2.4 Proteins Flashcards
What structure mediates and controls formation of polypeptides?
Ribosomes
What are the two RNA’s required for formation of polypeptides?
mRNA (messenger) and tRNA (transfer)
What is the reaction when two peptides join to make a dipeptide?
Condensation
What does the peptide bond consist of?
Double bond between C and O of first peptide + single bond between H and N of second peptide
How many different amino acids are known? (Including synthesized)
- 20 are ribosome-synthesized while 2 are artificially synthesized by humans
List some examples of amino acids
Histidine, Lysine, Cysteine, Glycine, Glutamine
What are the 3 key ideas that explain huge range of possible polypeptides?
- There are 20 amino acids
- They can be of any length
- They can be permutated and combined in any order
How many different polypeptides can be created of a polypeptide consisting of 5 amino acids?
20^5= 3,200,000 possibilities
Longest known polypeptide (+ number of amino acids)
Titin. Has approximately 30000-34000 amino acids
Central dogma of genetics
- Genes are codes for polypeptides
- Gene sequences are converted to polypeptide sequences by transcription + translation
- DNA + transcription–> RNA (+ translation)–> Proteins
- Everything happens in the cytoplasm
What are the properties an R group can possess?
Polar/Non-polar (Hydrophilic/phobic)
Positively/ Negatively charged (basic/acidic)
What does the R group determine?
Solubility and how polypeptides fold up into the protein
What is the primary structure of a protein?
The order or sequence of the amino acids the protein consists of
What are the bonds between adjacent amino acids?
Covalent peptide bonds
Primary structure: Fibrous or globular?
Neither as it is not yet folded
Secondary structure: What are the two stable configurations and what do they look like?
- Alpha helices: A spiral arrangement
- Beta-pleated sheets: A directionally oriented strand conformation
Secondary structure: What are the type of bonds?
H-H bonds between non-adjacent amine and carboxyl groups.
Also has peptide bonds
Secondary structure: What do H bonds provide?
Structural stability
Secondary structure: What are the parts of the secondary protein with no secondary structure called?
Random coil. They are just polypeptide chains
Secondary structure: Fibrous or globular?
Fibrous as they are long, thin and structural
Tertiary structure: What is the overall configuration?
3D
Tertiary structure: What is it determined by?
Protein’s interaction between R variable groups
Tertiary structure: What are the different bonds/interactions?
Hydrogen bonds, disulphide bridges, ionic/polar interactions
Tertiary structure: How does position of amino acids affect shape of chain?
Position determines whether an R chain has attraction or repulsion and hence affect the overall shape of the polypeptide chain
Tertiary structure: How is its function different from secondary structure?
Secondary determines structure while tertiary is important for function (catalytic, transport)
Tertiary structure: Why does it affect the function of a protein (eg. enzyme) ?
They way it folds will determine the specific active site for the enzyme
Tertiary structure: Fibrous or globular?
Globular, more round in shape
Quaternary structure: What is it?
It is the interaction between two or more polypeptide chains AND/OR a prosthetic group
Quaternary structure: Are all proteins quaternary?
No. They can remain at the tertiary level
Quaternary structure: What is a prosthetic group + example?
It is an inorganic compound involved in making of protein. Eg. Hemoglobin has a HEME group
Quaternary structure: Why is hemoglobin a quaternary structure?
It has 2 alpha and 2 beta chains (polypeptides) + oxygen binding heme groups
Quaternary structure: Fibrous or globular?
