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Biology Module 2 > Biological Molecules - Amino Acids > Flashcards

Biological Molecules - Amino Acids Flashcards

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1
Q

Describe the bonding in water

A

Hydrogen Bonding between molecules this is called intermolecular bonding
covalent bonding between the O and H, this is called intramolecular bonding
- Intramolecular is always stronger than intermolecular

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2
Q

Describe how hydrogen bonding happens

A
  • Hydrogen bonding happens because the water is polar and has a slight charge, the oxygen attracts more electrons making it negative whereas the hydrogen has a more positive charge.
  • opposites attract and create an intermolecular bond
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3
Q

List the properties of water

A
  • high specific heat capacity
  • high latent heat of evaporation
  • cohesive
  • solvent
  • ice
  • metabolism
  • liquid
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4
Q

Describe specific heat capacity (properties of water)

A

Hydrogen bonds between water, these can absorb the energy making it very hard for the bonds to break therefore there is a high specific heat capacity.
increasing the temperature increases the kinetic energy, a lot of energy is required to increase the kinetic energy and break the hydrogen bonds
- hydrogen bonds are stable

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5
Q

Why is the high specific heat capacity of water good for organisms

A
  • living things include prokaryotes and eukaryotes need a stable temperature for enzyme controlled reactions to happen properly
  • aquatic organisms need a stable environment in which to live
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6
Q

Describe High latent heat of vaporisation (properties of water)

A
  • hydrogen bonds are stable and require a lot of energy to break
  • the latent heat of evaporation is the energy required to get water from one state to another, this means a lot of energy is required to break the hydrogen bonds allowing it to change.
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7
Q

Why is high latent heat of vaporisation of water good of organisms

A

help keep cool living things and keep their temperature stable
- sweating and plants cool when the water evaporates from mesophyll cells

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8
Q

Describe Cohesion and surface area tension (properties of water)

A
  • cohesion tension theory
  • water molecules attract to each other because of their hydrogen bonds and create long columns of water
  • help water to glow as they stick together so pull one another along
  • good for transport medium and liquid as it flows
  • water molecules on the surface are all hydrogen bonded to the molecules beneath them and hence more attracted to the water molecules beneath than the air above, therefore the water contracts and this gives the surface of the water an ability to resit the force applied to it, this is known as surface tension
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9
Q

Why is Cohesion and surface area tension good for water molecules

A

Columns of water in plant vascular tissue are pulled up by the xylem tissue together from the roots
insects can walk on water for example pond skaters

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10
Q

Describe Ice (properties of water)

A
  • forms ice
  • hydrogen bonds spread the water molecules out and creates a lattice structure making the water less dense in a solid state than in a liquid state, this causes it to float and form a layer.
  • creates an insulating layer meaning organisms underneath do not freeze and can stay alive
  • can survive in a cold environment as water underneath does not survive
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11
Q

Describe metabolism (properties of water)

A

reactant - hydrolysis and photosynthesis
product - condensation and respiration
- important for the digestion and synthesis of large biological molecules

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12
Q

Describe proteins

A
  • used for structural components of animals in particular for example keratin and collagen
  • used as carriers
  • used as enzymes
  • used as hormones
  • antibodies
  • adopt specific shapes making them enzymes
  • membranes have protein constituents that act as carriers and pores for active transport across the membrane and facilitated diffusion
  • Animals can make some proteins but need to ingest others whereas plants can make all the amino acids that they need - but they need to have access to nitrogen.
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13
Q

What is an amino acid

A

basic building block of a protein

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14
Q

DRAW AN AMINO ACID

A

DRAW IT

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15
Q

Name the groups in an amino acid

A
  • amino group
  • carboxyl group
  • R group (variable)
  • contains carbon, hydrogen, oxygen and nitrogen (some contain sulfur)
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16
Q

Why is the R important in the structure of an amino acid

A
  • it is different for each amino acid group which makes it what it is
  • different R groups have different properties
  • they give amino acids their characterstics
    Ways in which they can vary:
  • polar or non-polar
  • ionic
  • Hydrogen bonds
  • some contain sulphur
  • hydrophobic - non-polar
  • hydrophilic - polar
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17
Q

How do amino acids do condensation reactions

A

two molecules join together to create a new bond and release a water molecules, when two Amino acid groups come together a covalent bond releasing water
- the OH of a carboxyl group and the H of a amino group

