biomed 3-5

proteins

multipurpose biopolymer molecules composed of amino acids acids

fibrous proteins

polypeptides arranged in long strands

globular proteins

polypeptide chains folded into spherical or globular form

structural proteins

type of protein used for support, in ligaments, tendons and bones

enzymatic proteins

type of protein used for the acceleration of chemical reactions

defensive proteins

type of protein used for the protection against disease

hormonal proteins

type of protein used for the co-ordination of an organism’s activities

membrane proteins

type of protein used for adhesion and cell growth

contractile and motor proteins

type of proteins used for movement

storage proteins

type of protein used for the storage of amino acids

central carbon

component of amino acid that is the centre.

amine group

component of amino acid on the LHS that is a nitrogen with a lone pair connected to 2 hydrogens. when a peptide is formed, on of these hydrogens is dropped to waste a H2O. this is the N TERMINUS END

carboxyl group

component of amino acid on the RHS which is COOH-. when a peptide bond is formed, the OH is dropped to form a waste H2O. this is the C TERMINUS end

r group

central component of amino acid: unique variable group attached to the central alpha carbon of an amino acid that gives each specific amino acid its distinct chemical identity and behavior

ribosome

organelle which is the site of polypeptide synthesis. composed of large complexes of RNA

mRNA

the messenger ___ which copies instructions in DNA and takes it to the ribosomes

tRNA

the transport ___ which reads ribosome codons and has anticodons. transports amino acids and joins them to the polypeptide chain

rRNA

the ribosomal ___ inside the ribosomes which reads mRNA to group into codons

protein primary structure

structure of protein which is a simple sequence of amino acids with a carboxyl terminus and amino terminus

protein secondary structure

protein structure differentiated by local and spatial interactions between functional groups of the protein backbone. defined by the patterns of hydrogen bonds between the main chain peptide groups

• α helix

• β sheet

alpha helix

protein secondary structure which is a spiral structure

beta sheet

protein secondary structure which is formed by mulitple side by side strands

tertiary protein structure

the protein structure defined by the 3d folding of polypeptides with many types of bonds between side groups. responsible for dictating biological activity

quaternary protein structures

protein structure which results From the aggregation of two or more polypeptide subunits held together by non-covalent interaction

methods of protein analysis

Biochemistry

• Molecular weight

  • Gel electrophoresis, polyacrylamide gels

• Western blots

• Enzyme assays

• Chromatography

• Mass spectrometry

 

Structure

• NMR

• X ray crystallography

 

Gel electrophoresis

• DNA and RNA - agarose gel for large molecules

• Proteins

  • Separate molecules like proteins

  • Proteins have no constant charge and can have any charge at a given pH

  • Proteins are coated with a detergent, sodium dodecyl sulphate

chromatography

method of protein analysis which separates the components of the mixture through a matrix

• components with lesser affinity towards the stationary phase moves fasted and gets eluted first

mass spectrometer

method of protein analysis:

1. neutral sample molecules are ionised in the ionisation chamber

2. mass analyser separates ions into mass to charge ratio

3. ion detector records ion current at each mass onto a spectrum

4. spectra are recorded in intensity of m/z

x ray crystallography

protein structural analysis to determine orientation of a protein.

1. irradiate the crystal of protein with x ray beam

2. crystals are used because it helps amplify the diffraction signal

3. x rays interact with the electrons surrounding the molecule and reflect

4. scattered beam is detected and the electron density is measured

5. end product is a resolution electron density map and model building to get a crystal structure

collagen

a major component of the extracellular matrix used in engineering to give structural support and treat injuries

elastin

a highly elastic protein which provides elasticity to tissues due to cross-linking of lysine residues produced by fibroblasts and smooth muscle cells

• used in engineering for skin healing, grafts, liver healing

carbohydrates

engineering includes vaccines, delivery systems, glycocoatings for implants.

• energy molecule storage in the body

• all over the surface of a cell membrane

• take message from outside the cell to inside

• compounds containing C, H and O

• classified based on number of sugar units, location of carbonyl groups, size of base carbon chain, stereochemistry

stereoisomers

molecules with the same molecular formular but arent mirror images and cant be overlapped. like look at your hands

• based on the chiral carbon furthest from the carbonyl carbon

chiral center

an asymmetric carbon with 4 different things attached to it.

• you need at least one assymetric carbon to have stereoisomers

glycogen

Energy storage of animals

glycosaminoglycans GAGS

long unbranched chains of repeating disaccharide units

• major function: forming a matrix that holds together protein components of skin and connective tissues

stem cells

a kind of cell that has the capacity to self-renew to produce additional cells by mitosis and also to differentiate into other, more mature cell types

potency

the measure of a stem cells ability to differentiate

totipotent

potency level: they can form all the cell types in a body, plus the extra embryonic or placental cells

pluripotent

potency level: they can give rise to all of the cell types that make up the body

multipotent

potency level: can give rise to multiple types of cells but all within a particular tissue, organ or physiological system

embryonic stem cells

pluripotent stem cells derived from embryos or placenta. when the fertilised egg undergoes cell division, forms the blastocyst, ICM differentiates into different cell types

• ideal for lab growth since these cells are meant to form whole organisms

• their derivation is ethically sensitive

• high potency

• very easy to keep alive

• allogeneic

tissue specific stem cells

Undifferentiated cells found among the differentiated cells in a tissue or an organ which differentiate to the specialised cell types of the tissue

haematopoietic stem cells

adult stem cells found in bone marrow and blood capable of producing all of the cells that make up the blood and the immune system

mesenchymal stem cells

adult stem cells found in several parts of the body, a promising therapeutic cell source. generally defined as adherent and elongated cells.

• low potency

• low numbers

• difficult to keep alive

• autologous

neural stem cells

• Specialised stem cells responsible for repairing nerve-insulating myelin in the brain

• NSCs ensure a life long contribution of new neurons

reasons for stem cell development

• Cell therapies

  • Transplantation of specific cells and precursors for treatment of various diseases

• New drug discovery and development

  • Testing the efficacy of the drugs

• Tissue repair and regeneration

• Fundamental research

  • Understand the tissue growth and development

  • Stem cell differentiation and the role of gene and proteins

  • Cell signalling

  • The role of microenvironment intwhich they are residing

  • Role of stem cecll secretory molecules

stem cell niche

the microenvironment which stem cells reside in

• artificial ones are used to understand the cues that derive stem cell fate decisions

• how can these factors active them or direct them towards self-renewal or differentiation?

• stiffness of substrate plays a part