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Biological Systems > Chapter 3 Nucleic Acids, Proteins and Enzymes > Flashcards

Chapter 3 Nucleic Acids, Proteins and Enzymes Flashcards

1
Q

What are nucleic acids, and what are the two types?

A

Polymers that store, transport and express hereditary information (genes)
Two types are DNA and RNA

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2
Q

What are nucleotides and what are its components?

A 
Monomer of nucleic acids.
Components
- Pentose Sugar (either ribose or deoxyribose)
- Phosphate Group
- Nitrogen containing base
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3
Q

What is the difference between a nucleoside and a nucleotide?

A 
Nucleoside = Nitrogen containing base + pentose sugar (no phosphate group)
Nucleotide = nucleoside + phosphate group
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4
Q

What are the two types of bases?

A

Prymidines (single ring)

Purines (double rings)

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5
Q

How do new nucleotides bond to nucleic acids?

A

One at a time. Pentose sugar bonds to phosphate on next nucelotide
Bonds at #5 carbon on one nucleotide to #3 carbon on next (5 –> 3 direction)

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6
Q

Define Oligonucleotides

A

Up to 20 nucleotides

e.g. small RNA molecules that regulate DNA replication and gene expression

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7
Q

What is an example of a polynucleotide?

A

DNA and RNA (longest polynucleotides in living world)

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8
Q

How are base pairs bonded and what makes them strong?

A

Bond via hydrogen bonds. Stronger due to number of hydrogen bonds (not as strong as covalent bonds)

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9
Q

What kind of helix is DNA?

A

Right handed helix (goes direction of fingers of a right hand if made into a fist with thumb pointing up)

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10
Q

What are the two primary functions of DNA?

A

Replication

Transcription

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11
Q

Describe transcription and translation

A

Transcription: Information from DNA is copied onto RNA
Translation: information then used to specify amino acid sequences in proteins

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12
Q

What are the major functions of Proteins?

A

Enzymes: catalyzing molecules
Defensive proteins: e.g. antibodies
Hormonal and regulatory proteins: e.g. insulin
Receptor Proteins: receive and respond to intra and extracellular signals
Storage proteins: Store amino acids for later use
Transport proteins: e.g. haemoglobin
Genetic respiratory proteins: regulate gene expression

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13
Q

What are the 2 components of amino acids?

A

Nitrogen containing amino group
Acidic carboxyl group
Distinct R group

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14
Q

What are the 3 special case amino acids?

A

Glycine - single H atom. able to fit in interior of protein molecules
Proline - ring structure. Limits H bonding and rotation. Stabilises bends or loops in protein.
Cysteine - can form covalent bonds called ‘disulfide bridges’ which affect how a protein molecule folds

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15
Q

Difference between an oligopeptide and a polypeptide.

A

Oligopeptide - 20 or fewer amino acids

Polypeptide - larger polymer. Functional proteins contain one or > polypeptides.

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16
Q

What is the range in number of amino acids in proteins?

A

51 (insulin) to 34,350 (titin) amino acids

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17
Q

How is the process of amino acids being added to an existing polypeptide similar to nucleotides being added to a nucleic acid chain?

A

Added one at time in a condensation reaction.

In the case of polypeptides it forms a peptide bond and goes in the direction of amino to carboxyl.

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18
Q

What is the primary stucture of a protein?

A

amino acid sequence

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19
Q

What is the secondary structure of a protein?

A

regular, repeate spatial patterns in different regions resulting from Hydrogen bonding
alpha helix - right hand coil
beta pleated sheet - 2 or more sequences extended and aligned

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20
Q

What is the tertiary structure of a protein?

A

bonds that form between polypeptide chains - resulting in definitive 3D shape
- Determined by R group interactions

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21
Q

Explain the 4 R group interactions that determine tertiary structure of a protein

A
  • Disulfide bridges hold folded polypeptides together
  • H bonds stabilize folds
  • hydrophobic side chains aggregate in interior
  • Van der Waals interactions between hydrophobic side chains
  • ionic interactions form salt bridges (deep in the protein)
22
Q

Define denaturing

A

Disruption of secondary and tertiary structures of a protein by heat or chemicals.
- Will normally return to normal when cooled or chemical removed

23
Q

What is the quarternary structure of a protein?

A

2 or more peptide chains (subunits) bonding together by hydrophobic and ionic interactiosn and H bonds
- Unique tertiary structure

24
Q

What are teh factors that cause denaturing?

A

Temperature
Change in concentration of H+ (pH)
High concentration of polar substances
Non-polar substances (in parts of protein where hydrophobic groups maintain structure)

25
Q

How do proteins interact with other molecules?

