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VM0052 Proteins > Proteins > Flashcards

Proteins Flashcards

1
Q

What is the main component of proteins? / the basic unit of a protein

A

Amino acids

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2
Q

What are proteins??

A

Polymeric Biomolecules composed of one or more Chains of Amino acids
linked covalently end to end by peptide bonds (amides).
Proteins have a very specific three-dimensional structure and carry essential functions in all biological process.

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3
Q

the 4 major biomolecules?

A

Lipids, proteins, carbohydrates, nucleic acid

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4
Q

What are biomolecules?

A

Molecules produced by living organisms that are essential to biological processes

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5
Q

What are polymers / polymeric molecules?

A

Macromolecules consisting of many small similar molecules covalently bonded together

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6
Q

Diff peptide and protein?

A

Peptides are smaller than proteins, consist of between 2 and 50 amino acids, whereas proteins >/=50 amino acids.

Peptides don’t have secondary, tertiary, and quaternary structures.

Proteins are formed from one or more polypeptides joined together. Hence, proteins essentially are very large peptides

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7
Q

The central dogma

A

the central dogma
DNA —> RNA —> Proteins
(more?? expl?)

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8
Q

where is the seq of amino acids encoded?

A

The sequence of amino acids in a protein is encoded in the DNA. Proteins
are one of the main effectors of genetic information.

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9
Q

Are proteins imp in cellular functions?

A

Yes!!!! Proteins participate in all cellular functions

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10
Q

How can proteins be divided into structural classes and which ones?

A

Based on 3D structure

Globular vs Fibrous

and

Membrane proteins and Intrinsically disordered proteins

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11
Q

Diff Globular vs Fibrous proteins

A

Globular:
- Compact, spherical
- Water soluble
- Various functions, eg catalytic functions

Fibrous
- Long, Linear
- Insoluble in water
- Structural functions

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12
Q

Membrane protein vs Intrinsically disordered protein

(????)

A

Membrane protein
- Soluble in membrane lipids
- Hydrophobic surface
- Diverse functions

Intrinsically disordered protein
- No stable structure
- Diverse functions

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13
Q

Examples of protein functions?

A

Proteins can perform an immense variety of functions

Enzymes
* Catalysis of chemical reactions

Structural
* Fibrous scaffolds of the cytoskeleton
and extracellular matrix

Motor
* Generate movement

Transport
* Binding and transporting of
important molecules

Signaling
* Receptors and messengers of
cell’s communication network

Regulatory
* Control the function of other
proteins

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14
Q
  1. Amino acids
    Expected learning outcomes:
    * What are α-amino acids
    * Why and how amino acids respond to changes in pH
    * What are the different side-chains and how can they be divided
    * What are the chemical properties of each group of side-chains (non-polar,
    polar neutral, polar positive and polar negative)
    * What are essential amino acids?
A
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15
Q

Proteins are polymers of which kind of amino acids?

A

Proteins are biological polymers of 20 α-amino acids (monomers)
ALFA amino acids

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16
Q

What are alfa-amino acids?

A

(α-amino acids. Amino-carboxylic acids.)
In α-amino acids, an amino group (NH2) in bound to the second carbon (α-carbon) after the carboxyl functional group (COOH). α-amino acids differ by their R group (side chain).

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17
Q

What make the diff amino acids diff?

A

The R-group / side chain

18
Q

What is the same for all amino acids and what do we call this?

A

They have an amino group and a carboxyl group

Backbone / ??????

19
Q

Why do amino acids display acid/base behavior and what does the charge of an amino acid depend on?

A

Amino acids have weak ionizable groups (amino and carboxyl), thus its overall charge is dependent on the pH and the protonation state of the functional groups

20
Q

What happens to the amino and carboxyl f grps when amino acid in water / neutral pH? (???)

A

carbonate is a weak acid –> neg ch ion
amino is weak base —> pos ion
when r w water

21
Q

Describe the “char” of the Carboxyl and Amino grp in terms of protonation at neutral pH.

A

Carboxyl group (COOH): is a weak acid (pKa«7.0). It has low affinity for H+ and is
deprotonated (COO-) at neutral pH (~7.0).

Amino group (NH2): is a weak base (pKa»7.0). It has high affinity for H+ and is
protonated (NH3+) at neutral pH (~7.0).

22
Q

What about the R-grp for net charge?

A
  • R group: Only amino acids with an acidic/basic at R group will have a net charge! = Only those that have ionizable grps in their R-chain will have a net charge!
    Zwitterionic form (no net charge) (excluding the R grp I think)
23
Q

WHat does the charge of free amino acid in solution dep on?

