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Body Cells And Structure > Structure And Function Of Proteins > Flashcards

Structure And Function Of Proteins Flashcards

1
Q

What do proteins do?

- brief explanation

A

They come in many shapes and sizes that have a variety of functions such as catalysis, defence, transport, motion, regulation and storage

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2
Q

Enzyme catalysis

- class, example and example of use

A

Class: enzymes
Examples: glucosidase, proteases, polymerises and kinases
Example of use: cleave polysaccharides, protein breakdown, synth nuclei acids and phospho prots

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3
Q

Defense

- class, example and example of use

A

Class: Ig, toxins, antigens
Example: MHC, antibodies and snake venom
Use: mark non-self for elim, block nerve function and self recog

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4
Q

Transport

- class, example and use

A

Circulating transporters: haem/myoglobin and cytochromes
Movement of O2 and CO2 in muscles and blood and movement of electrons
Membrane transporters: Na/K pump, proton pump and glucose transporter
Membrane potential, chemiosmosis and gluc transport

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5
Q

Support

- class, example and use

A

Fibres:
Collagen, keratin and fibrin
Forms cartilage, forms hair and nails and form blood clots

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6
Q

Motion:

- class, example and use

A

Muscles:
Actin and myosin
Contract muscle fibres

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7
Q

Regulation:

- class, example and use

A 
Osmotic proteins:
- serum albumin
- maintains osmotic conc of blood
Gene regulators: 
- Iac repressor 
- regs transcrip
Hormones:
- insulin, vasopressin, oxytocin
- control blood gluc, water retention and reg uterine contract and milk prod
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8
Q

Storage:

- class, example and use

A

Ion-binding:

  • ferritin, casein, calmodulin
  • store iron in spleen, store ions in milk and binds Ca
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9
Q

Ways to classify proteins

A

Size: port or pep
Class: fibrous or globular
Role: structural or functional
Location: intra/extracellular, soluble and membranal

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10
Q

Structural proteins

A

Such as actin/intermediate filaments of cytoskeleton

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11
Q

Intracellular vs extracellular

A

Intra: targeted to a specific organelle
Extra: lumen of RER

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12
Q

Integral vs peripheral

A

Integral proteins are within the membrane

Peripheral proteins are beneath the membrane

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13
Q

What are proteins made of?

A

Monomers such as amino acids
Polymers such as polypeptides
Cellular structure such as intermediate/actin filaments

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14
Q

The central dogma of molecular biology

A

DNA to RNA to polypeptide to functional protein (involving folding into 3D structure with chemical modification)

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15
Q

How can such a variety of shapes and functions arise from a string of amino acids?

A

Structure gives shape to key parts of amino acids, in specific position to aid in their function

  • to interact/bind with non-prot molecules or other proteins
  • taking part in chem reactions such as catalysis
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16
Q

Traditional enzyme characteristics

A

Enzyme contains an active site that is specific to the substrate, when it bind it become the enzyme-substrate complex (active site molded by 1/2/3 structure)

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17
Q

How many different amino acids exist

A 
20 different types: 
NON AROMATIC
-non polar: alanine, glycine (valine, isoleucine and leucine)
-polar uncharged: serine, asparagine, glutamine (threonine)
-charged: glutamic acid, arginine, aspartic acid (lysine)
AROMATIC
-non polar: (phenylalanine, tryptophan)
-polar uncharged: (tyrosine)
-charges: (histidine)
SPECIAL FUNCTION
-non polar: (proline, methionine)
-polar uncharged: (cysteine)
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18
Q

The amino acid structure

A

N-C-C

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19
Q

Forming a polypeptide

A

2 amino acid come together forming a dipeptide via creating a peptide bind, releasing water
Formed during translation
Polypeptide has an amino end (NH3) and carboxyl end (COOH)

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20
Q

Primary structure

A

One letter code, a culmination of many amino acids in a line such as S=Serine

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21
Q

Protein translation

A

The protein will start to fold whilst it is still being translated

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22
Q

First stage of folding

A

Nearby amino acids start to form regions of stable structure such as alpha-helix or beta-sheets
Amino acids form bonds that create the specific structures
Examples: bacterial porin (all beta) and ferritin (all alpha)

