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Biochem > 03 > Flashcards

03 Flashcards

1
Q

What do enzymes do

A

increase the rate of chemical reaction

rate = # in set amount of time

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2
Q

Describe an enzyme

A

specific for one reaction (depends on the amino acids that make up the enzyme)

not permanently changed in these reactions

bind the substances that are reacting (substrates) and release the (productcs) once the reaaction is complete

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3
Q

What are the steps to an enzyme catalyzed reaction

A
  1. binding of substrate
    E+S <-> ES
  2. conversion of the bound substrate into a still bound product
    ES <-> EP
  3. release of the product
    EP <-> E+P

*reversible reactions

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4
Q

What is the lock and key model
what are the limitations

A

enzyme and substrate fit together perfectly

this model explains the specificity of an enzyme
- not the ability of the enzyme to stablizie the transition state

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5
Q

What is the induced fit model

A

most accurate model

allows for flexibility of the enzyme in binding to the substrate

binding of the substrate induces changes in the shape/conformation of the enzyme

changes allow for enzyme catalysis to take place

explains changes in protein structure that occur when a substrate bidns to an enzyme

conromational change can stress the bonds –> allows for a reaciton to take place more easily

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6
Q

How do enzymes catalyze a reaction

A

lowers the activation energy needed to reach the final state
*doesn’t speed up the reaction progress, just the number of products made

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7
Q

What are the strategies used by enzymes to catalyze a reaction

A
  1. acid-base catalysis
  2. covalent catalysis
  3. metal-ion catalysis
  4. catalysis by approximation
  5. cofactor catalysis

enzymes can also use a combo of these

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8
Q

What are co-factors and co-enzymes

A

functional groups that help facilitate the enzymatic reaction

come from the enzymes themselves (aa side chains), other non-protein molecules or minerals that are part of the active site

  • can donate a function group to the reaction
  • stabilize the transition state of the reaction
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9
Q

What are examples of cofactors and coenzymes

A

zinc
iron
vitamin B6
Thiamine B1

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10
Q

How do cofactors work

A

incomplete enzyme + mineral cofactor join together to form an active enzyme

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11
Q

How do coenzymes work

A

incomplete enzyme + (vitamin + chemical group = functional coenzyme) join together to form an active enzyme

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12
Q

How is the rate of an enzymatic reaction measured

A

by how many products can be made in a period of time

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13
Q

What factors can impact the rate of reaction

A

pH
temp
substrate/enzyme/product concentration
inhibitors
protein modfications

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14
Q

What happens to an enzyme as pH is increased

A

each enzyme has an optimal pH
- below: not functioning to slow
- at pH: aa residues in the protein structure either protonaed or deprotonated –> can have correct structure // functional groups can catalyze
- above: denatured

most enzyme’s optimal pH = physiological pH or the pH of their environment

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15
Q

How does temp impact reaction rate

A

higher temp: more atoms and molecules vibrate

most human enzyme operate best at 37C

rate of reaction increases until the temperature at which the enzyme is denatured

temp increases = heat (vibrational) energy make it easier to break chemical bodns until the protein secondary and tertiary structure breaks down

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16
Q

What happens if there is little substrate, what is the impact of the rate of reaction

A

no substrate = no reaction

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17
Q

What happens if there is little enzyme, what is the impact of the rate of reaction

A

more enzymes = more product that can be made

enzyme concetration can be controlled by gene expression and protein degradation

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18
Q

What happens if there is little concentration of product, what is the impact of the rate of reaction

A

when a lot of product –> binds to active site and prevents the reaction from occuring, or go backwards to be converted back into the substrate

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19
Q

What are inhibitors

A

decrease the rate of reaction

reversible (competetive or noncompetetive or allosteric) or nonreversible

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20
Q

What are irreversible inhibitors

A

compounds that covalently modify an enzyme

permanent and not reversible and the enzyme is permanently changed

enzyme must be degraded and replaced with a new enzyme

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21
Q

What are reversible inhibitors

A

bind to enzymes, but not permanent

  • competitve
  • noncompetetice
  • allosteric
22
Q

What are competitive inhibitors

A

has similar shape to one of the substrates of an enzymes –> reactions can’t occur –> product is not produced

only inhibit when they are bound in the active site, many can be displaced by increasing the concentration of substrate

slower, gradually reaches vmax

23
Q

What are noncompetetive inhibitors

A

does not compete with substrates for binding
- binds elsewhere on an enzyme

results in conformation change inthe enzyme –> prevents the substrate from binding or the reaction from preceeding

Allosteric inhbition: inhibitor binds to allosteric site, active site changes shape so substrate can’t bind

loweres the vmax

24
Q

How do you turn off an enzyme

A

Location: keep the enzyme away from its substrate to prevent the reaction from happening

inactive enzyme: some enzymes are kept in an inactive state until they are needed

enzymes cna be modified to turn on and off (ex. post-translational modifications)

25
Q

How are metabolic pathways turned on and off

A

enzymes are always part of a pathway

when regulating these pathways, not every enzyme needs to be regulated (only the important ones)

when these reactions are regulated, the whole pathway turns off

26
Q

Which cell does not contain a nucleus or membrane bound organelles

A

prokaryotic (bacterial cells)

27
Q

How do prokaryotic cells differ from eukaryotic cells

A

compartments allow cells to concentrate molecules and proteins, controls when and how reactions take place

