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Cell and Molec > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

All proteins are enzymes

True or false

A

False

Many different functions

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2
Q

Transcription Regulators

A

Turn things on and off

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3
Q

Signal Proteins

A

Signal transduction

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4
Q

_______ drives function

A

Structure

Structure is MUCH more conserved than sequence data

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5
Q

The shape of a protein is specified by __________-

A

Its amino acid sequence

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6
Q

proteins fold into a conformation of ________ energy

A

Lowest

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7
Q

proteins come in a wide variety of complicated shapes

A

True

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8
Q

The alpha helix and Beta sheet are

A

Common folding patterns

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9
Q

Helices form ___________________-

A

Readily in biological structures

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10
Q

Beta sheets form ___________________________-

A

Rigid structures at the core of many proteins

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11
Q

Misfolded proteins can form _____________ that cause disease

A

Amyloid structures

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12
Q

proteins have _______ level(s) of organization

A

Several

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13
Q

Amino acids are linked together by __________ bonds

A

Peptide

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14
Q

Polarity

A

Has direction

i.e. DNA

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15
Q

Peptide bonds form by ___________-

A

Dehydration (removal of water)

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16
Q

A protein is made of amino acids linked together into a ___________

A

Polypeptide chain

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17
Q

Side chains of amino acids are

A

Different

i.e. can have negatively or positively charged, polar uncharged, nonpolar

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18
Q

The amino acids present in a chain will dictate how a protein will fold

A

Given interactions

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19
Q

3 types of noncovalent bonds help proteins fold

A

1) Electrostatic - held by charges
2) van der Waals attractions - close together
3) Hydrogen bonds - attachment b/w H and O, F, or N

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20
Q

Noncovalent interactions have a __________ effect

A

Additive

The more that’s there, the stronger the structure will be

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21
Q

Hydrophobic forces help the proteins fold into compact conformations

A

Hydrophobic forces will be w/in folds, protected from liquid environment

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22
Q

Hydrogen bonds w/in a protein help _________ its folded shape

A

Stabilize

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23
Q

Backbone to backbone

A

H-bond b/w atoms of 2 peptide bonds

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24
Q

Backbone to side chain

A

H-bond b/w atoms of a peptide bond and an amino acid side chain

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25
Q

Side chain to side chain

A

H-bond b/w atoms of 2 amino acid side chains

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26
Q

proteins fold in lowest energy conformation; dictated by amino acid sequence

A

Protein folding is an energetically favorable interaction

Most proteins need help fodling

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27
Q

Chaperones

A

Type of protein

Guide the folding of a newly synthesized polypeptide chain

Help proteins fold correctly; MOST assist in protein folding by keeping everything else in the cell AWAY during folding, it doesn’t know how the protein needs to be folded; SOME may prevent proteins from folding too early; SOME may create a chamber to isolate protein from everything else so it can fold correctly, then be released from this chamber

Found in ALL cellular life

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28
Q

Some chaperone proteins act as ________- that help a polypeptide fold

A

Isolation chamber

Proteins put in chaperone that is like a container to keep all other junk away while the protein folds

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29
Q

Proteins come in a ____________ of shapes and sizes

A

Wide variety

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30
Q

Secondary structures

A

Core elements of protein architecture

Stable arrangments of segments of a polypeptide chain held together by H-bonds b/w backbone amide and carbonyl groups

Propensity of a segment ot form any given secondary structure depends on its amino acid sequence

Alpha helices and Beta sheets

Formed STRICTLY with noncovalent H-bonding

In an average protein:
–60% of the chain = alpha helices and beta sheets with the remainder of the molecules existing as irregular structures, coils and turns

31
Q

Primary structure

A

Amino acid sequence

32
Q

Alpha helix

A

Some polypeptide chains fold into an orderly repeating form

Side chains protrude outward

Helix structure is very coordinated

Every amino acid is bound to another structure 4 residues down

Every amino acid in alpha helix takes part in H bonding EXCEPT those at N- and C-terminal ends

Held together STRICTLY by H bonds

Seen frequently in cells that cross the plasma membrane

Backbone forms a spiral structure stabilized by H bonds b/w the carbonyl oxygen atom to the amide hydrogen atom of the amino acid 4 residues downstream

ALL backbone amino and carboxyl groups are hydrogen-bonded (except at the beginning and the end of the helix)

Many membrane-bound proteins cross the lipid bilayer as an alpha helix

Form a stiff coiled-coil: join w/ other alpha helices to form this; alpha helices start reacting and twisting around each other to form coiled coild

Collagen is a coiled coil (strictly made of alpha helices)

33
Q

Beta Sheets

A

Formed STRICTLY by H bonds

Can form single polypeptide chain OR in multiple chains

Run parallel (connected via loops that come out) or antiparallel

Backbone forms laterally packed strands stabilized by H bonds b/w backbone amino and carboxyl groups of separate, but adjacent strands

Distinct Beta strands may be:

