Bio topic 2

Primary structure

The specific sequence of amino acids that make up the polypeptide chain

Secondary structure

The 3D structure formed as a result of interactions between amino acids such as alpha helix or beta plated sheet

Tertiary structure

The more specific 3D folding of the secondary structure

Quaternary structure

The 3D arrangement of more than one tertiary polypeptide

What is an amino acid made of

Amino group, carboxyl group, hydrogen and R group

Monomers proteins made of

Amino acids

How do amino acids join

Condensation reaction forming a peptide bond

Bonds in primary structre

Peptide bond

Bonds in secondary structure

Hydrogen

Bonds in tertiary and quaternary structure

Hydrogen, ionic, disulphide

Amino acid structure

Carbon, hydrogen, R group, amino group, carboxylic acid group

What does peptide bond look like

H O

| ||

N— C

Where you find polar R groups on protein

On the surface- hydrohphilic and attracted to water

Where you find non polar R groups on protein

Inside- hydrophobic and repel water

What are the 3 types of protein

Fibrous, globular, conjugated

Conjugated protein

Protein with another prosthetic group associated with their polypeptide chains

Fibrous protein

Polypeptide chains remain elongated

Little or no tertiary structure

Has repetitive sequences of amino acids

Has hydrophobic r groups on outside

Globular protein

Polypeptide chains are folded into spherical shape

Has tertiary structure

Does not have repetitive sequences of amino acids

Has hydrophilic r groups on outside

Overall function onpf fibrous protein

Important structural roles in organisms

Overall function of globular proteins

Important roles in metabolic reactions

Haemoglobin fibrous or globular

Globular

Collagen fibrous or globular

Fibrous

Is haemoglobin quaternary

Yes it has 4 polypeptide chains

Is collagen quaternary

Yes it has 3 polypeptide chains

Is haemoglobin conjugated

Yes it has a haem group

Is collagen conjugated

No

Is haemoglobin soluble

Yes

Is collagen soluble

No

Function of haemoglobin

Binds to oxygen and transports it

Collagen function

Structural strength and support

Polymer

Chain of many single monomers joined together in condensation reaction

How do plants and animals differ in amino acids they make

Plants can make all amino acids, animals only make some and get rest through diet called essential amino acids

Structure of phospholipid

Phosphate, glycerol and 2 fatty acids joined by ester bonds

Properties of phospholipid head

Hydrophilic, polar, soluble and attracts water

Properties of phospholipid tail

Hydrophobic, nonpolar, insoluble and repels water

Properties of cell membranes

Fluidity- gives membrane fluidity

Partially permeable- regulates substances in and out of cell

Flexibility

All parts of cell membrane

Phospholipid bilayer, glycoprotein, glycolipid, proteins, channel proteins, cholesterol

Function of glycoprotein

Role in cellular recognition and immune response

Act as receptors for hormones and neurotransmitters

Stabilise membrane

Function of glycolipid

Acts as surface receptors

Stabilise membrane structure

Function of protein in cell membrane

Role in cell signaling pathways and Stabilise membrane structure

Function of cholesterol in cell membrane

Disturbs close packing of phospholipids

Regulates membrane fluidity

Important for membrane stability

Function of channel protein

Control entry and removal of specifi molecules from a cell

Completely span bilayer

Gorter and grendel found and proves

Blood cell membranes contain enough phospholipis to cover the red blood cell twice- cell membrane is phospholipid bilayer

Davson and danielli found and proves

Electron microscope showed different layers- dark outer layers (thought protein) and lighter inner layer (thought lipid)

Freeze fracture found and proves

Showed bumps in centre of membrane- proteins found e,bedded in bilayer

Frye and edinin found and proves

Protein in 2 cells coloured and fused. Colours intermixed- membrane is fluid allowing protein to move

Unwin and Henderson found and proves

Some proteins only released using strong detergents but others more easily by ionic strength- integral proteins fully embedded and peripheral proteins loosely asociated

Lectin found and proves

Lectins(bind to carbohydrates) only bound to outside- carbohydrates only found on outside of cell membrane

Diffusion passive or active

Passive

Facilitated diffusion passive or active

Passive

Osmosis passive or active

Passive

Active transport passive or active

Passive

Active transport passive or active

Active

Exocytosis passive or active

Active

Endocyosis passive or active

Active

Diffusion

Net movement from a region of high concentration to a region of lower concentration until equilibrium is reached

Facilitated diffusion

Not movement from region of high concentration to region of lower concentration through channel or carrier proteins

