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Key Area 2 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What is genomics?

A

The study of the genome

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2
Q

What is the genome?

A

The total genetic material in a cell

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3
Q

What is the proteome?

A

The entire set on proteins expressed by a genome. The proteome is larger than the number of genes, particularly in eukaryotes

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4
Q

What are genes that do not code for proteins?

A

Non-coding RNA genes

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5
Q

What are non-coding RNA genes are transcribed to produce?

A

tRNA
rRNA
RNA molecules that control the expression of other genes

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6
Q

What factors affect the set of proteins expressed by a given cell type?

A
  • metabolic activity of the cell
  • cellular stress
  • the response to signalling molecules
  • diseased versus healthy cells
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7
Q

Eukaryotic cells have a plasma membrane. What is a plasma membrane?

A

It is the boundary around the outside of the cell. They also have a system of internal membranes, this increases the total area of the membrane.

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8
Q

Other structures which have a membrane in the cell are?

A

Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vesicles

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9
Q

What does the endoplasmic reticulum (ER) do?

A

It forms a network of membrane tubules with the nuclear membrane.

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10
Q

What are the 2 types of ER?

A
  • rough endoplasmic reticulum (RER)
  • smooth endoplasmic reticulum (SER)
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11
Q

What is the difference between the RER and SER?

A

RER has ribosomes on its cystolic face.
SER lacks ribosomes

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12
Q

What is the Golgi apparatus?

A

The Golgi apparatus is a series of flattened membrane discs.

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13
Q

What are lysosomes?

A

They are membrane bound organelles containing a variety of HYDROLASES.

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14
Q

What are hydrolases?

A

Hydrolases are enzymes that digest proteins, lipids, nucleus acids and carbohydrates

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15
Q

What are vesicles?

A

Vesicles transport materials between membrane compartments

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16
Q

What is the function of the smooth endoplasmic reticulum?

A

It’s where lipids are synthesised and inserted into its membrane.

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17
Q

What is protein synthesis?

A

The synthesis of all proteins begins in cystolic ribosomes- ribosomes in the cytoplasm not attached to the endoplasmic reticulum.

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18
Q

Where is the synthesis of cystolic proteins completed?

A

It is completed in the cystolic ribosomes and these proteins remain in the cytosol.

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19
Q

What do transmembrane proteins do?

A

They carry a signal sequence, which halts translation of the protein at the cystolic ribosome and directs the ribosome synthesising the protein to dock with ER forking RER.

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20
Q

What is a signal sequence?

A

A signal sequence is a short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.

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21
Q

Where do the proteins go after the ER?

A

Once proteins are made at a ribosome on the RER and is put into the lumen of the RER, they are transporter by vesicles that bus off from the ER and fuse with the Golgi apparatus.

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22
Q

How do molecules move through the Golgi apparatus?

A

Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack.

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23
Q

What happens to proteins as they move through the Golgi apparatus?

A

They undergo post- transitional modification.

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24
Q

What is post- transitional modification?

A

When the polypeptide chains have carbohydrates or phosphates added to them or are cleaved (cut) to make them an active protein

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25
Q

What happens after the Golgi Apparatus?

A

Vesicle that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes.

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26
Q

What does it mean when cells often secrete substances?

A

This means they release substances made inside the cell to the outside.

Peptide hormones e.g Insulin and digestive enzymes

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27
Q

What is the pathway of secreted substances?

A

The secreted substances are translated in ribosomes on the RER and enter its lumen. They bud off the RER in a vesicle and go to the Golgi apparatus.

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28
Q

What then happened to proteins?

A

They move through the Golgi apparatus and are then packaged into secretory vesicle and these vesicles move to and fuse with the plasma membrane, releasing proteins out of the cell.

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29
Q

What are many secreted proteins synthesised as?

A

They are synthesised as inactive precursors and require proteolytic cleavage to produce its active proteins.

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30
Q

What is proteolytic cleavage?

A

It is a type of post-transitional modification where the polypeptide is cut.

31
Q

What are amino acids?

A

They are the building blocks of proteins

32
Q

What are proteins?

A

They are polymers of amino acid monomers. Amino acids are linked by peptide bonds to form polypeptides.

33
Q

What is a peptide bond?

A

It is a strong covalent bond between a carbon atom of one amino acid and the Nitrogen atom of another amino acid. (Water is removed to allow to bond to form.)

34
Q

What are the 2 functional groups amino acids contain?

A

Amine group
Acid group

35
Q

What groups do amino acids contain?

A
  • carbon atom
  • hydrogen atom
  • amine group
  • carboxylic acid group
  • R group
36
Q

How do R groups vary?

A
  • size
  • shape
  • charge
  • hydrogen binding capacity
  • chemical reactivity
37
Q

What are the main categories that amino acids are split into?

A
  • polar
  • hydrophobic
  • acidic (negatively charged)
  • basic (positively charged)
38
Q

What are the properties of acidic R groups?

A
  • ends with a negatively charged group
  • hydrophilic
  • contain a carboxylic acid side chain
    Asp: aspartic acid + Glu: glutamic acid
39
Q

What are properties of basic R group?