  • W/in a single polypeptide chain
  • Different polypeptide chains

Can STACK to form an amyloid structure: misfolded proteins are beta sheets; can fold on top of each other to form these amyloid structures; have been found in MANY neurodegenerative diseases, recently found in type II diabetes

34
Q

Prion diseases

A

Caused by proteins whose misfolding is infectious

Induce misfolding of a protein

Amyloid fibers commonly found in these structures

Prions make protein go to a different kind of protein

35
Q

Levels of Protein hierarchy

A

Primary
Secondary
Tertiary
Quaternary

36
Q

Primary structure

A

Amino acid sequence

37
Q

Secondary structure

A

Alpha helices and Beta sheets

38
Q

Tertiary structure

A

Combination of different secondary structural elements (several alpha helices, several beta sheets)

Get DOMAINS in tertiary

39
Q

Quaternary structure

A

If protein interacts with another protein (2 or more polypeptide chains)

Some act as a monomer

NOT all proteins have quaternary structure

40
Q

Many proteins are composed of separate functional _______

A

Domains

41
Q

Domain

A

Section of a protein that serves specific function (part or section of protein)

Proteins can have many different domains

42
Q

Dimers

A

2 identical polypeptide chains must interact in order for this protein to be functional

Many protein molecules contain multiple copies of the same protein subunit

43
Q

Terms like dimer, tetramer, trimer indicate that it is a _________ structure

A

Quaternary

44
Q

Tetramer

A

Formed by interactions b/w 2 NONidentical binding sites on each monomer

45
Q

Dimer

A

Formed by interaction b/w single, identical binding site on each monomer

46
Q

Identical protein subunits can assemble into _____________

A

Complex structures

Transcription factors act as dimers: Have 1 domain that binds to DNA, one that binds to something else

SOmetimes proteins can form helix structures

47
Q

Tubules

A

Made up of repeating dimers

48
Q

Microfilaments/Actin

A

Part of cytoskeleton

VERY complex structure, repeat over and over

Made of one monomer that binds to another monomer over and over again

49
Q

The primary structure of a protein determines how it will fold

A

Hypothetical protein-folding pathway:
Primary -> secondary -> secondary -> pretertiary (with domains) -> tertiary

Proteins are very dynamic, always moving

50
Q

Proteins are often stabilized by ____________________

A

Covalent Cross-Linkages

Disulfide bonds help stabilize a favored protein conformation
-When you have an amino acid chain with CYSTEINE residues, potential for disulfide bonds to form

Reducing agent = breaks disulfide bonds = cysteine present

51
Q

Disulfide bonds are ______ bones

A

Covalent

52
Q

Oxidation

A

When disulfide bonds FORM

53
Q

Reduction

A

When disulfide bonds BREAK

54
Q

ALL proteins bind to

A

Other molecules

55
Q

Enzymes are powerful and highly specific catalysts

A

Enzymes greatly accelerate the speed of chemical reactions

56
Q

All proteins interact w/ other molecules in some way, VERY _________

A

Specific

57
Q

Ligand

A

Something a protein binds to

58
Q

If a protein binds to DNA, it will ____ bind to something else

A

NOT

59
Q

The binding of a protein to another molecule is highly ________

A

Selective

If a protein has several functional domains, it can binds to numerous ligands

Exemplified by Lock and Key model

60
Q

Binding sites allow proteins to interact with __________

A

Specific Ligands

61
Q

Binding b/w a protein and its ligand is

A

Very specific

62
Q

Side chains project into binding site; interact w/ _______________-

A

Noncovalent interactions

63
Q

Enzymes convert substrates to _________ while ______________

A

Products; remaining unchanges

64
Q

Hydrolase

A

General term for enzymes that catalyze a hydrolytic cleavage reaction

65
Q

Nucleases

A

Break down nucleic acids by hydrolyzing bonds b/w nucleotides

66
Q

Protease

A

Breaks down proteins by hydrolyzing peptide bonds between amino acids

67
Q

Isomerase

A

Catalyzes the rearrangement of bonds w/in a single molecule

68
Q

Polymerase

A

Catalyzes polymerization reactions such as the synthesis of DNA and RNA

69
Q

Kinase

A

Catalyzes the addition of phosphate groups to molecules

Protein kinases are an important group of kinases that attach phosphate groups to proteins

70
Q

Phosphatase

A

Catalyzes the hydrolytic removal of a phosphate group from a molecule

71
Q

Oxido-reductase

A

General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced; Enzymes of this type are often called oxidases, reductases, or dehydrogenases

72
Q

ATPase

A

Hydrolyzes ATP

Many proteins have an energy-harnessing ATPase activity as part of their function, including motor proteins such as myosin and membrane transport proteins such as the NA+ pump

73
Q

Enzymes can encourage a reaction in several ways:

A

1) Enzyme binds to 2 substrate molecules and brings them close enough to react
2) Binding of substrate to enzyme arranges electrons in substrate, creating partial negative and positive charges that favor a reaction

3) Enzyme strains the bound substrate molecule, forcing it toward a transition state that favors a reaction
- Changes bond angles

Cell and Molec (9 decks)

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