HL Bio - Microbiology #2 (Proteins, Enzymes, Metabolism)

Proteins essential questions

- How are amino acids linked together? - How many different amino acids are there? - How many different proteins are there? - What causes a protein to bind and coil into a 3D shape rather than a simple chain? - What happens if two or more polypeptide chains join together? - What are the functions of proteins in the cell, and also proteins which are secreted by living things? - How can an understanding of the proteins in living things help in the industry?

Why do we use the same 20 amino acids?

1.) These 20 were the ones produced by chemical processes on Earth before the origin of life. 2.) They are the ideal 20 amino acids making a wide range of proteins, so natural selection will always favor organisms that use them and do not use other amino acids. 3.) All life has evolved from a single ancestral species, which used these 20 amino acids.

How many different amino acids are used by ribosomes to make polypeptides?

20

If you have 21 amino acids, how many peptide bonds will you have?

20 peptide bonds, it is always one less

If a polypeptide contains just 7 amino acids how many possible polypeptides can be generated?

20^7 = 1,280,000,000 polypeptides

Explain properties of Hemoglobin

4 different polypeptides. Transport protein in red blood cells that transports oxygen and CO2

What codes the amino acid sequence of polypeptides?

Genes. Cell producers polypeptides with thousands of different sequences and stores the information to produce these within genes (DNA). The DNA sequence is transcribed to messenger RNA (mRNA) which brings this genetic code to the ribosomes

What can cause denaturation?

Heat and pH

Describe Packing DNA

Histone proteins are associated with DNA in eukaryotes and help chromosomes to condense during mitosis

Describe Insulin

Hormone - signals many cells to absorb glucose and help reduce the glucose concentration of the blood. Secreted by beta cells in the pancreas and transported by the blood. The pancreas of type I diabetics don't produce sufficient insulin and must inject insulin to correct their blood sugar concentration (endocrine)

What are the unique properties of amino acids?

Hydrophilic, hydrophobic, positively or negatively charged, contain sulfur

What makes fibrous proteins insoluble?

Hydrophobic R groups (so the hydrophilic R - groups would be inside) are exposed

What gives a polypeptide its distinctive properties?

R-groups

What is a substrate?

Reactant in chemical reaction

What is the active site?

Region on the surface of an enzyme to which the substrates bind and which catalyzes the reaction.

Properties of globular protein

Shape - Rounded / spherical. Role - Functional (catalytic, transport). Solubility - (generally) soluble in water. Sequence - irregular amino acid sequence. Stability - more sensitive to changes in heat, pH. Examples - Catalase (found in liver, breaks down chemicals found in our system), hemoglobin, insulin, immunoglobulin (anti-bodies)

Properties of a Fibrous protein

Shape - long and narrow. Role - structural (strength and support). Solubility - (generally insoluble in water). Sequence - repetitive amino acid sequence. Stability - less sensitive to changes in heat, pH. Examples - Collagen, myosin, fibrin, actin, keratin, elastin

A protein may consist of a _____ polypeptide or _____ _____ _____ polypeptide linked together

Single polypeptides, two or more polypeptides

What is insulin?

Small protein that contains two polypeptides (one with 21 amino acids and the other with 30 amino acids). They are receptors for sugar, without it, your body won't get the sugar. Absorbs glucose to help reduce the glucose concentration of the blood. Secreted by the pancreas

What is the induced it model?

Some enzymes can catalyze multiple reactions. As the substrate approaches the enzyme, it induces a conformational change in the active site in order to fit the substrate. This reduces the activation energy of the reaction by stressing the substrate

Describe spider silk

Spiders produce different types of silk with different functions, dragline silk is stronger than steel and tougher than kevlar. Makes the spokes of the web and the spiders lifelines. When first made it contains regions where the polypeptide forms parallel arrays. Some regions seem like a disordered tangle. When stretched the polypeptide gradually extends, making the silk extensible and very resistant to breaking.

How is the 3-D conformation of proteins stabilized?

They are stabilized by bonds or interactions between the R-groups of amino acids within the molecule. Most of these bonds are relatively weak and they can be broken.

What are ribosomes?

They are the molecules within cells that facilitate the formation of peptide bonds and are therefore where polypeptides are synthesized. Ribosomes = rRNA (ribosomal RNA) + Proteins

Describe immunity

This is the most diverse group of proteins, as cells can make huge numbers of different antibodies

Describe cytoskeleton

Tubulin is the subunit of microtubules that give animals cells their shape and pull on chromosomes during mitosis

What is a dipeptide?

Two amino acids joined

How can heat cause denaturation?

Vibrations within the molecule breaks intermolecular bonds or interactions. Example, you can un-boil and egg but you can't un-fry an egg

What is released as a byproduct of the dipeptide reaction?