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18
Q

Draw a condensation reaction of an amino acid

A

DRAW IT

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19
Q

What is the covalent bond in proteins called

A

A peptide bond

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20
Q

How is a peptide bond made

A

A peptide bond is made by a condensation reaction
a peptide bond is broke by hydrolysis
- protease enzymes in the intestines break peptide bonds during digestion and enzymes catalyse both condensation and hydrolysis
- two amino acids joint together are called a dipeptide, a longer chain is called a polypeptide

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21
Q

A protein may consist of…

A

a single polypeptide chain or more than one joined together

22
Q

Why is the primary structure of a protein important

A
  • determines what the protein will be if and the specific shape it turns into, if it does not have this shape it will not work
  • determines the sequence of amino acids
  • determines the function of the protein as it decides the shape of the protein
23
Q

why are some proteins not made in the body

A

Animals cannot make all proteins, therefore we have to eat them. the enzymes are then broken down by hydrolysis reactions into amino acids and rebuilt into polypeptide chains which we can use
- plants can make these essential amino acids through photosynthesis and the taking up of nitrate ions

24
Q

Why cant animals store amino acids

A

Animals cannot store amino acids due to the toxic amino group,
- to get rid of deamination happens which breaks down the amino acids which are gotten rid of in the urine

25
Q

Describe the secondary structure

A

If coiled - it is an alpha helix - 36 amino acids per 10 turns of the helix
if pleated - it is a Beta pleat - zig zag structure

26
Q

How is the secondary structure formed

A
  • Alpha - is occurs due to the hydrogen bonds, between the -NH group of one amino acid and -CO group another 4 places down the chain
  • Beta - occurs due to the hydrogen bonds, between the -NH group of one amino acid and -CO group of another one further down the strand to hold the sheet together
  • makes stable structures at optimal temperature and pH due to the many of them
27
Q

Describe the bonding used in tertiary structures

A
  • hydrogen bonding
  • ionic bonds
  • disulphide link
  • hydrophobic and hydrophilic interactions
28
Q

What are the two main types of tertiary structure

A
  • Globular and fibrous
29
Q

Describe Globular

A
  • rolled into spherical shapes
  • R groups turned inwards towards the centre of the molecule and the hydrophilic groups are on the outside - this makes the protein water soluble because the water molecules can easily cluster round and bind to them
  • usually soluble in water
  • metabolic roles
  • enzymes - due to specific shapes
  • antibodies - due to specific shapes
  • haemoglobin - due to specific shapes
30
Q

Describe Fibrous

A
  • regular repetitive sequences of amino acids
  • usually insoluble
  • structural roles due to the fibres that they form
  • collagen and Keratin
31
Q

Not all proteins have….

A

A quaternary structure

32
Q

Name two quaternary structures

A
  • Haemoglobin

- Collagen

33
Q

Describe Haemoglobin

A
  • Quaternary structure of protein is made up of four polypeptides: two alpha globin chains and two beta globin chains – each of these have its own tertiary structure put when they fit together they form a haemoglobin molecule
  • Interactions between the polypeptides give the molecules a very specific shape
  • On the outside of each chain there is shape where a haem group is held this group is called prosthetic group
  • They are essential part of the molecules – without it, it would not function, they are not made of amino acids and the haem group contains an iron ion. Protein associated with this group is called a conjugated protein
34
Q

Describe Collagen

A
  • fibrous
  • insoluble in water
  • 35% glycine
  • No prosthetic
  • left handed helix structures
35
Q

What is the secondary structure primarily held together by

A

hydrogen bonds

36
Q

What is the primary structure held together by

A

peptide bonds

37
Q

How do amino acids act as buffers

A
  • When dissolved in water the amino group and carboxyl group ionise, therefore the amino group accepts a H+ ion and changes from NH2 to NH3+, the carboxyl group gives up an H+ to change from COOH to COO-
  • At low pH the amino acid will accept H+ ions as there are lots of H+ ions in the solution
  • At high pH the amino acid will release H+ ions as there are fewer H+ ions in the solution
  • This means an amino acid has high acidic properties and is known as amphoteric
  • By accepting and releasing H+ ions amino acids regulate changes in pH this is known as buffering
38
Q

