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Cell Biology > LECTURE 2: Introduction to Macromolecules > Flashcards

LECTURE 2: Introduction to Macromolecules Flashcards

1
Q

Describe the reactions that add and remove monomers from a growing polymer.
a. List the specialized names we give to the linkages for each type of macromolecule

A

a) dehydration reaction- add
hydrolysis reaction- remove monomers

fats- ester bonds
carbs- glycosidic linkages
proteins- peptide bonds
nucleic acids- phosphodiester bonds

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2
Q

Explain why proteins have more structural diversity compared to other macromolecule

A

There are 20 different amino acids
• Average protein is 100 to 500 amino acids
• So there’s 20^500 combinations,
• A protein’s amino acid sequence makes it fold into a specific 3D structure due to chemical interactions
• Their final 3D structure gives them specific roles in the cell
• They have a variety of cellular functions.

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3
Q

Classify the different amino acids into their basic groups (polar, non-polar, etc).

A

polar uncharged: serine cytosine threonine glutamine asparagine tyrosine

non polar: glycine, leucine, isoleucine, valine, methionine. phenylalanine, tryptophan, proline

polar charged- lysine arginine histidine aspartic acid glutamic acid

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4
Q

List the experimental methods that we use to determine protein structures.

A
  1. X-ray crystallography
  2. Cryo-electron microscopy
  3. Nuclear magnetic resonance spectroscopy
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5
Q

Describe how the ABO blood system works.

a. List who can and can’t receive certain types of blood.

A

Sequence differences in the ABO glycosyltransferase gene means the encoded enzyme works differently in different people.

A person with type A RBCs has B antibodies in their blood, so can’t get B or AB blood transfusions. A person with type AB can get blood from anyone. A person with type O blood can donate their blood to anyone.

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6
Q

Describe the functions of different polysaccharides.

A
  1. Can serve as a energy source
    • starch in plants is made from linear alpha(1,4) linked glucose
    • glycogen in muscles and liver is made from branched alpha(1,4)&(1,6) glucose
  2. Can serve structural roles
    • cellulose in plant cell walls is made from beta(1,4) linked glucose
    • chitin is a more complex polysaccharide; main component of arthropod exoskeletons
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7
Q

Describe the differences between polar, non-polar, and amphipathic molecules.

A

Polar = different parts of the molecule have net negative or positive charge. From dipoles (e.g. water) or from + or – charges (e.g. acetic acid)

Hydrophobic (“water fearing”) because they contain significant regions with equal electron distribution (i.e. non-polar)

If a molecule has both hydrophilic and hydrophobic parts, it’s called amphiphatic.

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8
Q

. Describe the difference between a fatty acid, a fat and a phospholipid.
a. Describe how the degree of saturation of fatty acids impacts the melting temperature of fats.

A
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9
Q

List the biological roles of lipids in cells.

A
  1. Source of energy in the diet and serve to store energy in the body. Why? Because they’re highly reduced!
    e. g. fats and oils
  2. Some hormones (chemical messengers) are lipids.
    e. g. steroids and prostaglandins.
  3. Many vitamins are lipids. e.g. vitamins A, D, E
  4. The basic structural elements of biological membranes.
    e. g. phospholipids (later lecture!)
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10
Q

Describe the difference between a nucleobase, a nucleoside, and a nucleotide.

A

nucleobase- just the base ATCG
Nucleoside- sugar and base
nucleotide- sugar base and phosphate group

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11
Q

List and describe the biological roles of nucleotides in the cell.

A
  1. Nucleotides are monomeric units from which DNA and RNA are made
    (i. e. the molecules that encode and read out the genetic information of the cell)
  2. Regulatory molecules
    a) Second messengers in cell signaling (eg. cAMP)
    b) GTP can serve as a switch to activate some proteins (G-proteins)
  3. Agents of energy transfer for metabolism
    a) Cleaving of phosphate groups releases
    energy (ATP)
    b) Co-enzymes in energy transfer
    reactions (NAD)
    • Co-enzymes are non-protein
    compounds needed for enzyme
    action
    • NAD = nicotinamide adenine
    cyclic AMP (cAMP)
    dinucleotide
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12
Q

Compare and contrast the structural and chemical differences between RNA and DNA.