A
  • ends with a positively charged group
  • hydrophilic
  • contain an amino acid side chain (-NH2)
  • 3 base amino acids: Arg: arginine
    Lys: lysine His: histidine
40
Q

What are properties of polar R groups?

A
  • slightly charged
  • hydrophilic
  • key components are: carbonyl (CO), hydroxyl (OH) or amine (NH3) groups
  • Cys: cysteine, Thr: threonine, Asn: asparagine, Ser: serine, Tyr: tyrosine, Gln: glutamine.
41
Q

What are properties of hydrophobic R groups?

A
  • these R groups are sometimes known as non-polar R groups
  • do not have charges
  • key components are: a hydrocarbon group(-CH3), long chains of CH and rings.
  • 9 hydrophobic amino acids: Ala: alanine, Ile: Isoleucine, Pro: proline, Val: valine, Trp: tryptophan, Gly: glycine, Leu: leucine
42
Q

What are the levels of protein structure?

A

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

43
Q

What happens in the primary structure?

A

Amino acids link by peptide bonds to form polypeptides.

The primary structure is the sequence in which the amino acids are synthesised into the polypeptides.

44
Q

What happens in the secondary structure?

A

Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure.

45
Q

What are the 3 types of secondary structure?

A
  • alpha helix
  • beta sheets
  • turns
46
Q

How are alpha helix formed?

A

Formed by twisting the polypeptide chain into a spiral/ helix and then stabilising with hydrogen bonding.

47
Q

How are b-sheets formed?

A

B sheet has parts of the chain running alongside each other forming a sheet.

48
Q

What can B sheets be like?

A

They can be antiparallel or parallel

49
Q

What do turns do?

A

They reverse the direction of the polypeptide chain and the chain folds back on itself.

50
Q

What is the tertiary structure?

A

It is the final folded shape of the polypeptide.

51
Q

What are the different interactions between the R groups that stabilise the polypeptide.

A
  • hydrophobic interactions
  • ionic bonds
  • London dispersion forces
  • hydrogen bonds
  • disulphide bridges
52
Q

Where does the quaternary structure exist?

A

It exists in proteins with two or more connected polypeptide subunits which are linked by bonds between the R groups of the polypeptide chains.

53
Q

What are prosthetic groups?

A

A prosthetic group is a non-protein subunit tightly bound to a protein and necessary for its function.

54
Q

What effect does increasing temperature do to the interactions?

A

It disrupts the interactions that hold the protein in shape. The protein begins to unfold and eventually becomes denatured.

55
Q

What effect does increasing the pH have on the interactions?

A

As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost. This gradually changes the conformation of the protein until it is denatured.

56
Q

What is a ligand?

A

A ligand is a substance that can bind to a protein.

57
Q

What happens when a ligand binds to a protein- binding site?

A

The confirmation of the protein changes and this change in conformation causes a functional change in the protein.

58
Q

What is an allosteric enzyme?

A

It is an enzyme whose activity is regulated by altering its confirmation.

59
Q

What is the second type of site called?

A

It is called an allosteric site

60
Q

What is a modulator?

A

Modulators regulate the activity of the enzyme when they bind to the allosteric site.

61
Q

What are the 2 types of modulators?

A

Positive and negative

62
Q

What does the positive modulator do?

A

It increases the enzymes affinity for the substrate, therefore increases enzyme activity.

63
Q

What does the negative modulator do?

A

It deceases the enzymes affinity to the substrate, therefore decreases enzyme activity.

64
Q

What is cooperativity?

A

It is something that allosteric proteins with multiple subunits show in binding. Which changes in binding at one subunit alter the affinity of the remaining subunits.

65
Q

What happens when the binding of a substrate molecule to one active site of an allosteric enzyme?

A

It increases the affinity of other active sites for binding subsequent substrate molecules.

66
Q

What are properties of haemoglobin?

A
  • made of 4 polypeptide subunits
  • each subunit contains a haem group ( binds oxygen)
  • subsequent binding by other subunits is more likely when one of the subunits binds a molecule of oxygen
  • when oxy-haemoglobin releases oxygen the same process happens
67
Q

What happens when there is a decrease in pH on an increase in temperature?

A

The normal ionic interactions are lost and causes the shape of the protein to change and unfold and become denatured

68
Q

What promotes increased oxygen delivery to tissue?

A

Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin.

69
Q

What is a common form of post-transitional modification?

A

It is phosphorylation of proteins. This is when a phosphate group is added to the protein.

70
Q

What can the addition or removal of phosphate cause?

A

It can cause reversible conformational changes in proteins

71
Q

What do protein kinases do?

A

They catalase the transfer of a phosphate group from ATP to other proteins. The terminal phosphate of ATP is transferred to specific R groups.

72
Q

What do protein phosphates do?

A

They catalyse the reverse reaction. They catalyse the transfer of a phosphate group from proteins on to ADP to regenerate ATP.

73
Q

What does phosphorylation bring about?

A

It brings about conformational changes which can affect a protein’s activity.

Advanced Biology (5 decks)

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