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[h] IB DP Biology HL B1.2 Proteins Flashcards
[q] B1.2.1—What is the generalized structure of an amino acid?
[a] All amino acids have the same structure in terms of an amine group; and carboxyl group;
but different variable groups (R group);
[q] B1.2.2—How are amino acids linked together (what is the reaction?) to create longer chains of amino acids?
[a] Two amino acids are joined;
condensation reaction;
via carboxyl group of one amino acid;
and amine group of other;
creating a peptide bond; and water.
[q] B1.2.3—What are the dietary requirements for amino acids?
[a] Essential amino acids cannot be synthesized;
and must be obtained from food;
Non-essential amino acids can be made from other amino acids;
Vegan diets require attention to ensure essential amino acids are consumed;
[q] B1.2.5—Why is there an infinite variety of possible polypeptide chains?
[a] 20 different amino acids can be used; in any order;
long chains of amino acids can therefore have a huge number of different possible orders and combinations of the 20 amino acids; even 2 amino acids gives 400 possible combinations;
[q] B1.2.5—What is the effect of pH on protein structure?
[a] proteins have an optimum pH in terms of maintaining their structure and activity;
extremes of pH effect the interactions holding protein structure together;
this means they lose their structure; become insoluble;
in the process of denaturation;
most enzymes are proteins, so it can cause enzymes to lose their activity;
[q] B1.2.5—What is the effect of temperature on protein structure?
[a] increased temperature away from optimum leads to higher kinetic energy;
this can lead to breaking of bonds holding protein structure together;
causing denaturing;
most enzymes are proteins, so it can cause enzymes to lose their activity;
[q] B1.2.6 What are R-groups on amino acids?
How are they responsible for the diversity of proteins?
[a] R-groups are a variable group on amino acids;
R-groups determine the properties of assembled polypeptides;
R- groups are hydrophobic or hydrophilic;
hydrophilic R-groups are polar or charged, acidic or basic;
this leads to their interactions with other amino acids;
causing different shapes and structures to form;
accounting for the immense diversity of protein forms;
[q] B1.2.7 What is the primary structure of a protein?
How does it impact the conformation (shape) of proteins?
[a] primary structure is the order of amino acids in a polypeptide or protein;
all other levels of structure are determined by the primary structure;
because this determines which R-groups are present;
as the conformation (shape) is determined by interactions of the amino acids, which is determined by the sequence of amino acids;
[q] B1.2.8 What is the secondary structure of a protein?
How is it brought about?
What are the two structures often formed?
[a] Secondary structure is the folding patterns caused by nearby (local) interactions;
between amino acids;
e.g. Alpha helices are brought about by hydrogen bonding;
in regular positions;
which stabilize the structures;
beta-pleated sheets are also brought about by hydrogen bonding at regular positions;
[q] B1.2.9 What is the tertiary structure of proteins?
How is it brought about?
What kinds of bonds stabilize it?
[a] Tertiary is the folding pattern between more distant regions of the protein;
giving the three dimensional shape of the protein;
it is caused by hydrogen bonds;
ionic bonds; disulfide covalent bonds;
between cysteines;
and hydrophobic interactions between amino acid R-groups;
amine (NH2) and carboxyl groups (COOH) in R-groups can become positively or negatively charged by binding or dissociation of hydrogen ions;
and they can then participate in ionic bonding.
[q] B1.2.10—What is the effect of polar and non-polar amino acids on tertiary structure of proteins?
[a] In proteins that are soluble in water, hydrophobic amino acids are clustered in the core of globular proteins;
with the hydrophilic amino acids facing outwards towards the water;
Integral proteins have regions with hydrophobic amino acids, helping them to embed in membranes;
which have a hydrophobic central region;
[q] B1.2.11 What is the quaternary structure of non-conjugated and conjugated proteins?
Give an example of each.
[a] Quaternary structure is the interaction of more than one polypeptide chain to form the complete protein;
e.g. hemoglobin has two alpha subunits joined with two beta subunits;
hemoglobin is a conjugated protein, because it also requires the interaction with the heme group which has iron in it, as well as the polypeptide globin;
whereas insulin and collagen are non-conjugated proteins;
because they are created by the interaction of more than one polypeptide chain;
but no other groups or elements; insulin
[q] Nature of science – How has technology allowed us to visualize protein structure?
[a] Cryogenic (freezing) electron microscopy has allowed us to image single protein molecules and their interaction with other molecules;
[q] B1.2.12—What is a globular protein?
What is the relationship of form and function in globular proteins?
