Bio topic 2

What are the monomers of proteins?

Amino acids

Dipeptide

Two amino acids bonded together

Polypeptide

A polymer (chain) of more than two amino acids bonded together

What are proteins made of?

One or more polypeptides

What is the general structure of amino acids?

A carboxyl group, an amine/amino group, a carbon-containing R group

How many amino acids are there?

20

What is the difference between amino acids?

Their R group

How are amino acids linked?

Condensation reaction

What is released in a condensation reaction?

Water molecule

What type of bond is formed between amino acids?

Peptide bond

What are the 4 structural levels of proteins?

Primary, Secondary, Tertiary, Quaternary

What is the primary structure of a protein?

The sequence of amino acids in the polypeptide chain

What is the secondary structure of a protein?

The 2D arrangement of the chain of amino acids. Alpha helix or Beta pleated sheet

What determines the secondary structure of a protein?

Hydrogen bonds between amino acids

What is the tertiary structure of a protein?

The 3D structure of a protein

What determines the tertiary structure of a protein?

Hydrogen bonds, ionic bonds, disulphide bridges, hydrophobic and hydrophilic interactions

What is the quaternary structure of a protein?

Some proteins are made of more than one polypeptide chains linked together. The quaternary structure is the way these polypeptide chains are assembled together

What is the primary structure of proteins held together by?

Peptide bonds between amino acids

Ionic bonds in proteins

Attractions between negative and positive charges on different parts of the molecule

Disulphide bridge/bond in proteins

Covalent bond between sulphur atoms of two cysteine amino acids

Hydrophobic interactions in proteins

When hydrophobic groups are close together, they tend to clump together

Hydrophilic interactions in proteins

Hydrophilic groups get pushed to the outside

What do hydrophilic/phobic interactions affect tertiary structure?

They affect how the protein folds up

How does a proteins primary structure determine its 3D structure and properties

The amino acid sequence of a protein determines what bonds will form and how the protein folds into its 3D structure. The 3D structure determines its properties and function in the body

Globular proteins

* Round, compact proteins made up of multiple polypeptide chains.
* form colloids in water

How are the chains structured in globular proteins?

Coiled up so that hydrophilic parts are on the outside and hydrophobic parts face inwards

What are the two types of protein 3D structure?

Globular and fibrous

How does the structure of globular proteins make it good for their function?

Makes them soluble, so they're easily transported in fluids

Hydrogen bonds

Weak bonds between a slightly positively charged hydrogen atom in one molecule and a slightly negatively charged atom in another molecule

Example of globular protein

Haemoglobin

Haemoglobin strucutre

Globular protein made of 4 polypeptide chains. It has iron-contains haem groups that bind to oxygen

What is the function of haemoglobin?

Carries oxygen around the body

How is haemoglobin suited for its function?

Its soluble so can easily be transported in the blood

Collagen structure

Fibrous protein made up of 3 polypeptides

Fibrous proteins

* Long, insoluble polypeptide chains, tightly coiled round each other to form a rope shape
* chains are held together by lots of bonds,making the proteins strong
* little tertiary/quaternary structure
* occasional cross linkages which forms microfibres for tensile strength

How are fibrous proteins suited for their function?

They are strong so are often found in supportive tissue

How is collagen suited for its function?

High tensile strength due to hydrogen and covalent bonds and forms the structure of bones, cartilage and connective tissue in animals

What do enzymes do?

Catalyse metabolic reactions

Intracellular enzymes

Catalyse reactions inside the cell

Extracellular enzymes

Secreted by cells to catalyse reactions outside of cells

Are enzymes proteins?

Yes

Activate site of enzymes

Has a specific shape where the substrate molecules bind to

What makes enzymes specific?

Their tertiary structure

How do enzymes catalyse reactions?

They lower the activation energy needed for a reaction

Enzyme-substrate complex

A complex formed when an enzyme binds to its substrate molecule(s).

Activation energy

Energy needed to get a reaction started

How does an enzyme substrate complex lower activation energy?

* If 2 substrate molecules need to be joined, being attached to the enzyme holds them close together, reducing and repulsion between the molecules so they can bond more easily
* in a breakdown reaction,fitting into the active site puts a strain on the bonds in the substrate so the molecule breaks up more easily

Induced fit model

Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)

How do enzyme properties relate to their tertiary structure?

* Enzymes are very specific and usually only catalyse one reaction because only one complementary substrate will fit into the active site
* the enzyme’s active site is determined by its tertiary structure
* each enzyme has a diff tertiary structure so diff shaped active site

What can the tertiary structure of an enzyme be altered by?

Changes in pH or temperature

What is the primary structure of a protein determined by?