Water

When do most enzyme reactions occur?

When the substrates are dissolved in water -> hydrolisis

What is the optimal pH for the protein digesting enzyme pepsin found in the stomach?

pH 1.5 (the human stomach pH.) Very acidic it could burn your skin and that's why your throat burns when you throw up

What is the site of polypeptide synthesis?

ribosomes - but they need a specific sequence to make a polypeptide

Describe hormones

some such as insulin FSH and LH are proteins, but hormones are chemically diverse

What is optimal pH?

the pH at which the rate of enzyme activity is at its peak. Moving outside of optimal pH range will always result in a diminished rate of reaction. Different enzymes have different optimal pH's. Pepsin pH 2; Salivary Amylase pH 7.2

What is the lock and key hypothesis?

Enzymes are specific to their substrates. The substrate and the active site match each other in two ways. 1.) structurally: the 3D structure of the active site is specific to the substrate. Substrates that don't fit, won't react. 2.) Chemically: substrates that are not chemically attracted to the active site won't be able to react

How can pH cause denaturation?

Extremes of pH - charges on R groups are changed, breaking ionic bonds within the protein or causing new ionic bonds to form

What is Collagen?

A structural protein used to provide tensile strength in tendons, ligaments, skin and blood vessel walls

What is denaturation?

A change in the conformation of the protein. Denaturation is permanent

What is an enzyme?

A globular protein that increases the rate of a biological reaction by lowering the activation energy threshold

Describe Collagen

A number of different forms. All are rope-like proteins made of 3 polypeptides wound together. About a quarter of all protein in human body is collagen. Gives strength to tendons, ligaments, skin and blood vessel walls. Forms a mesh of fibers in skin and in blood vessel walls that resists tearing. fORMS PART OF TEETH AND BONES, HELPS TO PREVENT CRACKS AND FRACTURES

Describe rhodopsin

A pigment that absorbs light. Membrane protein of the rod cells of the retina (light sensitive region at the back of the eye). Rhodopsin consists of the opsin polypeptide. Retinal molecules absorb a single photon of light -> changes shape of the opsin -> the rod cells sense a nerve impulse to the brain. Even very low light intensifies can be detected.

Describe muscle contraction

Actin and myosin together cause the muscle contractions used in locomotion and transport around the body

What is a genome?

All of the genes of a cell, a tissue or an organism. it determines what proteins an organism can possibly produce. A genome is unique to most individuals (identical twins and clones share a genome)

What is a proteome?

All of the proteins produced by a cell, a tissue or an organism. It is the function of both the genome and environment to which the organism is exposed. It is both variable (over time) and unique to every individual

Describe immunoglobulins

Antibodies - Produced in response to antigens - proteins on a pathogen that causes an immune response. Two antigen binding sites - one on each 'arm' that bind to bacteria or other pathogens. Hypervariable - binding sites vary gently between immunoglobulins to enable them to respond a huge range of pathogens. Other parts of the immunoglobulin molecule cause a response. Antibiotics: destroying the cell wall of the cell development of the bacterial pathogen. Vaccine : injecting antigens

Describe receptors

Binding sites in membranes and cytoplasm for hormones, neurotransmitters, tastes and smells and also receptors for light in the eye and in plants (rhodopsin)

Why are there infinite possibilities of polypeptides?

Could be any length. There are 20 amino acids. Amino acids can be in any order or combination

What are the types of bonds formed in a polypeptide?

Covalent Bonds

What are fibrous proteins and globular proteins?

Fibrous have structural roles whereas globular proteins are functional (active in a cell's metabolism)

What are the functions of proteins?

Catalysis, muscle contraction, cytoskeleton, tensile strengthening/structure, blood clotting, transport of nutrients and gases, cell adhesion, membrane transport, hormones, receptors, packing of DNA, immunity

What is a polypeptide?

Chains of more than 20 amino acids

What happens when the temperature is high?

Enzyme stability to decrease, as the thermal energy disrupts the hydrogen bonds holding the enzyme together. The enzyme loses its shape, resulting in a loss of enzyme activity (denaturation)

How has biotechnology allowed us to use proteins in industry?

Enzymes are removing stains in clothing detergent. Monoclonal antibodies for pregnancy tests. Insulin for treating diabetic. Disease treatments

What is the central dogma of genetics?

DNA (gene) --> (Transcription(Nucleus)) mRNA(message) --> (Translation(cytoplasm ribosome)) Polypeptide(product)

Describe Rubisco

Enzyme - catalyzes the reaction that fixes carbon dioxide from the atmosphere. Provides the source of carbon to make all the macromolecules in living things. Found in high concentrations in leaves. Probably the most abundant enzyme in the world

Explain properties of Lysozyme

Enzyme found in nasal mucus and tears. It kills bacteria

What happens if you increase the temperature?