[a] Globular proteins have a roughly globe-like shape;
e.g. insulin;
this is caused by non-repetitive interactions giving a complex three-dimensional shape;
they are soluble in water and are often enzymes;
held together by hydrogen bonding, disulphide bridges and ionic bonds;
leading to a specific shape that can bind to receptors allowing it to act as a hormone;
[q] B1.2.12—What is a fibrous protein?
What is the relationship of form and function in fibrous proteins?
[a] Fibrous proteins are repetitive in terms of their primary sequence;
leading to a long, narrow shape;
causing them to be insoluble in water;
and to have high tensile strength;
e.g. collagen which is three polypeptides twisted together;
held together by hydrogen bonding;
[q] Functions of proteins:
[a] Proteins are biological molecules involved in chemical reactions, structures, transport, cell to cell communication, movement and immunity.
They are also the structural component of enzymes.
[q] Construction of proteins:
[a] Constructed from polymers of amino acids and are referred to as polypeptides – held together by peptide bonds.
[q] Linking of amino acids:
[a] Amino acids are subunits of proteins and they bond together to form polypeptides.
∙ There are 20 different amino acids
∙ Distinguished by their R-group
Know how to draw amino acid!
[q] What is the acid group also known as?
[a] Carboxyl group!
[q] Condensation of Amino acids (or dehydration synthesis):
[a] Condensation reactions can join two amino acids together to form dipeptides or polypeptides.
As each bond is formed, a molecule of water is produced.
This process is performed by ribosomes in a process known as translation.
[q] What do ribosomes do?
[a] ∙ ribosomes link amino acids together until a polypeptide is formed
∙ ribosomes can make peptide bonds between amino acids
[q] you should know how to draw the formation of peptide bonds.
[a] you should know how to draw the formation of peptide bonds.
[q] What is the sequence of the amino acids determined by?
[a] The protein.
[q] Sequencing of polypeptides:
[a] 20 different amino acids are used by ribosomes to make polypeptides.
The R groups give the polypeptide character.
For a polypeptide of n amino acids, there are 20^n possible sequences.
[q] How is amino acid sequences coded?
[a] The information needed to produce proteins is stored in DNA.
It is coded for by genes that contain three base pairs per amino acid.
The sequence of base pairs controls the building of polypeptides during translation.
[q] Proteins and polypeptides:
[a] Some proteins are single polypeptides, but others are composed of two or more polypeptides.
1 polypeptide: lysozyme: enzyme in secretions such as nasal mucus & kills some bacteria by digesting peptidoglycan in cell walls.
2 polypeptides: integrin: membrane protein used to make connections between structures inside and outside a cell
3 polypeptides: collagen: structural protein in tendons, ligaments, skin, provides high tensile strength
4 polypeptides: haemoglobin: transport protein in RBC.
[q] 4 levels of protein conformation:
[a] Primary structure
Secondary structure
Tertiary structure
Quaternary structure
[q] Primary structure:
[a] ∙ Sequence of amino acids of which protein is composed
∙ Formed by covalent peptide bonds
∙ Controls other levels of structure
[q] Secondary structure:
[a] ∙ Fold of amino acids upon themselves
∙ H bonds between amine and carboxylic groups
∙ H bonds give stability
∙ Fibrous proteins
[q] Tertiary structure:
[a] ∙ polypeptide folds and coils
∙ caused by interactions between R groups
∙ shape important for function
∙ globular proteins
[q] Quaternary structure
[a] ∙ interaction between multiple polypeptides
∙ sometimes involves prosthetic groups
∙ fibrous and globular
[q] What are fibrous proteins?
[a] Fibrous proteins have a long and narrow shape and are mostly insoluble in water.
Example: collagen.
[q] What are globular proteins?
[a] Globular proteins have a rounded shape, and they are mostly soluble in water.
Example: hemoglobin, insulin
[q] Rubisco + protein function
[a] Rubisco is an enzyme found in cells of plants which allow them to fix carbon dioxide from a gas in the atmosphere into carbon compounds during photosynthesis.
Function: catalyst.
[q] Insulin + protein function
[a] Insulin is produced in pancreas and released into the bloodstream.
It signals cells to absorb glucose to reduce amount of glucose in blood.
Function: hormone
[q] Immunoglobin + protein function:
[a] Proteins that bind to antigens on bacteria.
Causes a response which allows body to destroy pathogen.
Function: immunity
[q] Rhodopsin + protein function:
[a] Rhodopsin is a pigment found in retina of the eye which absorbs light and sends a nerve impulse to the brain.
Function: receptors
[q] Collagen and Spider silk + protein function:
[a] Collagen: rope-like protein found in skin, blood vessels,
Spider silk: protein-based silk produced by spider to make webs which are resistant to breaking.
Function: tensile strength
[q] What is a proteome?