Describe the tertiary structure

A
  • When coils and pleats start to fold along with areas of straight chain of amino acids this forms the tertiary structure
  • Has a very precise shape which is held firmly in place by bond between amino acids which lie close to each other
  • Supercoiled shape – fibrous proteins, or a spherical shape in globular proteins
39
Q

What is the quaternary structure

A
  • Many proteins are made up of more than one polypeptide chain
  • The quaternary structure is how multiple polypeptide chains are arranged to make the complete protein molecule
  • Hold together with the same bonds as the tertiary structure
40
Q

Describe hydrogen bonding

A
  • Hydrogen bonds form between hydrogen atoms with a slight positive charge and other atoms with a slight negative charge in amino acids they form in hydroxyl, carboxyl and amino groups
  • Hydrogen bonds may form between the amino acids and carboxyl group of another, may also form between polar areas of the R groups of different amino acids
  • Keep the tertiary and quaternary structure of the protein in the correct shape – presence of multiple hydrogen bonds give a lot of strength
41
Q

describe ionic bonding

A
  • Ionic bonds can form between carboxyl and amino groups that are part of R groups, these ionise into NH3+ and COO- groups
  • Positive and negative groups are strongly attached to each other and form an ionic bond
42
Q

Describe disulphide links

A
  • R group of the amino acid cysteine contains sulfur, they are disulfide bridges formed between the R groups of two cysteines which are strong covalent bond
43
Q

Describe hydrophobic and hydrophilic interactions

A
  • Hydrophobic parts of the R group associate together in the centre of the polypeptide this is so that they avoid water
  • Hydrophilic parts are found at the edge of the polypeptide to be close to the water
  • They cause the twisting of the amino acid chain which changes the shape of the protein
  • This is important as most amino acids are surrounded by water
44
Q

Describe the properties and functions of some fibrous proteins

A
  • In artery walls a layer of collagen prevents artery from bursting and withstands high pressure from blood being pumped by the heart
  • Tendons are made of collagen and connect muscles to bonds this allows them to pull on bones
  • Bones are made out of collagen then they are reinforced by calcium sulfate this makes them hard
  • Cartilage and connective tissue are made from collagen
45
Q

Describe keratin

A
  • Rich in cysteine so lots of disulphide bridges form between its polypeptide chains and with the hydrogen bonding it makes the molecule very strong
  • Found wherever a body part needs to be strong
  • Provides mechanical protection but also provides an impermeable barrier to infection and waterproof so water borne pathogens cannot enter
46
Q

Describe Elastin

A
  • Cross-linking and coiling makes the structure of elastin strong and extensible – found in living things where they need to stretch or adapt their shape
  • Skin can stretch around our bones and muscles because of elastin – without it, it will not go back to normal after being pinched
  • Elastin in lungs allows them to inflate and deflate in our bladder it helps to expand and hold urine
  • Helps blood vessels to stretch and recoil this maintains the pressure
47
Q

Describe insulin

A
  • Made up of two polypeptide chains
  • Chain A begins with a section of alpha helix and the B chain ends with a section of B-pleat
  • Both chains fold into a tertiary structure and are joined together by disulphide binks
  • Amino acids with hydrophilic R group are on the outside of the molecules therefore it is soluble in water
  • Insulin binds to glycoprotein receptors on the outside of muscle and fat cells to increase their uptake of glucose from the blood and to increase their rate of consumption of glucose
48
Q

Describe Pepsin

A
  • Digests protein in the stomach
  • Enzyme is made up of a single polypeptide chain of 327 amino acids but fold into a symmetrical tertiary structure
  • Pepsin has few amino acids with basic R groups whereas it has 43 amino acids with acidic R groups
  • This is why its very stable in an acidic environment – few groups to accept H+ ions therefore has little effect on enzymes structure – held together by hydrogen bonds and two disulphide bridges
49
Q

What is computer modelling used for

A
  • can predict the shape of a protein using computer modelling
  • based upon probability of an amino acid or a sequence of amino acids being in a secondary structure
50
Q

describe Ab initio protein modelling

A

the model is built based on the physical and electrical properties of the atoms in each amino acid sequence – can be multiple to the same amino acid sequence – other methods needed to reduce the number of solutions

51
Q

Describe comparative protein modelling

A

one approach is protein threading which scans the amino acid sequence against a database of solved structures and produces a set of possible models which match that sequence

Biology Module 2 (17 decks)

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