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23
Q

Alpha helix importance

A

Especially important in the structure of integrate membrane proteins

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24
Q

How does the polypeptide chain rapidly fold into a compact shape

A

This is done via hydrophobic exclusions, that pushes the hydrophobic amino acids into the middle of the protein and the hydrophilic amino acids into the outer protein, this starts to form the tertiary structure

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25
Q

Tertiary structure bonds

A 
Hydrogen bonds (O-H) weak
Disulphide bonds (S-S) strong, between 2 cysteines
Ionic bonds (+ve with -ve) strong
van see Waals (electron clouds) weak maximise contact of atoms
Hydrophobic exclusions (phobic inside and phillic outside)
This turns into the quaternary structure
26
Q

Quaternary structure

A

A dimer
A tetramer 2 alpha and 2 beta globins such as haemoglobin
Globular and fibrous

27
Q

Protein structure is hierarchical

A

Primary: structure is the protein sequence; the order of the amino acids from the N-term to the C-term
Secondary: structure describes the local structure of stresses of protein: alpha-helixes or beta-sheets
Tertiary: structure describes the relative positioning in the 3 dimensions of the secondary elements of a single molecule
Quaternary: structure describes proteins that contain more than one chain

28
Q

Protein degradation

A

Proteins can degrade via denaturation leading to a denature protein by breaking the secondary structure losing the 3D shape

29
Q

Anfinsen experiment

A

Native ribonuclease contains disulphides bonds these are then reduced forming reduced ribonuclease, with the addition of heat the protein will lose its structure, this can also be reversed by cooling and oxidising the disulphide bonds back to their original formation

30
Q

Chaperone protein

- function

A

They allow the repairing of midfielder protein forming the correctly folded protein
Chaperone protein: GroE

31
Q

Degrad of proteins

A

Aging: degrad over time as they are chemically altered

Half-life: variable between proteins

32
Q

Size of proteins

A

Describes in kDa or amino acid length
Is it a protein or a peptide
A peptide tends to be used for very small proteins (>50 aas)

33
Q

Fibrous or Globular

A

Usually describes as structural or functional
Functional proteins: instigate biochem change
Structural proteins: inside the cell such as the cytoskeleton or cell mem

34
Q

Location of proteins

- intracell vs extracell

A

Have key difference on their biochem
Extra cell prots: have to function without an energy supply, are extra tough and have disulphide bonds (structural support) mainly glycoproteins
Intra cell prots: have to be located to a specific organelle

35
Q

Soluble or membrane

A

Free proteins or those attaches to membrane by some mean

Membrane-bound are strongly bound and difficult to isolate and study

36
Q

Protein denaturation

A

By high temperature, changes in pH and certain chemicals

37
Q

Amino acid monomer structure

A

Amino group, carboxyl group and alpha carbon with side chain

38
Q

Peptide bonds

A

Broken down by proteases, high temperature and pH

39
Q

Entropy for hydrophobic exclusions

A

Consequence of water molecules wanting to remove themselves from the vicinity of the hydrophobic amino acids and the latter being forced into the close contact with each other

40
Q

Primary structure dictates 3D structure

A

One consequence of denaturation is that the protein becomes insoluble (individual proteins can’t be insoluble) individual mis-folded protein molecules bind to each other on a process called aggregation forming an insoluble lump of protein

41
Q

Lysosomes

A

Proteins are taken to them to be degraded by proteases broken down into amino acid monomers

42
Q

Prosthetic groups

A

Conjugated to proteins, inorganic such as Fe, Zn and Ca
Organic such as pyridoxal phosphate
Porphyrin ring: the haem group of haemoglobin, contains Fe

43
Q

Motifs and Domains

A

Immunoglobulins: Fab domain, Fc domain and the antigen-binding site
Domains can be structural or functional
Motifs such as helix-turn-helix and beta-alpha-beta, a combination of motifs are called folds

44
Q

Hydrolysis is peptide bond

A

Produces amino acids
Does not need energy input
Proteases speed the process up
Endoproteases can cleave polypeptide chain (from end of the chain)

45
Q

Dietary supply:

- amino acids

A

Begins in stomach via pepsin

Completed in intestine (trypsin, chymotrypsin in duo)

46
Q

Degrad of tissue protein:

- amino acid source

A

Normal turnover rate of proteins
2 methods: ubiquitin-proteasome pathway; abnorm prots on the cell cytosine (26S protease complex), gagged by ubiquitin, and ATP-depend step
Lysosomal pathway; long-lived proteins in the lysosomes
Degraded by proteases called cathepsins (broad spec and ATP-independ)
Enter lysosomes by endocytosis, and autophagy.