Both
Fibrous/Globular: Location of R groups
- Fibrous: Exposed on outside of the molecule
- Globular: Generally folded inside the core of the molecule
Fibrous/Globular: Shape
F: Long and narrow
G: Rounded/spherical
Fibrous/Globular: Solubility
F: Generally insoluble as hydrophobic R group is exposed
G: Soluble as R group is folded inside
Fibrous/Globular: Amino acid sequences
F: Repetitive sequences
G: Irregular sequences
Fibrous/Globular: Stability
F: Less sensitive to changes in heat, pH
G: More sensitive
Fibrous/Globular: Examples
F: Collagen, myosin, fibrin, keratin
G: Catalase, hemoglobin, insulin, immunoglobin
Protein function + example: Catalysis
Some enzymes are responsible for catalyzing specific chemical reactions within and outside the cell. eg. Rubisco
Protein function + example: Muscle contraction
Used for locomotion and transport around the body eg. Actin + myosin
Protein function + example: Cytoskeletons
Give animal cells their shape and pull on chromosomes during mitosis eg. Tubulin (Subunit of microtubules)
Protein function + example: Tensile strength
Fibrous proteins give strength/ elasticity required in skin, blood vessel walls, tendons and ligaments eg. Collagen
Protein function + example: Blood clotting
Plasma proteins help turn blood from liquid to gel in wounds eg. Fibrinogen
Protein function + example: Transport
Proteins in blood help transport oxygen, carbon dioxide, iron and lipids eg. Hemoglobin
Protein function + example: Cell adhesion
Membrane proteins cause adjacent animal cells to stick to each other in tissues eg. Glycoproteins
Protein function + example: Membrane transport
Facilitated diffusion, active transport, electron movement eg. Channel pumps and protein
Protein function + example: Hormones
Chemically diverse, they work as signaling molecules in the body eg. Insulin
Protein function + example: Receptors
Binding sites for hormones and neurotransmitters. Also receptor for light in retina and plants eg. Rhodopsin
Protein function + example: Packing of DNA
In eukaryotes, they aid chromosomes in condensing during mitosis eg. Histones
Protein function + example: Immunity
Most diverse as cells can make large numbers of different antibodies eg. Immunoglobulins
What is rubisco short for?
Ribulose bisphosphate carboxylase
What is function of rubisco?
Enzyme in plants that catalyzes reaction for fixing carbon dioxide from air. Found in leaves as it provides source required to make organic compounds
What is function of insulin?
Hormone that is secreted by beta cells and signals other cells to absorb glucose and reduce conc. in the bloodstream. Converts the glycose to glycogen for storage in liver cells.
What happens if insulin is not produce in sufficient amount?
Leads to diabetes as there is excess sugar in the blood leading to synthesized insulin injections
What are immunoglobulins?
Antibodies. Y shaped with 2 antigen binding sites to respond to multiple types of pathogens. Other parts can act as marker to phagocyte so pathogen can be engulfed later
What is rhodopsin?
A membrane protein in retinal rod cells that absorbs light.
How does rhodopsin work?
Molecule absorbs a photon of light and changes shape. This changes opsin protein and rod cell sends a nerve impulse to the brain.
What is collagen?
A rope like protein made of 3 polypeptides.
How does collagen work?
It forms a mesh of fibers that resist tearing and hence gives strength. Can also prevent fractures and cracks in teeth and bones.
What is spider silk and how does it work?
Stronger than steel and tougher than Kevlar. Contains regions where polypeptide forms parallel arrays. When stretched, polypeptide slowly extends, making it extensible and break-resistant
Genome
All genes present in an organism. Determines what proteins an organism will produce
Are genomes unique to an organism?
Yes except to identical twins and clones
Proteome
All proteins produced by a cell or organism. It is variable and unique
What is proteome the product of?
Genome + environment
What ways can environment affect proteome?
Influence what proteins are produced and in what quantity. Eg. nutrition, temperature, activity levels
Why is proteome larger and more varied than genome?
Larger in content and size as not all genes produce proteins. Polypeptides can also combine with prosthetic groups, be folded into different structures and modified hence giving proteomes more variety.
Denaturation
Structural change in a protein that usually results in a permanent loss of its biological properties.
Why does denaturation affect protein function?
Protein function is determined by the way it folds and so any change in tertiary structure will alter its activity
How does temp. affect denaturation?
High levels of thermal energy can disturb hydrogen bonds and cause protein to unfold. Optimum temp. varies but it’s usually 37 degrees Celsius for humans
How does pH affect denaturation?
Amino acids have +/-vely charged regions so changing pH alters charge and hence its solubility and overall shape. Optimal pH depends on environment of the protein