A

• DNA is an antiparallel double stranded helix
• Strands are held together by hydrogen
bonding between bases (‘rungs’ of the ladder)
• A pairs with T, G pairs with C
Note that a purine always pairs with a pyrimidine!
- No OH at 2’

RNA is single stranded (usually)
Can fold back on itself to form complex 3D structures (e.g. ribosomes) by base pairing (A with U, G with C)
Some RNAs have catalytic activity (ribozymes)
- OH at 2”

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13
Q

Macromolecules

A

are large molecule with over 1000 atoms
play many structural and functional roles in cells.
Often polymers: poly- aggregation of similar units (monomers)

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14
Q

What are the 4 categories of macromolecules?

A

proteins, nucleic acids, polysaccharides and lipids.

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15
Q

Small molecules

A

are those less than 1000 atoms (including monomers)

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16
Q

Macromolecule and monomer examples

A

Starch, glycogen, cellulose(ALL POLYSACCHARIDES); monomer- Monosaccharides
DNA; monomer- nucleotides
RNA; monomer- nucleotides
Protein; monomer- amino acids

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17
Q

Monomer

A

is a molecule that can react together with other monomer molecules to form a larger polymer chain o

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18
Q

Describe lipids

A

are diverse organic molecules that are insoluble in H2O but soluble in nonpolar organic liquids (e.g. chloroform).

are all hydrophobic

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19
Q

Describe how micelles form.

A

FA hydrophilic heads are towards the outside and interact with water and hydrophobic tales point inwards and interact with each other. A monolayer of lipid.

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20
Q

Why is H20 a dipole?

A

Water is a dipole because shared electrons spend more time by the electrophilic oxygen

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21
Q

Fats

A

are made of glycerol and linked by three ester bonds to three fatty acids (FAs).

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22
Q

fatty acids (FAs).

A

are unbranched hydrocarbons with one carboxyl group; they are amphipathic
can be saturated or unsaturated

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23
Q

Saturated FAs

A

FAs lack C=C double bonds and are solid at room temperature (closer packing of carbons, more van der Walls force)- high melting temp
Stearic acid is an 18 C saturated fatty acid

24
Q

Unsaturated FAs

A

have one or more C=C double bonds and are liquid at room temperature.- low melting temp
Oleic acid is an 18 C unsaturated fatty acid The double bond puts a kink in the chain

25
Q

Carbohydrates

A

include simple sugars and sugar polymers

are made of carbon, oxygen & hydrogen

26
Q

monosaccharides

A

Carbohydrate monomers
generally some combination of
CXH2XOX (eg glucose = C6H12O6)

27
Q

Describe the reaction that adds carbohydrate monomers

A

dehydration reactions by the loss of a hydroxyl from the a carbon of one monomer and a hydrogen from another carbon of the co-joining monomer (one oxygen & two hydrogens are lost to water). Forms a glycosidic bond.

28
Q

alpha

A

OH IS DOWN

29
Q

Beta

A

OH is up

30
Q

How can a Monosaccharide exist in solution?

A

can be linear (middle), or spontaneously close to form alpha- or beta-rings. The difference is whether the terminal hydroxyl (OH) is up or down (in red). A monosaccharide will ‘flip’ between these states rapidly.

31
Q

Oligosaccharide

A

oligo = ‘a few’)
Small chains of monosaccharides. Often many different types of monosaccharides in the chain with different branching combinations.

• Can be added onto lipids to make glycolipids and proteins to make glycoproteins. These often play a role in cell recognition (e.g. ABO blood type, displayed on red blood cells (RBCs))

32
Q

Polysaccharides

A

are long polymers of sugars

33
Q

What is the central dogma’ of molecular biology?

