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MCAT Pricenton Review Book biochem > Chapter 4 > Flashcards

Chapter 4 Flashcards

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1
Q

What is an amino acid?

A

They are biological molecules that allow for the creation of proteins, cells, horomones, antibodies, transporters, basically everything we need to survie on a biological basis

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2
Q

Basic Structure of an amino acid?

A
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3
Q

What are the classifications of Amino Acids?

A

Polar, Non Polar, Acidic, Basic

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4
Q

How many amino acids are there?

A

There are a total of 20 amino acids in the human body.

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5
Q

What are the two acidic amino acids? What are their structures?

A

Aspartic Acid and Glutamic Acid

They both have carboxylic acid functinoal group in their side chain with a PKA of 4

Rember glutamic acid glues on an extra CH2 to aspartic acid

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6
Q

What are the Basic Amino Acids? And their structures?

A

Lysine, Argeine, Histidine

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7
Q

hydrophobic (nonpolar) amino acids

A

Glycine, Alanine Valine Leucine Isoleucine phenylalanine tryptophan

GLY G, ALA A, VAL V, LEU L, Ile I, Phe F, Trp W

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8
Q

Polar Amino Acids and structures

A

Serine Threonine Tyrosine Asparagine Glutamine

Ser S, Thr T, Tyr Y, Asn N, Gln Q

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9
Q

Sulfur containg amino acids

A

Cysteine, Methionine

Cys C, Met M

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10
Q

Proline

A

Proline is unique the amino group is covalently bound to its non polar chain, which creates a secondar alpha amion group and ring structure. It causes kinks in protein folding due to this structure.

Pro P

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11
Q

what is the henderson hasselbalch equation?

what is this equation used for ?

A

Ph=pka+log [H-]/[HA] = PKA + log baseform/acidform

This equation is used to describe relationship between ph and pka and the postion of equilibirum.

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12
Q

what happesn when PH of soloutin is less than the pka of an acid group.

A

the acidic group will be in its protonated form.

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13
Q

what happens when the ph of the soloution is more than the pka of the acidic group?

A

the acidic group will be in its deprotonated form

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14
Q

What is the isoelectric point?

A

The isoelectric point is considered the zwitterion. This is when the PH is considered uncharged. It is designated by pI where there is a postive and negative charge.

Zwitter in german means hybrid

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15
Q

How do you calculate the zwitter ion?

A

add the first pka with the second pka and divide by two

pKa1 + pKa2 /2 = pI

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16
Q

What are the two common types of covalent bonds between amino acids?

A

Peptide bonds and disulfide bridges

17
Q

What is the peptide bond? How is this bond formed?

A

The pepetide bond links amino acids to one another. This bond is formed though a dehydration rxn with the loss of water. It is formed between the caroxyl group of one amino acid and the alpha amion group. Pictured is the rxn

18
Q

What is the polypetide bond pattern for the formation ?

A

n c c n cc

19
Q

What is an individual amino acid called?

A

Residue

20
Q

What is it called when a protein hydrolysis another protein?

A

This is called proteolysis or porteolytic cleaveage.

21
Q

What is the protein called that cleaves another protein

A

Protease , or Proteolytic enzyme

22
Q

Disulfide Bond

A

Disulfide bonds are formed between two cysteine amino acides to make a cystine. This is done through a oxidation rxn. with the loss of hydrogen on both cysteine amino acids.

23
Q

What is it called when a protein is broken down.

A

The term is dentauration

24
Q

What are the ways that a protein can be denatured?

A

Increase in heat, decrease in pH, chemical

25
Q

Primary structure 1

A

This is the first structure in creation of proteins, this is the polypetide backbone of the protein.

refered to as a sequene

26
Q

Secondary Structure

A

This is the intial folding of the chain, which folds into shapes to stabilze. This is done with hydrogen bonding. Two common alpha helix and beta pleated sheats

27
Q

How does proline cause an issue in peptide chain?

A

Forces the chain to kink, due to the bonding of one hydrogen on the nitrogen not being able to complete the chian.

28
Q

Tertiary Structure

A

Concerns with distant amino acids interactions

This is done through van der walls forces between nonpolar side chains, hydrogen bonds between polar sidechians and cysteing disulfide.

29
Q

What is the hydrophobic effect concering proteing folding?

A

The hydrophobic effect concering proteins, has to do with the folding during the tertiary stages. The exterior of the protein becaums hydrophili, while they hydrophobic R groups fold inwards.

30
Q

Quaternary Structure

A

Is the interaction between various polypetide subunits. Example is hemoglobin which is 4 proteins together.

Forces stabilizing the are similar to teritary, besides the peptide chain which only is in primary.

31
Q

Define each Term

Hydrolase

Isomerase

Ligase

Lyase

A

Hydrozels chemical bonds

rearranges bonds withing a molecule to form an isomer

Forms ca chemical bond (glue)

Breaks a chemical bond by means other than oxidation or hydrolsis

32
Q

Define each term

Kinase

Oxidoreductase

Polymerase

Phophsatase

A

transfers a phosphate group to amolecule from a high energy carrier such as ATP

runs redox rxns

polymerization additon of nucleotids to the leading strand of dna by dna polmerase 3

removes a phosphate group

33
Q

Define Each Term

Phopshorlylase

Protease

A

transfers a phosphate group to a molecule from inorganic phosphate

hydrolyzes pepetide bonds

34
Q

Reaction Coupling

A

This allows for thermodynamically unfavorbale rxns to occur through coupling with ATP hydrolsis.

ATP to ADP + PO 4 2- ^G -12

the properties are additve so by adding the ATP hydrolsis it can push a rxn to the negative Delta G

35
Q

Active Site Model (Lock and Key)

A

Binding no conformation change

36
Q

Induced fit model

A

Active site and substrate are different,and they go through a conformational change

37
Q
A
38
Q
A

MCAT Pricenton Review Book biochem (2 decks)

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