1.3 Proteins Flashcards
α-helix
definition: a prevalent type of protein secondary structure
description: a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O
stabilized by: hydrogen bond between CO and NH groups of the main chain to stabilize.
formed by: formed by hydrogen bonds within protein strands
β-pleated sheet
definition: series of anti-parallel chains of covalently-linked amino acids, with adjacent chains linked by hydrogen bonds.
description: The regular folding of each amino acid chain leads to a regular pleated pattern across chains.
stabilized by:
formed by: formed by hydrogen bonds between protein strands
•Amino acid
monomeric units that are teh buildingblokcs of protein; that are capable of existing in ionized and unionized forms composed of: 1. amino group 2. alpha carbon 3. r-group side chain 4. hydrogen atom 5. carboxyl group
C-terminus
the end of the peptide chain aka the 5’ end of the chain
Chaperones
a protein that assists the folding/assembly of other proteins.
Condensation reaction
Monomers polymerize through condensation reactions
Denaturation
Definition: structural change in a protein (caused by either pH or temp) that results in the loss (usually permanent) of its biological properties
Because the way a protein folds determines its function, any change or abrogation of the tertiary structure will alter its activity
- —>temp
1. High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
2. As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
3. Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)
Dimer
a macromolecular complex formed by two protein monomers
Disulfide bonds
an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups
Folding
the process by which a protein structure assumes its functional shape or conformation
Hydrolysis
these reactions involve the breaking of polymers into individual monomers by splitting water
Macromolecule
a very large molecule, such as a protein
Monomer
these subunits polymerize thru condensation reactions
Oligopeptide
a short peptide chain used to refer to peptides with less than 20–25 amino acid residues.
Peptide bond
The carboxyl group of one amino-acid reacts with the amino group of another to form this type of bond
Polymer
3 classes of macromolecules are ____
which are composed of repeating subunits called monomers that are covalently bonded together
Polymerization
process in which relatively small molecules, called monomers, combine chemically to produce a very large chainlike or network molecule, called a polymer.
Polypeptide
a chain of many amino acids
Primary structure•
the unique sequence of amino acids residues in a protein
description: amino acid monomers are joined, forming polypeptide chains
stabilized by: peptide bonds
Protein•
are long polymers containing many freely rotating binds which allow for tremendouse confirmational flexibilty
monomer: amino acid
bond type: peptide bond
Quaternary structure•
the overall 3d shaped formed from 2 or more polypeptide chains (subunits)
description: 2 or more polypeptides assmeble to form larger protein molecules
stabilized by: h-bonds, ionic interactions, hydrophobic interactions, disulfide brdiges
R-group•
a side chain specific to each amino acid that confers particular chemical properties to tha
Residue
Any of the monomers comprising a polymer
Secondary structure•
the localized fooding of a polypeptide chain into regualr structures (alpha helices and beta-pleated sheets)
description: polypeptide chains may form a-helices or B-pleated sheets
stabilized by: h-bonds between components of the peptide backbone results in secondary structure
Side-chain
a chemical group attached to the main chain or backbone of a molecule, such as a protein
Tertiary structure•
the overal 3d sturcture of single polypeetide chain, resulting form multiple interactiosn amongst teh amisno acid side chians and the peptide backbone
description: polypeeptide fold, forming specific shapes
stabilized by: h-bonds; disulfide bridges; hydrophobic interaction
Tetramer
protein with a quaternary structure of four subunits (tetrameric).
trimer
A structure composed of three identical or similar units
Sketch the basic structure of an amino acid
Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.
Explain why proteins are essential to cell function by giving examples of their function.
- Digestive enzyme–> Break down nutrients in food into small pieces that can be readily absorbed
ex: Amylase, lipase, pepsin - Transport–>Carry substances throughout the body in blood or lymph
ex: Hemoglobin - Structure—>Build different structures, like the cytoskeleton
ex: Actin, tubulin, keratin - Hormone signaling—>Build different structures, like the cytoskeleton
ex: Insulin, glucagon - Defense—>Protect the body from foreign pathogens
ex: Antibodies - Contraction—>Carry out muscle contraction
ex: Myosin - Storage–> Provide food for the early development of the embryo or the seedling
ex: Legume storage proteins, egg white (albumin)
•Describe two ways that protein folding can be regulated.
chaperones help proteins fold when they become trapped in an incorrectly folded state.
.•Explain how and why proteins are properly folded
chaperones help proteins fold when they are first formed
Explain the four levels of protein structure, and give examples of each.
- Primary
- Secondary
- Tertiary
- Quarentary
Explain how amino acid monomers polymerize to form proteins
Monomers polymerize through condensation reactions. Monomers are released from a polymer by hydrolysis reactions.
Describe why and how the side chains affect the function and structure of each amino acid.
The gene, or sequence of DNA, ultimately determines the unique sequence of amino acids in each peptide chain. A change in the nucleotide sequence of the gene’s coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and therefore function.
nucleic acid
monomer: nucleotide
bond type: phosphodiester bond
complex carbohydrate
monomer: monosaccharide
bond type: glycolic linkage
N terminus
the beginning of the peptide chain aka the 3’ end of the chain
Why are beta-pleated sheets more stable than alpha-helices?
Unlike the α helix, the ß sheet is formed by hydrogen bonds between protein strands, rather than within a strand. … Antiparallel ß sheets are slightly more stable than parallel ß sheets because the hydrogen bonding pattern is more optimal.
how do change in the temperature result in changes in the tertiary structure of proteins?
- High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
- As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
- Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)
how do changes in the pH result in changes in the tertiary structure of proteins?
- Amino acids are zwitterions, neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions
- Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
- All proteins have an optimal pH which is dependent on the environment in which it functions (e.g. stomach proteins require an acidic environment to operate, whereas blood proteins function best at a neutral pH)