A

DNA-> RNA>PROTEINS

A gene is transcribed by RNA polymerase to make RNA (either mRNA to make a protein, tRNA, or rRNA)
RNAs are then exported from the nucleus.
If it’s an mRNA, it gets translated by the ribosome to make a protein of a specific amino acid sequence that’s based upon the original DNA sequence

34
Q

Gene

A

stretch of DNA which encodes a protein or RNA

DNA is stored in nucleus

35
Q

Nucleic acids

A

are polymers of nucleotides that store and transmit genetic information.

36
Q

What is a nucleotide composed of?

A

consists of three parts:
• A five-carbon sugar (ribose in RNA, 2’ dexoxyribose in DNA)
• A phosphate group linked to the 5’ carbon of the sugar
• A nitrogenous base linked to the 1’ carbon of the sugar

37
Q

Describe nitrogenous bases

A

– Bases are either purines or pyrimidines.
– The purines are adenine and guanine in both DNA and RNA.
– The pyrimidines are cytosine and uracil in RNA; uracil is replaced by thymine in DNA.

38
Q

Deoxyribonucleic acid (DNA

A

olds the genetic information in all cellular organisms and some viruses.
Four bases: A, C, T, G

39
Q

Ribonucleic acid (RNA)

A

encodes the message of DNA and is the genetic material in some viruses. Four bases: A, C, U, G

40
Q

How are nucleotides connected?

A

Nucleotides are connected by 5’-3’ phosphodiester bonds between the phosphate of one nucleotide and the 5’ carbon of the next. Thus nucleic acids have a direction (5’ phosphate end to 3’ hydroxyl end)

41
Q

Proteins

A

are the most chemically diverse macromolecules in the cell

are polymers of amino acids

42
Q

What are the 2 major classes of proteins?

A
  1. Globular proteins are usually inside the cell
  2. Fibrous proteins are usually exported
    outside the cell (extracellular matrix)
43
Q

Describe what roles proteins play

A

Enzymes –catalysts that perform chemical reactions

Structural elements – e.g. tubulin

Contractile elements – e.g. myosin in
muscle cells

Control of gene transcription
– Transcription factors bind to DNA and control if a gene is transcribed
– Ribosomes (rRNA protein hybrids)

Transport proteins – move material across membranes (e.g. glucose transporters)

Carriers – hemoglobin

Hormones – e.g. insulin

Antibodies – defense against invaders

44
Q

How are proteins made

A

made by linking together amino acids
Amino acids have an α carbon, an amine group, a carboxyl group, and a variable R group.
Amino acids are linked together (dehydration rxns) by peptide bonds into a polypeptide chain to make a protein.
Like DNA, they have a direction. From “N-terminus” to “C-terminus”

45
Q

Describe Primary structure

A

is the sequence of amino acids in the polymer. This is the order that the polypeptide will be made by the ribosome, from N-terminus to C-terminus

46
Q

Describe secondary structure

A

refers to the conformation of adjacent amino acids into α- helix, β-sheet, hinges, turns, turns, loops, and ‘disordered’ sections.

Alpha-helix

a) 360 degree turn of the helix = 3.6 amino acid residues
b) H bonds between the carbonyl group and the imine group (H-N) of the backbone hold the helix together

Beta-sheet

a) Residues go in a pleated pattern called a β- strand, with the R groups sticking up and down
b) H bonds between the backbone carbonyl groups and the imine group (H-N) hold the adjacent strands together

47
Q

Describe the Tertiary structure

A

is the overall 3D
conformation of a single protein polymer.
• Driven largely by R-group chemistry:
Hydrophobic R-groups in the centre of the protein, hydrophilic R-groups on the exterior
• It is stabilized by noncovalent bonds.
• e.g. van der Walls’ bonds, salt bridges
• NOT static… protein parts move around!!
• Conformational changes are non-random
movements triggered (for example) by the binding of a specific molecule.