Osmosis

Net movement of water from a region of high concentration (lower concentration of solute) to a region of low concentration high concentration of solute) through partially permeable membrane

Active transport

Movement of molecules from low to high concentration using ATP to drive protein pumps in membrane. Carrier proteins act as pumps and have complementary bases

Exocytosis

Bulk transport out of a cell. A membrane bound vesicle with the substance enclosed fuses with cell membrane and releases contents outside cell

Endocytosis

Bulk transport into a cell. Membrane budget inwards, wraps around substances and pinches off to form a vesicle

What are the 4 bases

Adenine, thymine, cytosine and guanine

Nucleotide structure

Phosphate, deoxyribose sugar, base

How many hydrogen bonds between A and T

2

How many hydrogen bonds between C and G

3

Bond between nucleotides to form polynucleotide chains

Phosphodiester bonds

Whynis complementary base pairing important

So double helix is uniform width of 3 rings forming each rung

Gene

Sequence of bases on DNA that codes for a sequence of amino acids in a polypeptide chain

DNA

Contains genetic code which dictates all inherited characteristics of an organism

What type of replication is dna replication

Semi conservative

DNA replication process

Dna helicase breaks hydrogen bonds between dna strands. 2 strands act as templates. Free nucleotides line up along dna strands and hydrogen bonds from between complimentary bases. Dna polymerase joins adjacent nucleotides with phosphodiester bonds to form complimentary strand. Dna ligasenhelps close any gaps in strand that have been missed

Dna polymerase role in dna replication

Enzyme to join adjacent nucleotides with phosphodiester bonds to for new dna strands

Dna helicase role in dna replication

Breaks hydrogen bonds between dna strands

3 possible ways for dna replication

Semi conservatively, conservatively and fragmentary

First result of meselson and stalls dna proof

One band at bottom after grown in heavy nitrogen

Second result of meselson and stahl dna proof

One band in middle after a cycle in light nitrogen

Third result of meselson and stahls dna proof

One band in middle and one at top after second round in light nitrogen

Expected results of fragmentary

Medium, medium

Expected results of conservatively

Heavy and light

Expected results of semiconservatively

Medium, one light and one medium

Stages of protein synthesis

Transcription and translation

Similarities between DNA and RNA

Both have phosphate, base and pentose sugar. Both made of nucleotides joined by phosphodiester bonds. Both contain A C and G

Differences between DNA and RNA

Rna is single stranded, dna is double. Rna has a ribose sugar, dna have deoxyribose sugar. mRNA has uracil, DNA and tRNA have thymine

Process of transcription

RNA helicase breaks hydrogen bonds between bases and dna strands unwinds. Antisense strand only uses as template. Free rna nucleotides pair with exposed complimentary bases on antisense. Rna polymerase joins nucleotides with phosphodiester bonds in condensation reactionscto form mrna. Mrna detaches and exits nucleus pore to cytoplasm carrying copy of genetic code

What strand is used as template in transcription

Antisense strand

Process of translation

Ribosome attaches to mRNA at start codon and moves along reading 3 bases at a time. Trna attaches to specific amino acids ans carries them to ribosome. Complimentary base pairing between anticodon and codon with hydrogen bonds. Amino acids join by peptide bond in condensation reaction. Trna releases from mrna. Ribosome moves along and detaches at stop codon. Polypeptide chain detaches from Ribosome.

Nature of genetic code

Triplet- three bases code for one amino acid

Degenerate- more than one triplet code can code for the same amino acid

Non-overlapping- each base is only part of one triplet

Biological catalyst

Enzyme produced by cell which increases rate of biological reactions without being changed or used up

Activation energy

Energy required to break or form bonds which is needed by and reduced by enzymes for a reaction to take place

Enzyme

Globular protein which is a biological catalyst that increases rate of biological reactions by lowering activation energy required to start reaction

Lock and key theory

Shape of active site fits substrate exactly

Induced fit theory

Flexible active site that changes shape slightly to fit substrate more closely

How enzyme works

Substrate fits into and binds to enzyme active site. Shape of active site fits shape of substrate. An enzyme substrate complex form and bonds are broken or formed and lowers activation energy. The product is released and enzyme is unchanged.

Intracellular enzyme

Inside cells

Extracellular enzymes

Outside cells

Catabolic

Break down

Anabolic

Build up

Rate of diffusion is ______________ to surface area

Directly proportional

Rate of diffusion is ___________ to difference in concentration

Directly proportional

Rate of diffusion is ____________ to the thickness of surface

Inversely proportional