterial ribosomes are small (17-23nm)

Question 10

How are eukaryotic ribosomes and prokaryotic ribosomes similar or different

Answer 10

They have differential sensitivity to drugs (antibiotics)

Question 11

What are enzymes typically? (1)

What are they essentially? (3)

How do they relate to cell chemistry?

Answer 11

• Typically proteins (some RNA molecules have enzyme activity)
• Catalysts (participate in chemical reactions)
  
  • Increase reaction rate but do not alter the final equilibrium
  • Recyclable (do not get consumed)
  • Regulated (Can make reaction speed up or slow down)
• Achieve cell chemistry by coupling endergonic reactions with exergonic reactions (Energy from exo to endo)

Question 12

Examples of exo (2) and endo (3) reactions

Answer 12

Exo:

• Cell respiration
• Catabolism

Endo:

• Active transport
• Cell movement
• Anabolism

Question 13

Properties of enzymes (What reactions, how many) (3)

How are enzymes specific (1)

Answer 13

• Enzyme for almost every cellular reaction
• ~ 10,000 different enzymes in an animal cell
• Multiple copies of each enzyme
• Active site: “lock and key” type fit for each substrate. Catalysing process:
  
  • Substrate fits in an enzyme
  • Enzyme-substrate complex
  • Yields product
    
    • (Each enzyme for one reaction - Enzyme specificity)

Question 14

How do we measure evolution distance? (1)

What are some tenets that allow us to do this? (3)

Answer 14

Difference between two DNA sequences (or proteins encoded by two genes) is a measure of the amount of evolution (distance) that separates them

• All organisms have genes (DNA)
• DNA contains a history of evolution (early drafts of the programme)
• Compare genes to define relationships

Question 15

What are the 2 main types of cells

Answer 15

• Prokaryotes (no nucleus) Older
• Eukaryotes (nucleus) Newer

Question 16

The higher classification of cells by Woese and Fox (3). Called Domains

Answer 16

Prokaryotes

• Domain Bacteria
• Domain Archaea
  
  • Archea are more related to us (Eurkaya)

Eukaryotes

• Domain Eurkaya

Question 17

The function of Bacteria/Archaea in herbivores (1) and humans (3)

Answer 17

Herbivores

• Bacteria & Archaea allow herbivores to break down the sugars in plants

Humans

• Bacteria in our intestines help to make essential vitamins
• Harmless bacteria in our skin protect us from attack by other invaders
• Gut microbiome: >30,000 species of Domain Bacteria & Domain Archaea in the human gut

Question 18

What kind of food contains prokaryotes

Answer 18

Fermented foods (Yogurt, Cheese)

• Produced via the action of microbes

Question 19

How does life depend on bacteria (2) and some other pros (2)

Answer 19

• More than 50% of the earth’s free oxygen is generated by bacteria
• About 70% of biologically available nitrogen is processed by bacteria
• Produce chocolate? Waste treatment?

Question 20

Are all bacterias good?

Answer 20

Some bacteria cause diseases.