A

R groups on surface may form weak interactions with groups on surface of another molecule.
- can change tertiary structure of protein
Or chemical group can covalently bond to side chain of 1 or more of its amino acids

26
Q

What is the function of catalysts in living systems

A

Living systems depend on reactions that occur spontaneously at slow rates.
Catalysts speed up the reactions without being permanently altered (DO NOT make reactions that would not occur otherwise)

27
Q

What are biological catalysts

A

Proteins (enzymes) and a few RNA molecules (ribosomes)

28
Q

What is free energy (G) and how is it released

A

The amount of energy in a system that is able to do work.

Released by exergonic reactions

29
Q

What is activation energy?

A

The input of energy that initiates a reaction by putting reactants into transition state.
Can come from heat (molecules have increased kinetic energy)

30
Q

Why is it not possible for heat to be used to speed up reactions by creating activation energy in living systems

A

Because it speeds up all reactions, including destructive ones

31
Q

How do enzymes act on activation energy?

A

Lower threshold of activation energy by enabling reactants to come together and react more easily

32
Q

What allows enzymes to be very specific

A

Individual 3D shape of active site

33
Q

What is the name of the bond between enzymes and reactants and how is it held together?

A

Enzyme-substrate complex. Held together by H bonding, ionic attraction or temporary covalent bonding

34
Q

How do enzymes catalyze a reaction?

A
  • Inducing strain: bonds in substrate are stretched (causing transition state)
  • Substrate orientation: substrates are brought together so bonds can form
  • Adding chemical groups: R group may be directly involved
35
Q

Define induced fit

A

enzyme changes shape when substrate bonds to make the binding tight

36
Q

What are cofactors?

A

Other molecules that help proteins function

  • metal ions: participate in enzyme catalyzed reaction
  • Coenzymes: add or remove chemical group from substrate. NON-Specific
  • Prosthetic group: molecules permanently bound to their enzyme
37
Q

What factors affect the rate of catalyzed and uncatalyzed reactions

A

Uncatalyzed directly proportional to concentration of substrate
Catalyzed - concentration of enzymes (rate levels out as enzymes become saturated)

38
Q

What are metabolic pathways?

A

Multiple enzyme catalyzed pathways where the product of one reaction is the substrate for the next and each step is catalyzed by a specific enzyme

39
Q

What is systems biology?

A

A new field that describes the components of metabolic pathways mathematically

40
Q

How do cells regulate metabolism

A

Controlling amount of an enzyme (turning synthesis on or off)
OR
Regulating enzyme ACTIVITY (faster option)

41
Q

How is enzyme activity regulated?

A

Chemical inhibitors bind to enzyme and slow rates through reversible and irreversible inhibition.

42
Q

What are the functions of natural and artificial inhibitors

A
  • Natural inhibitors regulate metabolism

- Artificial inhibitors are used to treat diseases, kill pests and study enzyme function

43
Q

Explain the process of irreversible inhibition

A

Inhibitor covalently bonds to side chain in active side permanently deactivating enzyme

44
Q

What are the two types of reversible enzyme inhibors

A

Non-competetive:similar shape to enzyme substrate binds at site distinct form active site causing change in enzyme shape and function (slows or prevents bonding)
Competetive: binds at active site but no reaction occurs (competes with substrate)

45
Q

What is allosteric regulation

A

Non-substrate molecule binding to a site other than the active site (allosteric site)

  • Enzyme chagnes shape and alters affinity of active site for substrate
  • can activate or deactivate enzymes
46
Q

What types of bonds can modify allosteric sites

A

covalent or non-covalent (both are reversible)

47
Q

Explain the process of Phosphorylation

A

By the protein kinase.

  • can change hydrophobic regions to hydrophilic, causing enzymes to twist and expose active sites
  • Protein phosphatases reverse the process by removing a phosphate group
48
Q

What are key steps in metabolic pathways

A

Commitment step - first reaction

Feedback inhibition - final product acts as inhibitor for first enzyme

49
Q

What are 2 factors that change protein shape in living systems

A

pH and temperature

50
Q

What is the law of mass attraction?

A

Higher H+ concentration, the more the reaction is driven to the left (less hydrophilic form)

51
Q

How does temperature affect protein shape

A

temperature increases rate of chemical reactions. If temperature is too high, noncovaelent bonds can break and inactivate proteins (denature)

52
Q

What are isozomes

A

enzymes that catalyze the same reaction but have different composition and physical properties
- May have different optimal pH or temperature allowing an organism to adapt to its environment

Biological Systems (20 decks)

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