The sequence of nucleotides in the gene encoding for amino acids

How does enzyme concentration affect enzyme activity?

The more enzyme molecules there are in a solution, the more active sites present and the more likely a substrate molecule is to collide with an active site and form an enzyme-substrate complex

What is the limiting factor in enzyme catalysed reactions?

Substrate concentration

What does DNA stand for?

Deoxyribosenucleic Acid

What does RNA stand for?

Ribonucleic acid

What are mono nucleotides made from?

* Pentose sugar
* nitrogenous base
* phosphate group

Pentose sugar

Sugar with 5 carbon atoms

DNA and RNA are polymers of what?

Mononucleotides

What is the pentose sugar in a DNA mononucleotide called?

Deoxyribose

Each DNA mononucleotide has the same \_____ and a \_________/\_____

* Sugar
* phosphate group

What varies between DNA/RNA mononucleotides?

Their base

4 bases (DNA)

* Adenine (A)
* Thymine (T)
* Cytosine (C)
* Guanine (G)

What is the pentose sugar in a RNA mononucleotide called?

Ribose

Each RNA mononucleotide has the same \_____ and a \_________/\_____

* Sugar
* phosphate group

4 bases (RNA)

* Adenine (A)
* uracil (U)
* cytosine (c)
* guanine (G)

Polynucleotide

A polymer consisting of many mononucleotide monomers in a chain

What are polynucleotides joined by?

Condensation reaction between the phosphate of one mononucleotide and the sugar group of another

How many polynucleotide strands is DNA made up of?

Two

How many polynucleotide strands is RNA made up of?

One

How do two DNA polynucleotide strands join together?

Hydrogen bonding between bases

What are the DNA base pairs?

Adenine - Thymine (A-T)

Cytosine - Guanine (C-G)

Complementary base pairing

Hydrogen bonding between particular pyrimidines and purines

Pyrimidines

* Cytosine
* thymine
* uracil

How many hydrogen bonds form between A and T?

Two

How many hydrogen bonds form between C and G

Three

DNA double helix

Two antiparallel polynucleotide strands twist to form the DNA double-helix

Who and when determined the double-helix structure of DNA

Watson and Crick - 1953

Gene

Sequence of mononucleotide bases on a DNA molecule that codes for the sequence of amino acids in a polypeptide

Different proteins have a different \______ and \_____ or amino acids

* Number
* order

How many bases code for one amino acid?

Three

Does DNA move out of the nucleus?

No, It is too large so is copied into mRNA (transcription). The mRNA leaves the nucleus and joins with a ribosome in the cytoplasm, where it can be used to synthesise a protein (translation)

Two types of RNA

* Messenger RNA (mRNA)
* transfer RNA (tRNA)

When and where is mRNA made?

In the nucleus during transcription

What does mRNA do?

Carries the genetic code from the DNA to a ribosome in the cytoplasm, where it's used to make a protein during translation

Codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

Where is tRNA found?

The cytoplasm

What does tRNA have at each end?

Amino acid binding site at one end and an anticodon at the other end

Anticodon

A sequence of three bases of a tRNA molecule that pairs with the complementary three-nucleotide codon of an mRNA molecule during protein synthesis.

What does tRNA do?

Carries the amino acids that are used to make proteins, to the ribosomes during translation

What are codons and anticodons sometimes referred to as?

Triplets

Genetic code

The sequence of base triplets (codons) in DNA or mRNA which codes for specific amino acids

Features of genetic codes

* Degenerate (more than one genetic code corresponds to one amino acid)
* Non overlapping (base triplets don't share their bases,each is separate from the triplet before)

How many possible triplets are there?

64

Start and Stop codons

Triplets used to tell the cell when to start and stop the production of the protein. Found at the beginning and end of the gene

What is the first stage of protein synthesis called?

Transcription

Stage 1 of transcription:

Transcription starts when RNA polymerase attaches to the DNA double-helix at the beginning of a gene (start codon)

Transcription starts when RNA polymerase attaches to the DNA double-helix at the beginning of a gene (start codon)...

Stage 2 of transcription:

The hydrogen bonds between the two DNA strands in the gene break, separating the stands and causing the DNA molecule to unwind.

The hydrogen bonds between the two DNA strands in the gene break, separating the stands and causing the DNA molecule to unwind...

Stage 3 of transcription:

One of the strands is used as a template to make an mRNA copy

Stage 4 of transcription:

RNA polymerase lines up free RNA mononucleotides alongside the template strand. Complementary base pairing means the mRNA ends up being a complementary copy of the DNA strand (with T being replaced with U)

Stage 5 of transcription:

Once the RNA mononucleotides have paired with their specific bases on the DNA strand they're joined by RNA polymerase, forming an mRNA molecule