Descr protonation based on pH

EXCLUDING the R-grps

A

The charge of an amino acid in solution changes according to the pH!

pH &laquo_space;7 — Fully protonated (positive charge) — NH3+ and COOH

pH ~ 7 — Zwitter ion form. — NH3+ COO-

pH&raquo_space; 7 — Fully deprotonated (negative charge) — NH2 COO-

24
Q

What are most proteins in living organisms synthesized from?

A

The majority of proteins in living organism are synthesized from a set of 20 amino acids (proteinogenic), each one with a different side chain

25
Q

What attributes a proteins’ chemical properties?

A

The side chain!

26
Q

“Proteinogenic amino acids” means?

A

= amino acids that are incorporated biosynthetically into proteins during translation.
“protein creating”.
Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code

27
Q

How are amino acids grouped/classified?

A

Proteinogenic amino acids can be grouped according to the properties of their side chain (polarity and charge at physiological pH)

28
Q

What are the 4 diff grps of amino acids based on the properties of their side chain?

A

Non-polar
Polar neutral
Polar positive
Polar negative

Polar ones are water soluble – hydrophillic, non-polar hydrophobic (right???)

(polar neutral has net charge = 0, polar charged have net charge diff than 0)

29
Q

Expl the diff polar grps of proteins (neutral, pos, neg) how & why charge

A

Neutral – dont have weak a/b in the side chain

Pos — have weak base in side chain — at around pH 7 —> protonated —> pos

Neg — have weak acid in side chain — at around pH 7 —> deprotonated –> neg

30
Q

Which amino acid’s side chain is considered borderline polar/non-polar?

A

Cysteine

*The S-H bond in cysteine is borderline between polar and non-polar and will be considered both thorughout this course

31
Q

How do the non-polar side chains interact with water?

A

They don’t!!

HYDROPHOBIC —> want to avoid contact w water

32
Q

Name the amino acids with non-polar side chains
+ some props/characteristics of their str

A

All w. non-polar:

Gly (G)
Ala (A)
Val (V)
Leu (L)
Ile (I)
Phe (F)
Trp (W)
Met (M)
Pro (P)
(Cys*** (C))

Gly – the simplest amino
acid (R = H) – only one that doesn’t have a C in its side chain

Val, Leu, Ile
– branched chain amino acids (BCAA)

Pro
– secondary amino group (cyclic side chain)

Phe, Trp
– aromatic amino acids = have benzene ring in the R-grp

33
Q

What amino acids have polar uncharged side chains?

A

Side chains (polar uncharged)
Ser (S)
Thr (T)
Tyr (Y)
Asn (N)
Gln (Q)
(Cys** (C))

Tyr – aromatic amino acid
Cys* – thiol containing amino acid. Can form
disulfide bonds

34
Q

How do amino acids w. polar uncharged side chains interact w water?

A
  • Interact with water
    (hydrophilic)
  • Form hydrogen bonds
35
Q

Which are the aa w polar charged side chains? & which are pos/neg

Descr their protonation at neutral pH

A

Side chains (polar charged)
- His (H)
- Lys (K)
- Arg (R)
- Asp (D)
- Glu (E)

  • Asp, Glu – deprotonated at
    neutral pH (negative)
  • Lys, Arg, His – protonated
    at neutral pH (positive)
36
Q

What kinds of interactions do aa w polar charged side chains partake in?
Do they interact w water?
What particular beh do they have?

A
  • Interact with water
    (hydrophilic)
  • Form hydrogen bonds
  • Electrostatic interactions

interact w water but since also have a charge, they can have ionic interactions, eg neg and pos amino acids tgthr…

  • Acid/base behavior (pK3)
37
Q

Expl what is meant by “essential aa” & give examples of such.

A

Essential amino acids
= amino acids that animals cannot synthesize from
other precursors and therefore must be obtained in appropriate amounts from the diet

  • The remaining amino acids, can be synthesized
    endogenously, to a certain amount
  • CYS an TYR can be synthesized from MET and PHE
  • Birds, cats and ferrets: Arginine (R) is essential
  • Ruminants: rumen microbial metabolism can synthesize all essential
    amino acids, but…

Valine (V)
Leucine (L)
Isoleucine (I)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
Threonine (T)
Histidine (H)
Lysine (K)
(+ Arginine for Fe, birds, ferrets)

38
Q

Is it only essential amino acids that should/must be obtained from food?

A

No! Not nec.
To sustain growth and reproduction and depending on the species, age, physiological and environmental factors and pathological states the essential and non-essential amino acids must also be obtained in sufficient amounts from the diet!

non-essential only means we CAN prod it
just bc of that doesnt mean dont need to consume, may not prod enough

39
Q

Why do we need to consume proteins?

A

we need to consume to use their amino acids to make our own proteins – not to use them as they are
break down —> amino acids —> make our own proteins

40
Q
A

VM0052 Proteins (1 decks)

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