48
Q

What was the First Globular Proteins Whose Tertiary Structure Was Determined?

A

Myoglobin
• Stores oxygen in muscle cells.
• Has a heme prosthetic group that binds O2.
• Structure derived using X-ray crystallography
3-D structure of myoglobin. Heme group is located in red in the center of the protein.

49
Q

Describe Quaternary structure

A

structure refers to protein complexes composed of more than one protein
refers to the manner in which subunits interact.

Homodimer = 2 proteins encoded by the same gene
Heterodimer = 2 or more different

proteins encoded by different genes
There are proteins that have many different subunits encoded by different genes!

when the individual polypeptides are bound to each other for the protein complex to work. Like hemoglobin, which has strong protein-protein interactions between the polypeptides.

50
Q

Describe the Quaternary structure of hemoglobin.

A

α is encoded by one gene, and there are two units in the final complex (α1 and α2). Globin β is encoded by a different gene, and there are also two units in the final complex (β1 and β2).

51
Q

What do proteins often do?

A

very often interact with each other

  • proteins will be separate
  • and then transiently come together to form an active complex

Separate proteins (which may or may not have activity on their own) transiently come together to form an active complex. This is still ‘quaternary structure’, but the protein-protein interactions are weaker

52
Q

i

A

proteins can become physically associated to form a multiprotein complex.
– Which proteins interact can be determined using the yeast two-hybrid (Y2H) assay
– The Y2H is an indirect assay and includes lots of uncertainties.
– Results from large-scale studies can be presented in the form of a network.
– A list of potential interactions can be elucidate unknown processes.

53
Q

Why is protein structure important?

A

A protein’s structure determines its function!
– Subtle changes in a protein’s structure can have a huge impact on its ability to perform its function within the cell

– Cells routinely modify protein structures (phosphorylation, etc) to regulate activities

– The structure is based upon the chemistry of the amino acids, the order of the amino acids are determined by the gene that encodes the protein

– Mutations in DNA can be (but are not always) damaging to the protein’s function

54
Q

Briefly describe how X-ray crystallography works.

A

Tertiary and quaternary structures can be determined using a variety of methods: 1. X-ray crystallography
1. Get your proteins to form into a crystal.
(all proteins in crystal are arranged as a lattice)

  1. Put your protein crystal into a strong Xray beam
  2. The Xrays will interact with atoms as they pass
    through the crystal, and will be diffracted
    depending on how the protein atoms are lined up
  3. Capture the diffracted xrays with a detector
  4. Rotate the crystal a bit (new atoms are now in row)
    and repeat 3&4
  5. Do crazy math (Fourier transformations)
  6. This gives an electron density map
  7. With help of a computer, ‘fit’ amino acid shapes
    and the backbone in the electron densities

*Myoglobin and hemoglobin were discovered this way

55
Q

Describe how Cryo-electron microscopy works?

A

Proteins ‘fixed’ in a crystal may not have the same conformation as they do in a cell.
Also, crystallography doesn’t work with really huge complexes and integral membrane proteins. Cryo-EM solves these problems!
2017, the Nobel Prize in Chemistry was awarded for this

protein is flash frozen, done in a liquid ethane and in a way that the protein freezes but its done so quick that water droplets dont form so it gives you a clear image of the protein and then with transmission electron microscopy and help of computer you can get 3D structure of protein

56
Q

Describe how Nuclear magnetic resonance spectroscopy works and what are the limitations associated with it?

A

Stick your protein(native protein) (in solution) in a really strong magnet.
Magic chemistry happens
Limitation: only works for really small proteins (and small molecules)
advantage- get to see how protein functions in native state

57
Q

What is a problem associated with x- ray crystallography?

A

you have to crystallize the protein and some don’t crystalize well or structures change during

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