[a] A proteome is defined as all the proteins produced by a cell, a tissue or an organism.
Variable from cell to cell since cells differ in functions and activities.
[q] Why do peptide bonds break easily?
[a] The structure is maintained by bonds between R groups of amino acid.
These bonds are weak and can be broken easily.
[q] What causes denaturation of proteins?
[a] Heat: vibrations in molecule breaks bond
Changes in pH: causes changes in R groups which breaks bonds or causes new bonds to form.
This will alter the structure of proteins. (exception: stomach enzyme pepsin)
[q] Amino acids build _____
[a] proteins.
[q] Alpha carbon in amino acids and with what bonds and name each specific bond:
[a] Central carbon atom with 4 single covalent bonds to:
-nitrogen atom of amine group
– carbon atom of carboxyl group
– Hydrogen atom
-R group
[q] Why is the carboxyl group acidic on alpha carbon?
[a] they can donate protons
[q] Why is the amine group basic on alpha carbon?
[a] Because it can accept proteins.
[q] Are amino acids amphiprotic?
[a] Yes, they are amphiprotic.
[q] How is a dipeptide formed?
[a] Two amino acids are linked by a condensation reaction.
[q] How can amino acids be linked in general? (through what reaction)
[a] Condensation reaction
[q] Oligopeptide
[a] Chains of amino acids fewer than 20.
[q] How many amino acids can polypeptides contain?
[a] Any number
[q] Polypeptide
[a] A chain of amino acids.
[q] What are the main components of proteins?
[a] Polypeptides
[q] Generally what bonds are amino acids linked with?
[a] Peptide bonds.
[q] How are peptide bonds formed for the linkage of amino acids?
[a] Condensation reaction between the amine group (-NH₂) of one amino acid and carboxyl group (-COOH) of another.
[q] Where is the condensation reaction to form peptide bonds catalyzed and by whom?
[a] -Cells
-By ribosomes
[q] How many different amino acids are used to make polypeptides?
[a] 20
[q] How do animals obtain their amino acids?
[a] Food
[q] Essential amino acid?
[a] One that cannot be synthesized in sufficient quantities by the animal so must be obtained by diet.
[q] Non-essential amino acid and what does it transform?
[a] can be synthesized by the animal using metabolic pathways that transform one amino acid to another
[q] What type of foods have the best balance of amino acids?
[a] Animal based foods.
[q] What type of foods/diets are deficient in amino acids? (2)
[a] -Plant-based foods
– Protein diet
[q] 2 essential amino acids for humans?
[a] – Lysine
-Methionine
[q] What type of bonds can ribosome make and between what?
[a] -Peptide bonds
-Amino acids
[q] How do ribosomes make sequences of amino acids?
[a] They receive instructions in the form of genetic code.
[q] How many amino acids are included in the genetic code?
[a] 20
[q] How can amino acid sequences be calculated starting with dipeptides?
[a] Can be any of 20 so would be (20ⁿ)
[q] Proteome
[a] The complete set of proteins expressed by an organism.
[q] 4 Examples of polypeptides:
[a] -Beta endorphin- polypeptide of 31 amino acids
– Insulin- contains two short polypeptides (one with 21 amino acids, another with 30)
-Alpha amylase- single polypeptide with 496 amino acids
-Titin- largest polypeptide ever (34k amino acids)
[q] How are proteins stabilized?
[a] -Bonds/Interactions between R-groups of amino acid and molecule.
[q] denaturation of proteins
[a] When bonds in proteins are disrupted or broken and the conformation of the protein changes.
[q] Is denaturation permanent?
[a] Yes denaturation permanent.
[q] When denaturation happens what usually happens to the soluble proteins and why?
[a] -Become insoluble and form a precipitate
– Due to hydrophobic R groups in the center of the molecule becoming exposed to water by change in conformation
[q] How can heat cause denaturation?
[a] Causes vibrations within the molecules that can break bonds.
[q] What temperature does heat cause denaturation at usually and give a specific #?
[a] -lower temperatures
-Around 80 c
[q] How can extremes of pH cause denaturation of proteins?
[a] The positive and negative charges on the R-groups are changed by the acids or bases breaking the ionic bonds and forming new ionic bonds.
[q] What happens when amino acids are linked up into a polypeptide?
[a] Their amine and carboxyl groups are used to make peptide bonds.
[q] When amino acids are linked into polypeptide what is left?
[a] -Amine group (-NH2) and carboxyl group at the other end (-COOH).
[q] Does the hydrogen atom attached to the alpha carbon of each amino acid have effect on the protein?
[a] No not really
[q] What determines chemical characteristics of a protein?
