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Biochem/ metab > lecture 5 > Flashcards

lecture 5 Flashcards

1
Q

what is the overview of protein synthesis?

A

DNA–transcribed–> mRNA–>translated–> protein
transcription occurs in the nucleus
translation occurs in the cytoplasm

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2
Q

protein is formed by what in the cell?

A

ribosome

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3
Q

what is the definition of a peptide?

A

<50 amino acids= peptide

>50 amino acids= polypeptide

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4
Q

what are amino acids?

A 
building block of protein 
function as individual units in metabolic processes
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5
Q

what is an Alpha amino acid?

A

amino acid that is on the adajecent carbon to the carboxyl group

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6
Q

what does amphoteric mean?

A

acts as an acid or a base

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7
Q

what are 3 factors relevant to amino acids

A

amphortic
buffers
3rd pKa value

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8
Q

how do proteins act as a buffer?

A

2 biologically relavant ph values
COOH= 2 (acidic)
NH3= 10 (basic)

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9
Q

what are the 3 different pKa values locations on the amino acid?

A

NH3
COOH
Rgroup

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10
Q

how are amino acids classified?

A

based on:

  1. capacity to interact with water
  2. based on R group properties
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11
Q

what are the classes of amino acids?

A
  1. neutral non-polar
  2. neutral polar
  3. acidic
  4. basic
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12
Q

describe the neutral non-polar amino acid

A

side chain does not have charge

  • r group is mainly hydrocarbons
  • hydrophobic
  • maintain 3-d structure
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13
Q

describe neutral polar amino acids

A

side-chain not charged
functional group capable of h bonding
hydrophilic

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14
Q

describe acidic amino acids

A

negative charge on the R group

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15
Q

describe basic amino acids

A

postive charge on the amino acids

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16
Q

what are the neutral non-polar amino acids

A 
GAP PIL MTV
Glycine 
alanine 
Phenylalanine 
proline 
Isoleucine 
Leucine 
methionine 
Tryptophan 
valine
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17
Q

list the neutral polar amino acids

A 
Samuel glutamine asparagine threw that cat 
serine 
glutamine 
asparagine 
tyrosine 
threonine
cysteine
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18
Q

list the acidic amino acids

A

Gil ate asparagus

  • glutamate
  • aspartate
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19
Q

list the basic amino acids

A

Lice are hot
Lycine
arganine
histadine

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20
Q

what do basic and acidic amino acids do?

A

basic- accept protons/ hydrogens

acidic- donate protons/ hydrgogens

21
Q

what are stereocenters?

A

alpha carbons

22
Q

what do all protein derivative have/ are

A

-stereocenter
chiral
stereoisomers

23
Q

which configuration is most common?

A

L-configuration

NH3–>

24
Q

what is the least common configuration?

A

D-configuration

–NH3

25
Q

Define stereoisomers

A

molecules with all the same elements (# of molecules) like C3H6O2but the arrangement is different

26
Q

define enantiomers

A

the mirror image forms of amino acids * cant be superimposed*

  • L configuration
  • R configuration
27
Q

how does pH influence structure?

A

amino acids can be ionized –> react with charged particles and can change shape
pH–> # of H+ ions in environement

28
Q

what determines the structure

A

pH concentration of the envrionment

29
Q

what is the concentration of H+ with a low pH and a high pH?

A

low pH= high concentration

high pH= low concentration

30
Q

what 2 parts of an amino acid can be ionized? and what can they do?

A

Amino group: accept protons

carboxyl group: donate protons

31
Q

what does the charge on the NH3+ say?

A

NH3+ has accepted a proton
that the concentration of H+ in the environment is high so the
pH is low and
acidic solution

32
Q

what does say when there is a charge on the NH3+ and the COO-?

A

that the NH3+ still have its proton but the COO- has donated the proton
the H+ concentration has decreased the pH is rising
net charge = 0
neutral environment

33
Q

what is zwitterion?

A

when an amino acid has a + and - charge

net charge= 0

34
Q

what is pI?

A

isoelectric point , when the net charge is 0

35
Q

what does a - sign in the COO say?

A

that the carboxyl group has donated it proton
the H+ concentration is low so
the pH is high= basic solution

36
Q

how do you calculate pI?

A

adding the pKa values
pKaN
pKaC
& sometimes pKaR

37
Q

how do you know which pKa values to use?

A

if there is only 2 the use those 2

If there are 3 then always use the pKaR and the other functional group that matches with the R group

38
Q

what is pKa with respect to pKaR, pKaC, pKaN?

A

the pH when the proton is lost from that location

39
Q

which side chains can be ionized?

A 
Cat Thought Luke Had All Amino Groups 
cysteine-np
tyrosine-nnp
lysine-nnp 
histidine-b
arginine-b
aspartate-a
glutamate- a
40
Q

what determines the predominant ionic form

A

pH solution

41
Q

what does titration tell?

A

reactivity of the side chain

42
Q

what are 2 rxn proteins

A
  1. peptide bond formation

2. cysteine oxidation rxn

43
Q

what is the peptide bond formation

A

a covalent bond between 2 amino acids *by the ribosome

44
Q

how are proteins used in the body?

A 
perform most actions in the body 
- structure 
metab reg
transport 
defense 
catalysis
45
Q

what do biological activity proteins act in?

A

chemical messengers

  1. neurotransmitters
  2. hormones
46
Q

how do amino acids act as precursors or nitrogen-containing molecules

A

nitrogenous bases

Heme/chlorophyll

47
Q

what metabolic intermediate is an amino acid found in?

A

urea cycle

48
Q

all amino acids are chiral except which one?

A

glycine

49
Q

describe the titration curve

A

tells the pKa which is determined based on the average of the two structures that are present between the forms

Biochem/ metab (4 decks)

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