28
Q

Describe the plasma membrane

A

all cells enclosed

phospholipic bilayer that contains proteins and other molcules

proteins embedded in the membrane and/or anchored to tje membrane

allows cellular communication and transport between either side

29
Q

What are phopholipids

A

amphiphatic molecuels
- hydrophillic and hydrophobic regions

dual nature allows phospholipids to form a bilayer that is hydrophillic on the outsdie nad hydrophobic on the inside

30
Q

What are integral proteins

A

transmembrane proteins

embedded in the membrane with hydrophobic and hydriphillic regions on either side

can connect the outside and insdie of the cell

channels, transporters, receptors for hormones, neurotransmitters

31
Q

What are peripheral proteins

A

attach to integral membrane proteins or to the edges of the lipid bilayer temporarily and crry out a specific function

32
Q

How are products transported across the membrane

A

using proteins

establishes an electorchemical gradient
- concentration gradient
- charge gradiant

33
Q

What are the modes of transport

A
  1. passive transport
    - simple diffusion
    - facilitative difussion
  2. active transport
    - primary
    - secondary
  3. bulk transport (endocytoriss)
34
Q

Describe simple diffusion

A

movement of molcules from jhigh to low concentrations

no energy required

small non-polar molecules
small polar (water) can move, but slowly

35
Q

Describe facilitated diffusion

A

movmenet of molecules from high to low

larger polar moele
molecules must bind to its transport protein

36
Q

Describe active transport

A

uses a lot of energy
ex. sodium potassium pump

37
Q

Describe secondary active transport

A

transports a molecue from a low to high contraction area

no energy used riectly – connects transport of on molecule to the tranport of another with its concentraction gradant

38
Q

What does the nucleus do

A

the library and command centre

largest organlle

has double membrane that is connected to the endoplasmic reticulum

most of the NDA is in the nucleus, with small amount located in the mitochondria

DNA replication and transcription of the DNA into RNA both occur in the nucleus

once mRNA transcribed and processed it travels out of the nucleus through nuclear pores for translation

39
Q

Describe nuclear transport

A

proteins, RNA, nucleotides all need to move in and out of the nucleus

involves the movement through nuclear pores

proteins made in the cytoplasm, specific sequences on the protein direct the protein to where they are needed

nuclear proteins –> nuclear localization sequences (NLS)
nuclear export sequences (NES)

40
Q

What is the endoplasmic reticulum

A

the protein factory

made up of smooth and rough (ribosomes attached) areas

rough ER: site of translationg of proteins bound for outside the cell or within the membrane or organelles
(where post-translation modifications occur)

smooth ER: contains enzymes for lipid synthesis and the cytochrome P450 oxidative enzymes of drug metabolism as well as the site of glycogen storage in the liver

41
Q

What are ribosomes

A

protein synthesis factories that are found in the cytoplasm and attached to the ER

42
Q

What is the golgi complex

A

“amazon warehouse”

golgi complex modifies, sorts and distributes proteins around the cell

proteins translated in the rough endoplasmic reticulum move the golgi where they receive post-translational modifications and are transported to where they need to go

43
Q

What is the mitochondria

A

the powerplant

sites of energy production

consist of an outer and inner membrane (double membrnae)
- inner membrane: site of the enzymes invovled in cellular respiration, while the TCA cycle and other oxidative pathways occur in the matrix

mitochonrdria has its own DNA, seperate from the nucleus

44
Q

What are lysosomes

A

recycling depot

membrnae-bound organelles containing enzymes that can breakdown molecules that can be re-used

lysosomes break down:
- anything the cell doesn’t need
- foreign invaders

pH is maintained at about 5.5 so that the enzyme encolsed in the organelle can function

pH maintained by transporters that use energy (ATP) to pump H+ into the lysosome

45
Q

What is cellular signaling

A

cells need to communicate iwth each other to maitain homeostasis
- sharing info across different cells and cell types

46
Q

What are the steps to cellular signaling

A
  1. secretion of a messenger molecule
  2. binding of the messenger to a receptor outside or inside the cell
  3. a change occuring in the cell
  4. termination of the signal/degredation of the messenger
47
Q

What are the types of cellular signalling

A
  • endocrine hormones and messengers are secreted into the blood and travel to target cells
  • paracrine messengers act on cells nearby
  • autocrine messengers bind on the same cell from which they are released
  • juxtacrine are direct cell to cell interactions
48
Q

What determines the type and location of a cell receptor

A

type and the location of receptor determined by the messenger molecule

49
Q

What does it mean if a cell receptor can cross the membrane or if it cannot

A

mol can cross the plasma membrane: receptor will likely be inside the cell

mol cannot cross the plasma membrane: the receptor will need to be on the cell surface

50
Q

What are intracellular receptors

A

bind to messengers that can diffuse across the plasma membrane

messengers need to be hydrophobic

steroid/thyroid hormone superfamily of receptors are examples
- diffuse through the plasma membrane, bind to their receptor in the cytoplasm and move to the nucleus where they alter gene expression

51
Q

What are extracellular receptors

A

bind to messengers that cannot diffuse across the plasma membrane

usually hydrophillic and can be large

bind to receptor proteins embedded in the plasma membrane

causes a conformational change that starts signlaing cascade inside the cell

Biochem (11 decks)

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