Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Y1 Cellular Biochemistry and Biology > L1: Charge and Shape in Biological Systems > Flashcards

L1: Charge and Shape in Biological Systems Flashcards

1
Q

What determines the structure and function of biological molecules, cells, organs, and organisms?

A

Determined by the interactions of the atoms they are made from

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is it that nature is able to achieve so well and is so remarkable?

A

Able to produce many different molecules from very few building blocks - use very similar elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What does the nucleus of an atom consist of?

A

Protons and neutrons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What mass and charge do protons and neutrons have?

A

Both has a mass of 1
Protons have a charge of +1
Neutrons have a charge of 0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What property results from the nucleus having both protons and neutrons?

A
  • The nucleus is very dense - most of the mass is concentrated here
  • Accounts for very little of the volume
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What surrounds the nucleus? How are these arranged?

A

Cloud of electrons arranged in shells which can contain 2, 8, or 18 electrons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What charge and mass do electrons have?

A

Mass of 0
Charge of 1/1836

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What do all atoms of an element have in common?

A

All have the same number of protons (same atomic number)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Why are partially filled electron shells not preferable? How is this resolved?

A

Not as energetically preferable as filled shells
Atoms donate and accept electrons in order to achieve the octet rule, to become more stable

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is a cation?

A

Atoms which have lost electrons from their outer shell to become positively charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is an anion?

A

Atoms which have gained electrons in their outer shell to become negatively charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Define ionic bonding

A

Electrostatic attraction between a metal and non-metal, formed from the transfer of electrons, to form a giant ionic lattice structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Which is the cation and which is the anion? Why?

A

Na+ is the cation - loses electron to Cl
Cl- is the anion - gains electron Na

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What ion does hydrogen form? How?

A
  • Loses an electron to form H+
  • No electrons so is just a proton
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What chemical property does H+ cause?

A

Responsible for acidity - pH is a measure of the concentration of free H+ ions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Define covalent bonding

A
  • Localised electrostatic attraction between a shared pair of electrons and the nuclei of the bonded atoms. There is overlap of the atomic orbitals, where the electrons are shared
  • Covalent bonding is very strong
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Why is covalent bonding a favourable process?

A

By sharing electrons this brings the molecule to a lower energy level overall

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Why can water form?

A
  • Oxygen has a slight negative charge and hydrogen has a slight positive charge
  • Oxygen is more electronegative than hydrogen, meaning the shared pair of electrons are more greatly attracted to oxygen
  • This creates a polar bond
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What type of bonding can form as a result of water being a polar molecule?

A

Hydrogen bonding between water molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What two types of bonding are found in liquid water? Where?

A
  • Covalent bonds (sharing electrons between oxygen and hydrogen)
  • Hydrogen bonds attraction between non-bonding electrons on oxygen and hydrogens on adjacent water molecules)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is one of the most important functions of hydrogen bonding other than in water?

A
  • Between base pairs in DNA
  • Specificity of the base-pairing results from specific hydrogen bonding patterns between A/T and C/G
22
Q

Why does water have a high latent heat capacity?

A

Lots of hydrogen bonds in water, means it requires a large amount of kinetic energy to break the hydrogen bonds, which gives water stability

23
Q

Why can ice float?

A
  • Ice is less dense than water
  • Most substances are more dense in a solid form. The hydrogen bonds in the water molecule fix at lower temperatures, causing the polar molecules to move further apart than in the liquid state to form a lattice structure
  • This produces a giant covalent structure, which oxygen atoms at the centre of a tetrahedral structure.
24
Q

Why is ice floating so important?

A
  • Important to evolution
  • Allows ice to be an insulator and life to survive underneath, which allowed life to survive and evolve over generations
25
Q

Why is water being a polar molecule beneficial?

A
  • Makes water a good solvent
  • Able to solubilise polar regions of molecules (or polar species like ions)
  • Driver of the conformation of biological structures
26
Q

What can water not solubilise? Why?

A
  • Non-polar molecules
  • Because water is polar and repels non-polar molecules so H bonding does not occur
27
Q

What is meant by hydrophilic/lipophobic?

A

Areas of molecules with charge, good hydrogen-bonding potential and/or a low proportion of carbon atoms tend to sit in or face water

28
Q

What is meant by hydrophobic/lipophilic?

A

Areas of molecules with high proportion of carbons tend to be pushed out of the aqueous phase

29
Q

What is one of the biggest examples of a structure formed due to differences in polarity?

A

Phospholipid bilayer - negatively charged polar head which is hydrophilic and a neutrally charged non-polar fatty acid tail which is hydrophobic/lipophilic

30
Q

What are two other examples of phospholipid structure which are determined by polarity?

A

Liposome - bilayer of phospholipids in a sphere
Micelle - monolayer of phospholipids in a sphere

31
Q

Define what an acid is

A
  • Acids are compounds that can lose an H+ ion (proton), in the process they become negatively charged
  • Fully dissociate in an aqueous solution but will remain associated as the covalent molecule in a less polar solvent
32
Q

Name some strong inorganic acids

A

Hydrochloric acid
Sulphuric acid

33
Q

Why can equilibrium occur in a weak organic acid?

A

The energy difference between the two states can be relatively small, allowing a shift in equilibrium between each side of the reaction, and a back and forth between the form, possible in the physiological pH range

34
Q

What is an example of a weak organic acid?

A

Any carboxylic acid

35
Q

Define what a base is

A

Bases are compounds that can (reversibly) form covalent bonds by taking an H+ ion to become positively charged

36
Q

Can equilibrium occur in weak bases like with with acids?

A
  • Yes
  • At a physiological pH
  • Energy difference between the two states is relatively small
37
Q

Which two acidic amino acids are predominantly ionisable at a physiological pH?

A

Glutamic acid and aspartic acid

38
Q

What charge do acidic amino acids have at a physiological pH? What is the pKa value?

A

Negatively charged
Low pKa - less than 7.4

39
Q

Which two basic amino acids are predominantly ionisable at a physiological pH?

A

Lysine and Arginine

40
Q

What charge do basic amino acids have at a physiological pH? What is the pKa value?

A

Positively charged
High pKa above 7.4

41
Q

What property do the acidic and basic amino acids have when charged?

A

VERY hydrophilic
When something is charged it is very soluble in water

42
Q

What structure do the backbone amines and carboxylic acids combine to form in peptides?

A

Amides /amide linkages

43
Q

Giver an overall equation for the formation of an amide

A
44
Q

What property is significant about amides?

A

Neutral across the physiological pH range, so DO NOT ionise

45
Q

What groups have an impact on the structure of the protein?

A

Side/ R-groups

46
Q

What can influence the side/R-group structures?

A

The ionisation states on the amino acids

47
Q

What is the primary structure of a protein?

A

The order of the amino acids - the polypeptide sequence

48
Q

How does the primary structure of a protein influence the secondary structure?

A
  • Arrangement of primary structure into defined regions, e.g. alpha helix and beta sheets
  • Determined by the shape (conformational preference) of the residues due to their hydrophobicity/hydrophilicity preference (determined by the R groups) and maintained by regular hydrogen bonding pattern
49
Q

What is the tertiary structure of a protein?

A
  • Higher order of folding from secondary structure which gives the overall shape of a protein
  • Conformation of residues influences the structure ( the most common is proline-induced turns)
  • More bonding interactions (ionic and H bonding are the most important) and disulfide bridges/bonds between cysteines
50
Q

How does hydrophilicity play a role in the folding of a protein?

A

Lipophilic/hydrophobic residues prefer to be at the center of the protein (away from water) and will influence structure

Y1 Cellular Biochemistry and Biology (25 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions