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Biochemistry CH3 Flashcards

1
Q

What do proteins do (generally)

A

Perform nearly all the work in cells and organisms

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2
Q

Name 5 things proteins do

A

Structure
Catalysis
Immunology
Transport
Storage

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3
Q

At least how many different proteins are found in human cells?

A

20000

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4
Q

Transport

A

Proteins help to move molecules around the cell and organism. Hemoglobin is a blood-based protein that carries oxygen from the lungs to tissue.

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5
Q

Hormones

A

These molecules communicate messages between cells. Relaxin is a protein hormone that helps women during childbirth by relaxing pelvic ligaments to make delivery easier.

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6
Q

Catalysis

A

Enzymes speed up, or catalyze, chemical reactions. Protease, an enzyme, breaks down proteins in cells to help organisms recycle unneeded proteins. This enzyme is also added to laundry detergent to degrade stains with protein (i.e. blood or food).

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7
Q

Structure

A

These proteins give strength to cells, organelles, and tissues. Collagen is the structural protein found in cartilage, skin, and tendons.

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8
Q

Protection

A

The human body protects itself from outside proteins and toxins by making proteins called antibodies to fight the foreign invaders.

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9
Q

All proteins are constructed from the same 20 standard _____ _____

A

amino acids

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10
Q

Which carbon are the functional (R) groups attached to?

A

Ca (alpha carbon)

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11
Q

What are the same groups that all amino acids have and what do they do?

A

NH3, CH, and COO-

It permits all amino acids to link together in a protein

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12
Q

Non-polar aliphatic amino acids

A

GAVPLIM - Great Adventures Very Predictably Lead Into Mountains

Glycine Alanine Valine Proline Leucine Isoleucine Methionine

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13
Q

Non Polar Aromatic amino acids

A

PWY - People Want Yachts

Phenylalanine Tryptophan Tyrosine

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14
Q

Polar neutral amino acids

A

STCNQ - Some Tiny Creatures Need Quests

Serine Threonine Cysteine Asparagine Glutamine

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15
Q

Acidic amino acids

A

Aspartic and glutamic acid (D and E)

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16
Q

Basic amino acids

A

RKH - Really Kind Hearts

Arginine Lysine Histidine

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17
Q

Disulfide bonds

A

Link amino acids together and form covalent bonds

When present, stabilize a proteins structure

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18
Q

Protein keratin

A

Protein component

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19
Q

Long chain of amino acids

A

polypeptide

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20
Q

Basic amino acids side chains are normally _______ charged.

A

positively

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21
Q

Condensation reaction

A

Formation of a peptide bond with the loss of water

Typically between one oxygen from the carboxylic acid group and two hydrogens from the amino group

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22
Q

Oligopeptide

A

Short chain of amino acids typically 2-20 amino acids

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23
Q

Peptide

A

amino acids linked together by peptide bonds

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24
Q

When the number of residues is 99 or less, we say its a

A

polypeptide

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25
What makes a protein attain its status
After 100 residues have been added together.
26
When a protein has 100 amino acids, the protein has a mass of...
10,000 g/mol or 1 Da
27
__________ _______ is the term used to describe the chemistry of large compounds.
Supramolecular chemistry
28
Dipeptide
Amino functional group of one amino acid reacts with the carboxylic acid function group of a second, 2 monomers are joined together producing a dipeptide with the release of water.
29
Protein backbone
Connection of amino acids via peptide bonds, this is a protein backbone what links all amino acids together.
30
C terminal vs N terminal
31
Why are amino acids called residues?
To reflect the molecule remaining after the condensation reaction takes place.
32
Conformation
Proteins can have hundreds or thousands of amino acids joined together into a three dimensional structure.
33
Fibrous vs globular protein
Biologically active structures Fibrous - Long extended structure of alpha helices Globular - thick
34
Portions of proteins may exist in a random conformation, or, as they are often called...
intrinsically disordered
35
Four standard levels or protein structure...
Primary (1degree) Secondary (2 degree) Tertiary (3 degree) Quaternary (4 degree)
36
Primary structure refers to...
The order of amino acids covalently bonded together including disulfide bonds, in a polypeptide chain. N->C
37
Secondary Structure
Examine local three dimensional structure of amino acid residues close in linear sequence. Alpha helices, beta sheets, and beta turns.
38
Alpha helices
Coiled structures of amino acids where backbone atoms form hydrogen bonds to stabilize this sequence.
39
A standard helix has ___ amino acids or residues per each turn while rising ___ angstroms per turn.
3.6 5.4 1 angstrom = 1E-10 m
40
The interior of a helix has no
space
41
Beta sheet is
Repetitive sheetlike structure. Zig zag orientation.
42
Beta sheets form when
Individual beta strands that interact by hydrogen bonding to one another.
43
Anti parallel beta sheets and parallel
Two versions Anti-parallel beta-sheets form when one beta-strand ends and the amino acid sequence turns back around on itself. Then, an additional beta- strand can join other strands to form anti-parallel sheets.
44
anti parallel vs parallel sheets
H bonding partners are different and the distance of each repeat is unique. Parallel repeats every 6.5 angstroms Antiparallel repeats every 7.0 angstroms
45
What percent of amino acids are found in turns in a protein?
30% Changes in the direction of the N à C direction of the primary sequence.
46
One type of common turn is the ____-____ , which is a four residue unit that turns 180 degrees.
beta turn
47
Beta turns are a different category than ____ _____
beta sheets
48
Beta turns can form with both
alpha helix and beta sheets.
49
Motif
Collections of particularly stable groups of secondary structures are often referred to as a motif. For example, one motif is a helix-turn-helix motif composed of an alpha helix, followed by a turn, and then another alpha helix.
50
Motifs occupy a position between secondary and tertiary structures but are not one of the...
four levels specified by scientists
51
Tertiary Structure
Overall three-dimensional structure of a folded polypeptide
52
Prosthetic group
Help with some function of a protein In myoglobin it helps bind the oxygen that it stores.
53
Myoglobin
Critical in our muscle cells for binding and storing oxygen. Prosthetic helps bind oxygen that it stores.
54
A heme ring is a ________ _____, which is a non-amino acid portion of the molecule necessary for the structure and function of a protein.
prosthetic group
55
Myoglobin and protease inhibitor fits in what class of protein structure
globular
56
Strength of covalent bond compared to protein stability range
400 kJ/mol (covalent bond) 20-65 kJ/mol (protein)
57
Protease
Protein enzyme that degrades other proteins, so a protease inhibitor regulates the activity of a protease.
58
What type of protein is this?
beta barrel protein
59
Quaternary Structure
Macromolecules that have two or more independent polypeptide chains that associate with one another. The number and orientation of these chains constitute the quaternary structure.
60
Example of quaternary structure
Staphylokinase - has two identical polypeptide chains
61
Dimer
Two polypeptides protein structure, two subunits.
62
Hemoglobin is another example of a...
protein quaternary structure it is a tetramer
63
Tetramer
Four subunits two subunits are the same called alpha subunits while the other two are beta subunits. (uncommon) Ex: hemoglobin
64
Protein complex lumbricus erythrocruorin from an earthworm has ___ subunits as part of its quaternary structure
180
65
The "-in" ending is used for proteins that are not ______. ex: hemoglobin, myoglobin, etc.
enzymes
66
Enzymes typically have the "___" ending.
ase Ex: protease, staphylokinase, etc.
67
Enzymes
proteins that accelerate speeds of chemical reactions lower activation energy
68
The result of a enzymes speeds up the reaction _____ times or even more compared to the rate of the uncatalyzed reaection.
1000
69
Enzymes work better in organic or inorganic catalysts
inorganic - due to their complementary structure
70
Hydration reaction adds
water across a double bond
71
Generalized reaction equation to illustrate an enzyme catalyzed reaction:
E + S ---> ES ---> E + P P - product ES - enzyme substrate complex
72
lyase
class of enzymes that creates double bonds or adds molecules to double bonds
73
Cofactor
Non protein component that are critical for activity, metal ions can be cofactors
74
Organic compounds function as cofactors as well and when they do they are called
coenzymes lack of a coenzyme generally makes an enzyme non functional
75
examples of coenzymes
Vitamin C and Niacin
76
Apoenzyme
An enzyme without the cofactor (either ion or coenzyme)
77
Active site
Specific spot in their structure where catalysis takes place.
78
When the cofactor is added to the apoenzyme to produce a functional enzyme, this is called the
holoenzyme
79
Most active sites have about __ amino acid residues defining the space.
10 fraction of 100+ amino acids in a typical protein
80
Non covalent interactions between the active site and the amino acids do...
interact with the substrate which helps to generate a favorable energy change to enhance the reaction Gives enzymes great specificity for one molecule and also provides energy to initiate the reaction
81
These interactions provide energy to change the conformation of the enzyme to accommodate this substrate, this is called an _____ ___
induced fit
82
Transition State
The structure of the molecule in its transition into a new molecule high in potential energy and that it is the most unstable part of the reaction.
83
Increasing the concentrration of enzyme generally increases the ____
rate
84
Increasing the substrate concentration increases the rate up to a certain point?
yes, because the active sites fill up
85
The ph of the solution influences the rate?
yes, most enzymes have a particular pH range that is most active and hence has the most complementary shape for activity.
86
Temperature related to rate.
Critical factor for both the reaction conditions and for enzyme conformation. Reaction rates for uncatalyzed reactions increase with increasting temperature (10 degrees C increase doubles the reaction) (more temperature more collisions)
87
Unfolding
renders enzyme inactive, too much increase in temperature can cause this.
88
Inhibitors
Slow down or stop enzyme reactions. Bind to the enzyme and prevent the reaction from taking place.
89
When the binding occurs through non covalent interactions we say these are
reversible inhibitors
90
Reversible inhibitors have three types:
competitive uncompetitive mixed
91
Competitive inhibitors
Compete with the natural substrate for the active site. When a competitive inhibitor binds, it takes the place that a natural substrate would occupy. Since the substrate is not being acted upon, it slows down the reaction rate and less reactant is turned into product.
92
Uncompetitive inhibitors
Bind at a spot distinct from the active site and prevent catalysis from taking place. Interestingly, the inhibitor only binds to the enzyme- substrate complex.
93
Mixed inhibitors
Can bind either to the lone enzyme or the enzyme-substrate complex. Like the uncompetitive inhibitor, the mixed inhibitor binds at a site distinct from the active site, so it does not compete with the substrate.
94
What type of inhibitor are found when an enzyme has two or more substrates
Uncompetitive or mixed
95

Biology (14 decks)

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