[a] R-groups
[q] Are R groups hydrophobic or hydrophilic?
[a] Some are hydrophobic
Some are hydrophilic
[q] Some R groups are also polar and become charged by…
[a] acting like an acid or base.
[q] Four levels of complexity structure for proteins:
[a] -Primary
-Secondary
-Tertiary
-Quaternary
[q] primary structure of protein
[a] Linear sequence of amino acids in a polypeptide
[q] Backbone of polypeptide is a ________________ linked by _______________
[a] -repeating sequence of atoms
-covalent bonds
[q] Bond angles in primary structure proteins:
[a] -Tetrahedral
[q] What the purpose of rotation about the bonds between the alpha carbon atoms and adjacent nitrogen/carbon atoms?
[a] Allows polypeptides to fold into any three-dimensional shape.
[q] protein conformation
[a] three-dimensional arrangement of atoms in a polypeptide
[q] What determines most proteins assembly into a specific conformation?
[a] Sequence of amino acids and their R groups.
[q] What 2 things does protein conformation determine?
[a] – Function and behavior of cells
[q] What are the C=O and N-H groups along a polypeptide chain?
[a] -Remains of carboxyl and amine groups after they have been used to make peptide bonds.
[q] How are the C=O and N-H groups polar?
[a] Oxygen has a slight negative charge and hydrogen a slight positive charge.
[q] Why can hydrogen bonds form between the C=O and N-H groups?
[a] Because the groups are polar.
[q] C=O and N-H groups allow hydrogen bonds to form, and the bonds are strong enough to…
[a] stabilize distinctive conformation strictures within protein molecules.
[q] two commonly occurring structures that are stabilized by hydrogen bonding:
[a] -A-helix
-B-pleated sheet
[q] What is the A-helix?
[a] polypeptide is a helical shape, with hydrogen bonds between turns of the helix.
[q] B- Pleated sheet?
[a] —two or more sections of polypeptide are arranged in parallel with hydrogen bonds between them
[q] Bond angle of B-pleated sheet?
[a] Tetrahedral
[q] Tertiary structure:
[a] the folding of a whole polypeptide chain into a three-dimensional structure
[q] How is tertiary structure stabilized?
[a] Interactions between R-groups
[q] 4 Main types if interactions within tertiary structure:
[a] -Ionic bonds between + charged and – charged R-groups.
– Hydrogen bonds between polar R-groups.
A hydrogen atom forms a link between two electronegative atoms such as O or N.
-Disulfide bonds between pairs of cysteines.
– Hydrophobic interactions between any of the non-polar R-groups.
[q] ____________ groups become positively charged by accepting a proton.
______________ groups become positively charged by donating a proton.
[a] -Amine
-Carboxyl
[q] Disulfide bonds:
[a] -Covalent
– Strongest of all interactions.
[q] What will the chaperones do in regard to tertiary structure?
[a] Ensure that the protein is fully functioning and folded correctly.
[q] Fibrous proteins- what are they? what structure do they not have?
[a] -polypeptides that do not become folded and instead remain elongated
– do not have tertiary structure
[q] What categories can amino acids be divided into?
[a] – Non-polar and hydrophobic
-Polar/charge and hydrophilic
[q] Why do many globular proteins need to be soluble in water?
[a] Because they carry out their function in the cytoplasm or in an aqueous solution outside the cell.
[q] Globular proteins have …
[a] -hydrophilic amino acids on their surface where they are in contact with water.
-hydrophobic amino acids clustered in the center where no water.
[q] Globular protein arrangement
[a] -stabilizes tertiary structure
– maximizes hydrophobic interactions between amino acids in the center and hydrogen bonding between amino acids on the surface and the water around the protein
[q] channel proteins allow
[a] hydrophilic solutes or water to diffuse across the hydrophobic core of the membrane
[q] Channel proteins have a tunnel lined with what and where?
[a] -tunnel lined with hydrophilic amino acids
-through the center of the protein
[q] Channel Proteins let what come through?
[a] -Specific hydrophilic ions/molecules
[q] quaternary structure of a protein
[a] a protein that consist of more than a single polypeptide
[q] what 1 thing is in a non-conjugated protein?
[a] polypeptide subunits
[q] How is quaternary structure formed?
[a] polypeptides are linked by the same types of interaction as in tertiary structure
[q] What do Conjugated proteins have?
[a] One or more non-polypeptide subunits in addition to their polypeptides
[q] What the does the function of a protein depend on?
[a] Its form
[q] Polypeptides in fibrous structures do not develop secondary structures such as…
[a] alpha helices
[q] Ribose carbon atoms
[a] 5
[q] Glucose carbon atoms
[a] 6
[x] Exit text
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