Increases the speed and motion of both enzyme and substrate, resulting in a higher enzyme activity

What do low temperatures result in?

Insufficient thermal energy for the activation of a given enzyme-catalyzed reaction to be achieved

What is an example of a Peptide?

Insulin, Titin, etc.

Example of two or more polypeptides

Integrin

What does the condensation reaction involve (hint: which groups)?

It involves the amine group (-NH2) of one amino acid and the carboxyl group (-COOH) of another

What is Hydroxyproline?

It is a modification of the amino acid

Why is Vitamin C so important?

It is essential for proper formation of amino acids, it is needed for collagen. Without it you would get swollen bleeding gums, opening of previously healed wounds, tired/weak all the time, severe joint pain, anemia, skin that bruises easily. It holds teeth in gums.

What is another use of Vitamin C?

It is required to convert proline into hydroxyproline . The modification increases the stability of the collagen triple helix

Denaturation in proteins means charging on R-groups are changed breaking ionic bonds within the protein or causing new ionic bonds to form. What does a change in structure mean for enzymes?

It means that there is a change in the active site. If the active site changes shape the substrate is no longer able to bind to it.

What happens when you change the pH?

It will alter the charge of the enzyme, which may affect protein solubility and change the shape of the molecule.

What will happen if the charge or shape of the molecule has changed?

It will diminish its ability to bind to the substrate, halting enzyme function

What is Titin?

Largest peptide discovered. Contains 34,500 amino acids; found in humans. A part of muscle structure (located in the sarcomere of striated muscle) (movement)

What are Polypeptides?

They are molecules consisting of many amino acids (more than 20) linking by peptide bonds. Chains of amino acids joined by peptide bonds

Example of a single polypeptide

Lysozyme

Describe membrane transport

Membrane proteins are used for facilitated diffusion and active transport, and also for electron transport during cell respiration and photosynthesis

Describe cell adhesion

Membrane proteins cause adjacent animal cells to stick to each other within tissues

Explain properties of Integrin

Membrane proteins used to make connections between structure in cells.

What happens when there is a higher kinetic energy?

More frequent collisions between enzyme and substrate

What is the process of substrate and enzyme?

Once the substrate has been locked into the active site, the reaction is catalyzed. The products are released and the enzyme is used again.

What are Thermophiles?

Organisms that live in relatively hot conditions and their proteins are able to maintain their structure in these extreme conditions

Describe blood clotting

Plasma proteins act as clotting factors that cause blood to turn from a liquid to a gel in wounds

How are amino acids attracted to substrates?

Polar regions of amino acids attract substrate and active site of the enzyme

Describe transport of nutrients and gases

Proteins in blood help transport oxygen, carbon dioxide, iron and lipids (hemoglobin)

Explain properties of Collagen

Structural protein of tendons, ligaments, skin, blood vessel walls. Provides high tensile strength

What is one of the central ideas of biology?

Structure dictates function

What is the optimum concentration?

Substrate molecules, all active sites are full and working at maximum efficiency. Any increase in concentration past the optimum will have no added effect as there are no extra active sites to be used.

What determines the three-dimensional conformation of a protein?

The amino acid. The properties of the amino acids determine how a polypeptide folds up into a protein and determines its 3-D shape (R-Group)

What is DNA?

The blueprint for the protein being made

What is Scurvey?

The breakdown of collagen tissue due to the lack of Vitamin C in the diet

What is collision?

The coming together of a substrate molecule and an active site

What are the environmental factors that influence proteins?

The environmental influences what proteins an organism needs to produce and in what quantity. Example factors would be nutrition, temperature, activity levels and anything else that affects a cell's activities.

What makes the globular proteins soluble?

The hydrophobic R groups are folded into the core of the molecule, away from the surrounding water molecules

Which is larger the proteome or the genome?

The proteome because it is a combination of both the genome and environmental factors. Not all genes produce polypeptides. Multiple polypeptides and prosthetic groups can interact. Amino acids can be modified (e.g. collagen). A polypeptide can fold into different levels of structure (e.g. insulin, hemoglobin)

What happens if you increase the substrate concentration?

The rate of reaction will increase

What needs to happen in order for the collision to be successful?

The substrate and active site must be correctly aligned.

What is the optimal temperature?

The temperature at which the rate of enzyme activity is at its peak; this is different for each enzyme

Describe Catalysis

There are thousands of different enzymes to catalyze specific chemical reactions within living things (rubisco, catalase)

What are immobilized enzymes?

enzymes that are attached to material so that their movement is restricted. Ex, alginate beads

Describe tensile strengthening/structure

fibrous proteins give tensile strength needed in skin, tendons, ligaments and blood vessel walls (collagen)

What are the two theories on how enzymes work?

lock and key hypothesis and induced fit model