2.4 Amino Acids Flashcards
What are proteins composed of?
Proteins are comprised of long chains of recurring monomers called amino acids
What is the structure of a generalised amino acid? (5 components) Draw the structure
Amino acids all share a common basic structure, with a central carbon atom bound to:
An amine group (NH2)
A carboxylic acid group (COOH)
A hydrogen atom (H)
A variable side chain (R)
How many different amino acids are there?
There are 20 different amino acids which are universal to all living organisms
How are proteins created?
Amino acids are joined together on the ribosome to form long chains called polypeptides, which make up proteins
How do amino acids differ?
Each type of amino acid differs in the composition of the variable side chain
Why do the side chains affect the type of protein?
These side chains will have distinct chemical properties (e.g. charged, non-polar, etc.) and hence cause the protein to fold and function differently according to its specific position within the polypeptide chain
How can amino acids be joined together to form a protein?
Amino acids can be covalently joined together in a condensation reaction to form a dipeptide and water
What is the covalent bond between amino acids is called?
The covalent bond between the amino acids is called a peptide bond
What are long chains of amino acids called?
long chains of covalently bonded amino acids are called polypeptides
How can polypeptide chains be broken down?
Polypeptide chains can be broken down via hydrolysis reactions, which requires water to reverse the process
Where are peptide bonds formed?
Peptide bonds are formed between the amine and carboxylic acid groups of adjacent amino acids
What is the chemistry behind the formation of a peptide bond?
The amine group loses a hydrogen atom (H) and the carboxylic acid loses a hydroxyl (OH) – this forms water (H2O)
What is the primary structure?
The order of the amino acid sequence is called the primary structure and determines the way the chain will fold
Do all amino acids fold the same? Why?
NO
Different amino acid sequences will fold into different configurations due to the chemical properties of the variable side chains
What two types of secondary structures are there?
Alpha helices
Beta-pleated sheets
When do amino acids fold in alpha-helices?
Alpha helices occur when the amino acid sequence folds into a coil/spiral arrangement
When do amino acids fold into beta-pleated sheets?
Beta-pleated sheets occur when the amino acid sequence adopts a directionally-oriented staggered strand conformation
What causes alpha helices or beta-pleated sheets to form?
Both α-helices and β-pleated sheets result from hydrogen bonds forming between non-adjacent amine and carboxyl groups
What happens if the protein does not have a secondary structure?
Where no secondary structure exists, the polypeptide chain will form a random coil
What is tertiary structure?
The overall three-dimensional configuration of the protein is referred to as the tertiary structure of the protein
What determines the tertiary structure of a protein?
The tertiary structure of a polypeptide chain will be determined by the interactions between the variable side chains
What are examples of interactions of side chains which result in a tertiary structure?
These interactions may include hydrogen bonds, disulphide bridges, ionic interactions, polar associations, etc.
What affects the overall shape of a protein?
The affinity or repulsion of side chains will affect the overall shape of the polypeptide chain and are determined by the position of specific amino acids within a sequence
What structure affects the overall folding process?
Hence, the order of the amino acid sequence (primary structure) determines all subsequent levels of protein folding
What type of proteins have quaternary structures? (2 conditions)
Quaternary structures are found in proteins that consist of more than one polypeptide chain linked together
Alternatively, proteins may have a quaternary structure if they include inorganic prosthetic groups as part of their structure
Do all proteins have a quaternary structure? Why?
NO
Not all proteins will have a quaternary structure – many proteins consist of a single polypeptide chain
What is an example of a protein with a quaternary structure?
An example of a protein with a quaternary structure is haemoglobin (O2 carrying molecule in red blood cells)
What is the structure of haemoglobin?
Haemoglobin is composed of four polypeptide chains (two alpha chains and two beta chains)
What groups does haemoglobin contain?
It is also composed of iron-containing haeme groups (prosthetic groups responsible for binding oxygen)
What is denaturation?
Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties
What does denaturation affect?
Because the way a protein folds determines its function, any change or abrogation of the tertiary structure will alter its activity
What two conditions can cause denaturation?
temperature and pH
How may high temperatures affect bonds in proteins?
High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
What happens when bonds in proteins are broken (by high temp)?
As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
What (for most human enzymes) is the temp at which proteins denature?
Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)
What type of molecule are amino acids? (relating to polarity?
Amino acids are zwitterions, neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions
Why does a change of pH denature proteins?
Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
When do proteins function best? (pH)
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)
What is a gene?
A gene is a sequence of DNA which encodes a polypeptide sequence
What two processes are required to convert a gene sequence into a polypeptide sequence?
transcription and translation
What is transcription?
making an mRNA transcript based on a DNA template (occurs within the nucleus)
What is translation?
using the instructions of the mRNA transcript to link amino acids together (occurs at the ribosome)
Typically, how many polypeptides does one gene code for?
one gene will code for one polypeptide
What are 3 exceptions for one gene coding for one polypeptide sequence?
Genes may be alternatively spliced to generate multiple polypeptide variants
Genes encoding tRNA sequences are transcribed but never translated
Genes may be mutated (their base sequence is changed) and consequently produce an alternative polypeptide sequence
What is a proteome?
The proteome is the totality of proteins expressed within a cell, tissue or organism at a certain time
Is the proteome unique for every organism?
YES
The proteome of any given individual will be unique, as protein expression patterns are determined by an individual’s genes
Is the proteome larger/smaller than the number of genes?
The proteome is always significantly larger than the number of genes in an individual
What are 2 reasons for the proteome being larger than the number of genes?
Gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene
Proteins may be modified (e.g. glycosylated, phosphorylated, etc.) following translation to promote further variations
What are the 7 functions of proteins?
Structure – e.g. collagen, spider silk Hormones – e.g. insulin, glucagon Immunity – e.g. immunoglobulins Transport – e.g. haemoglobin Sensation – e.g. rhodopsin Movement – e.g. actin, myosin Enzymes – e.g. Rubisco, catalase
What are examples of a structural protein?
Collagen: A component of the connective tissue of animals (most abundant protein in mammals)
Spider silk: A fiber spun by spiders and used to make webs (by weight, is stronger than kevlar and steel)
What are examples of hormones + definitions?
Insulin: Protein produced by the pancreas and triggers a reduction in blood glucose levels
Glucagon: Protein produced by the pancreas that triggers an increase in blood glucose levels
What are examples of immunological proteins + definitions?
Immunoglobulins: Antibodies produced by plasma cells that are capable of targeting specific antigens
What are examples of transport proteins + definitions?
Haemoglobin: A protein found in red blood cells that is responsible for the transport of oxygen
Cytochrome: A group of proteins located in the mitochondria and involved in the electron transport chain
What are examples of proteins associated with sensation + defintion?
Rhodopsin: A pigment in the photoreceptor cells of the retina that is responsible for the detection of light
What are examples of proteins associated with movement + definition?
Actin: Thin filaments involved in the contraction of muscle fibres
Myosin: Thick filaments involved in the contraction of muscle fibres
What is an example of an enzyme associated with photosynthesis?
Rubisco: An enzyme involved in the light-independent stage of photosynthesis