47
Q

Fate of amino acids

A

Synth of prots: DNA, RNA and ribosomes
Synth other compounds: purines, pyrimidines and NuTs
Remainder: provide energy/energy stores, no amino acid storage and they mainly stay in the liver or muscles

48
Q

Excess protein

A

Protein’s amino group is removed to form ammonia, and is converted to urea leaving the carbon skeleton (alpha-ketoacid)

49
Q

Urea cycle:

- stages

A

Transamination: amino acid + alpha ketoglitarate reversibly forms glutamate + alpha-keto acid
Require co-factor of pyridoxal phosphate (derived from vit B6)

50
Q

AST and ALT

A

Aspartate transaminase: forms aspartate from glutamate (liver)
Alanine transaminase: many amino acids and muscle prots are transaminated to alanine for transport to the liver, then is further converted to glutamate

51
Q

Nitrogen disposal:

- routes of disposal

A

Oxi deamination: prod NH4
- direct removal of the amino group to form ammonia, catalysed by glutamate dehydrogenase (GluDH)
Glutamate —> alpha ketoglutarate
Ammonia enters the urea cycle, and a-ketonwill be transaminated
Transamination to aspartate:
- formation of aspartate form glutamate
- aspartate enters urea cycle and a-Leto same as above

52
Q

Nitrogen disposal:

  • urea characteristics
  • urea cycle
A

Small, uncharged and highly water soluble (easily diffuse) and little energy requirement
1. Urea + arginine + water = ornithine + urea
2. ornithine + carbamoyl phosphate from the mito matrix (ammonia prod in mito)
3. Citrulline + aspartate + 2ATP = Argininosucciate
4. Argininosucciate loses fumarate prods arginine
Overall reaction: aspartate + NH4 + CO2 + H2O + 4ATP reversibly forming urea + fumarate + 4ADP

53
Q

Fate of urea

A

Transferred in blood to kidneys, can regen oxaloacetate via Malays in the cytosine using AST reaction (Malate dehydrogenase reaction), generating a net 1.5 ATP

54
Q

Amino acid synthesis:

- process

A
  1. Starts with a C skeleton from central metabolism
  2. Use transamination reaction to add amino group
  3. Further step to final amino acid structure
55
Q

Essential amino acids

A

Lysine, methionine, threonine, valine, leucine, leucine, isoleucine, phenylalanine, tryptophan and histidine

56
Q

Purine and pyrimidines

A

Purine: adenine and guanine
Pyrimidines: cytosine, uracil and thymine

57
Q

Amino acids are precious ones for important biomolecules

A

Histidine to histamine
Tyrosine forming hormones such as thyroxine, adrenaline, melanin and dopamine
Tryptophan: serotonin
Arginine: nitric acid
Serine: phospholipids
Glycine: creative, bile salts and porphyrins

58
Q

Amino acids feed into the TCA cycle

A

Added into each step of the cycle

59
Q

Metabolically classifies into 2 classes:

- glucogenic and ketogenic

A

Glucogenic: TCA cycle intermediate are gen and used for ATP or converted to glucose
Ketogenic: acetyl CoA gen to be converted to ATP or triglycerides for storage in adipose tissue (ketone bodies fuel)

60
Q

Energy metabolism in muscle cells:

  • overview
  • excess protein
  • high exercise
A

Excess protein:
- excess not stored, broken down for ATP generation or storages as glycogen or triglycerides (formation to amino acids via ALT)
- muscle cells take up branches chain amino acids from the blood and use carbon skeleton for fuel/storage (BCAA aminotransferase)
High intensity exercise:
- rate of cycling between ATP to ADP
- using creatine P used to replenish ATP

Body Cells And Structure (8 decks)

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